AlDubayan SH, Giannakis M, Moore ND, Han GC, Reardon B, Hamada T, Mu XJ, Nishihara R, Qian Z, Liu L, Yurgelun MB, Syngal S, Garraway LA, Ogino S, Fuchs CS, Van Allen EM
Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018 03 01; 102(3):401-414.
Inherited DNA-Repair Defects in Colorectal Cancer.
Hazar-Rethinam M, Kleyman M, Han GC, Liu D, Ahronian LG, Shahzade HA, Chen L, Parikh AR, Allen JN, Clark JW, Kwak EL, Faris JE, Murphy JE, Hong TS, Van Seventer EE, Nadres B, Hong CB, Gurski JM, Jessop NA, Dias-Santagata D, Iafrate AJ, Van Allen EM, Corcoran RB
Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in BRAFV600E Colorectal Cancer. Cancer Discov. 2018 04; 8(4):417-427.
Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in BRAFV600E Colorectal Cancer.
Edelman G, Rodon J, Lager J, Castell C, Jiang J, Van Allen EM, Wagle N, Lindeman NI, Sholl LM, Shapiro GI
Phase I Trial of a Tablet Formulation of Pilaralisib, a Pan-Class I PI3K Inhibitor, in Patients with Advanced Solid Tumors. Oncologist. 2018 04; 23(4):401-e38.
Phase I Trial of a Tablet Formulation of Pilaralisib, a Pan-Class I PI3K Inhibitor, in Patients with Advanced Solid Tumors.
Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM
The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018 05; 50(5):645-651.
The long tail of oncogenic drivers in prostate cancer.
Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell. 2018 04 19; 173(3):624-633.e8.
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.
One day later. Continuing psychological stress after a cardiac intensive care rotation. J Gen Intern Med. 2010 Aug; 25(8):882-3.
One day later. Continuing psychological stress after a cardiac intensive care rotation.
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N
Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10.
Oncogenic Signaling Pathways in The Cancer Genome Atlas.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L
Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 04 05; 173(2):371-385.e18.
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Manier S, Park J, Capelletti M, Bustoros M, Freeman SS, Ha G, Rhoades J, Liu CJ, Huynh D, Reed SC, Gydush G, Salem KZ, Rotem D, Freymond C, Yosef A, Perilla-Glen A, Garderet L, Van Allen EM, Kumar S, Love JC, Getz G, Adalsteinsson VA, Ghobrial IM
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun. 2018 04 27; 9(1):1691.
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma.
Dissecting Genomic Determinants of Response to Platinum-based Chemotherapy in Advanced NSCLC and Colorectal Cancer
McKay RR, Bossé D, Xie W, Wankowicz SAM, Flaifel A, Brandao R, Lalani AA, Martini DJ, Wei XX, Braun DA, Van Allen E, Castellano D, De Velasco G, Wells JC, Heng DY, Fay AP, Schutz FA, Hsu J, Pal SK, Lee JL, Hsieh JJ, Harshman LC, Signoretti S, Motzer RJ, Feldman D, Choueiri TK
The Clinical Activity of PD-1/PD-L1 Inhibitors in Metastatic Non-Clear Cell Renal Cell Carcinoma. Cancer Immunol Res. 2018 07; 6(7):758-765.
The Clinical Activity of PD-1/PD-L1 Inhibitors in Metastatic Non-Clear Cell Renal Cell Carcinoma.
Integrative Somatic and Germline Computational Biology to Redefine Clinical Actionability in Solid Tumors
Sowalsky AG, Ye H, Bhasin M, Van Allen EM, Loda M, Lis RT, Montaser-Kouhsari L, Calagua C, Ma F, Russo JW, Schaefer RJ, Voznesensky OS, Zhang Z, Bubley GJ, Montgomery B, Mostaghel EA, Nelson PS, Taplin ME, Balk SP
Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations. Cancer Res. 2018 08 15; 78(16):4716-4730.
Neoadjuvant-Intensive Androgen Deprivation Therapy Selects for Prostate Tumor Foci with Diverse Subclonal Oncogenic Alterations.
Gopal RK, Calvo SE, Shih AR, Chaves FL, McGuone D, Mick E, Pierce KA, Li Y, Garofalo A, Van Allen EM, Clish CB, Oliva E, Mootha VK
Proceedings of the National Academy of Sciences of the United States of America
Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma. Proc Natl Acad Sci U S A. 2018 07 03; 115(27):E6283-E6290.
Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma.
Hanna GJ, Kofman ER, Shazib MA, Woo SB, Reardon B, Treister NS, Haddad RI, Cutler CS, Antin JH, Van Allen EM, Uppaluri R, Soiffer RJ
Integrated genomic characterization of oral carcinomas in post-hematopoietic stem cell transplantation survivors. Oral Oncol. 2018 06; 81:1-9.
Integrated genomic characterization of oral carcinomas in post-hematopoietic stem cell transplantation survivors.
Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 07 12; 174(2):433-447.e19.
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.
Sheng W, LaFleur MW, Nguyen TH, Chen S, Chakravarthy A, Conway JR, Li Y, Chen H, Yang H, Hsu PH, Van Allen EM, Freeman GJ, De Carvalho DD, He HH, Sharpe AH, Shi Y
LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade. Cell. 2018 07 26; 174(3):549-563.e19.
LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade.
Li Q, Damish AW, Frazier Z, Liu D, Reznichenko E, Kamburov A, Bell A, Zhao H, Jordan EJ, Gao SP, Ma J, Abbosh PH, Bellmunt J, Plimack ER, Lazaro JB, Solit DB, Bajorin D, Rosenberg JE, D'Andrea AD, Riaz N, Van Allen EM, Iyer G, Mouw KW
Clinical cancer research : an official journal of the American Association for Cancer Research
ERCC2 Helicase Domain Mutations Confer Nucleotide Excision Repair Deficiency and Drive Cisplatin Sensitivity in Muscle-Invasive Bladder Cancer. Clin Cancer Res. 2019 02 01; 25(3):977-988.
ERCC2 Helicase Domain Mutations Confer Nucleotide Excision Repair Deficiency and Drive Cisplatin Sensitivity in Muscle-Invasive Bladder Cancer.
Klega K, Imamovic-Tuco A, Ha G, Clapp AN, Meyer S, Ward A, Clinton C, Nag A, Van Allen E, Mullen E, DuBois SG, Janeway K, Meyerson M, Thorner AR, Crompton BD
Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors. JCO Precis Oncol. 2018; 2018.
Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L
Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 08 09; 174(4):1034-1035.
Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM
Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 12; 36(11):1056-1058.
Intron retention is a source of neoepitopes in cancer.
Shulman DS, Klega K, Imamovic-Tuco A, Clapp A, Nag A, Thorner AR, Van Allen E, Ha G, Lessnick SL, Gorlick R, Janeway KA, Leavey PJ, Mascarenhas L, London WB, Vo KT, Stegmaier K, Hall D, Krailo MD, Barkauskas DA, DuBois SG, Crompton BD
Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2018 08; 119(5):615-621.
Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.
Mateo J, Chakravarty D, Dienstmann R, Jezdic S, Gonzalez-Perez A, Lopez-Bigas N, Ng CKY, Bedard PL, Tortora G, Douillard JY, Van Allen EM, Schultz N, Swanton C, André F, Pusztai L
Annals of oncology : official journal of the European Society for Medical Oncology
A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol. 2018 09 01; 29(9):1895-1902.
A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT).
Miao D, Margolis CA, Vokes NI, Liu D, Taylor-Weiner A, Wankowicz SM, Adeegbe D, Keliher D, Schilling B, Tracy A, Manos M, Chau NG, Hanna GJ, Polak P, Rodig SJ, Signoretti S, Sholl LM, Engelman JA, Getz G, Jänne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman P, Van Allen EM
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat Genet. 2018 09; 50(9):1271-1281.
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors.
Nava Rodrigues D, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreira A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke KP, Sumanasuriya S, Fontes MS, Bianchini D, Zafeiriou Z, Teixeira Mendes LS, Mouw K, Schweizer MT, Pritchard CC, Salipante S, Taplin ME, Beltran H, Rubin MA, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D'Andrea A, Sawyers CL, Chinnaiyan AM, Alimonti A, Nelson PS, Drake CG, Van Allen EM, de Bono JS
Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 10 01; 128(10):4441-4453.
Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer.
Bellmunt J, Lalani AA, Jacobus S, Wankowicz SA, Polacek L, Takeda DY, Harshman LC, Wagle N, Moreno I, Lundgren K, Bossé D, Van Allen EM, Choueiri TK, Rosenberg JE
Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma. Br J Cancer. 2018 09; 119(6):707-712.
Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma.
Harshman LC, Drake CG, Haas NB, Manola J, Puligandla M, Signoretti S, Cella D, Gupta RT, Bhatt R, Van Allen E, Lara P, Choueiri TK, Kapoor A, Heng DYC, Shuch B, Jewett M, George D, Michaelson D, Carducci MA, McDermott D, Allaf M
Transforming the Perioperative Treatment Paradigm in Non-Metastatic RCC-A Possible Path Forward. Kidney Cancer. 2017 Jul 26; 1(1):31-40.
Transforming the Perioperative Treatment Paradigm in Non-Metastatic RCC-A Possible Path Forward.
A piece of my mind. Paracentesis by moonlight. JAMA. 2011 Apr 27; 305(16):1635-6.
A piece of my mind. Paracentesis by moonlight.
A Common Language for Transformative Healthcare Networking. New England Journal of Medicine. 2012.
A Common Language for Transformative Healthcare Networking
Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 11 01; 175(4):984-997.e24.
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Rodrigues DN, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreira A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke KP, Sumanasuriya S, Fontes MS, Bianchini D, Zafeiriou Z, Mendes LST, Mouw K, Schweizer MT, Pritchard CC, Salipante S, Taplin ME, Beltran H, Rubin MA, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D'Andrea A, Sawyers CL, Chinnaiyan AM, Alimonti A, Nelson PS, Drake CG, Van Allen EM, de Bono JS
Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer. J Clin Invest. 2018 11 01; 128(11):5185.
Conway JR, Kofman E, Mo SS, Elmarakeby H, Van Allen E
Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine. Genome Med. 2018 11 29; 10(1):93.
Genomics of response to immune checkpoint therapies for cancer: implications for precision medicine.
A role in transition. Ann Intern Med. 2009 Sep 15; 151(6):427-8.
Transcriptomic Correlates of Response to Immune Checkpoint Therapies in Melanoma
Expanding accessibility of a molecular oncology almanac for precision cancer medicine
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
The paradox of positive thinking. J Clin Oncol. 2011 Jul 01; 29(19):2730-1.
Nassar AH, Umeton R, Kim J, Lundgren K, Harshman L, Van Allen EM, Preston M, Dong F, Bellmunt J, Mouw KW, Choueiri TK, Sonpavde G, Kwiatkowski DJ
Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites. Clin Cancer Res. 2019 04 15; 25(8):2458-2470.
Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites.
Molecular and immune drivers of immunotherapy responsiveness in prostate cancer
The Cellular Geography of Therapeutic Resistance in Cancer
AlDubayan SH, Pyle LC, Gamulin M, Kulis T, Moore ND, Taylor-Weiner A, Hamid AA, Reardon B, Wubbenhorst B, Godse R, Vaughn DJ, Jacobs LA, Meien S, Grgic M, Kastelan Z, Markt SC, Damrauer SM, Rader DJ, Kember RL, Loud JT, Kanetsky PA, Greene MH, Sweeney CJ, Kubisch C, Nathanson KL, Van Allen EM, Stewart DR, Lessel D
Association of Inherited Pathogenic Variants in Checkpoint Kinase 2 (CHEK2) With Susceptibility to Testicular Germ Cell Tumors. JAMA Oncol. 2019 Apr 01; 5(4):514-522.
Association of Inherited Pathogenic Variants in Checkpoint Kinase 2 (CHEK2) With Susceptibility to Testicular Germ Cell Tumors.
Molecular origins and evolution to chemoresistance in germ cell tumors
Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group. Br J Cancer. 2019 Apr; 120(8):869.
Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.
Genomic correlates of response to immune checkpoint blockade. Nat Med. 2019 03; 25(3):389-402.
Genomic correlates of response to immune checkpoint blockade.
Clinical analysis and interpretation of cancer genome data. J Clin Oncol. 2013 May 20; 31(15):1825-33.
Clinical analysis and interpretation of cancer genome data.
Hamid AA, Gray KP, Shaw G, MacConaill LE, Evan C, Bernard B, Loda M, Corcoran NM, Van Allen EM, Choudhury AD, Sweeney CJ
Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer. Eur Urol. 2019 07; 76(1):89-97.
Compound Genomic Alterations of TP53, PTEN, and RB1 Tumor Suppressors in Localized and Metastatic Prostate Cancer.
Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, Sboner A, Fedrizzi T, Mosquera JM, Robinson BD, De Sarkar N, Kunju LP, Tomlins S, Wu YM, Nava Rodrigues D, Loda M, Gopalan A, Reuter VE, Pritchard CC, Mateo J, Bianchini D, Miranda S, Carreira S, Rescigno P, Filipenko J, Vinson J, Montgomery RB, Beltran H, Heath EI, Scher HI, Kantoff PW, Taplin ME, Schultz N, deBono JS, Demichelis F, Nelson PS, Rubin MA, Chinnaiyan AM, Sawyers CL
Genomic correlates of clinical outcome in advanced prostate cancer. Proc Natl Acad Sci U S A. 2019 06 04; 116(23):11428-11436.
Genomic correlates of clinical outcome in advanced prostate cancer.
Fares CM, Van Allen EM, Drake CG, Allison JP, Hu-Lieskovan S
American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting
Mechanisms of Resistance to Immune Checkpoint Blockade: Why Does Checkpoint Inhibitor Immunotherapy Not Work for All Patients? Am Soc Clin Oncol Educ Book. 2019 Jan; 39:147-164.
Mechanisms of Resistance to Immune Checkpoint Blockade: Why Does Checkpoint Inhibitor Immunotherapy Not Work for All Patients?
Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2019 Jul; 51(7):1194.
Publisher Correction: The long tail of oncogenic drivers in prostate cancer.
Jerome and Nancy Kohlberg Professor of Medicine
Amin-Mansour A, George S, Sioletic S, Carter SL, Rosenberg M, Taylor-Weiner A, Stewart C, Chevalier A, Seepo S, Tracy A, Getz G, Hornick JL, Nucci MR, Quade B, Demetri GD, Raut CP, Garraway LA, Van Allen EM, Wagner AJ
Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res. 2019 08 15; 25(16):5135-5142.
Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma.
Assistant Professor of Radiation Oncology
Gurjao C, Liu D, Hofree M, AlDubayan SH, Wakiro I, Su MJ, Felt K, Gjini E, Brais LK, Rotem A, Rosenthal MH, Rozenblatt-Rosen O, Rodig S, Ng K, Van Allen EM, Corsello SM, Ogino S, Regev A, Nowak JA, Giannakis M
Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res. 2019 08; 7(8):1230-1236.
Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer.
Kamran SC, Lennerz JK, Margolis CA, Liu D, Reardon B, Wankowicz SA, Van Seventer EE, Tracy A, Wo JY, Carter SL, Willers H, Corcoran RB, Hong TS, Van Allen EM
Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer. Clin Cancer Res. 2019 09 15; 25(18):5561-5571.
Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer.
A statistical framework to systematically characterize cancer driver mutations in noncoding genomic regions
Kehl KL, Elmarakeby H, Nishino M, Van Allen EM, Lepisto EM, Hassett MJ, Johnson BE, Schrag D
Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports. JAMA Oncol. 2019 Oct 01; 5(10):1421-1429.
Assessment of Deep Natural Language Processing in Ascertaining Oncologic Outcomes From Radiology Reports.
Braun DA, Ishii Y, Walsh AM, Van Allen EM, Wu CJ, Shukla SA, Choueiri TK
Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma. JAMA Oncol. 2019 Nov 01; 5(11):1631-1633.
Clinical Validation of PBRM1 Alterations as a Marker of Immune Checkpoint Inhibitor Response in Renal Cell Carcinoma.
Finding the edge of the seat. Nat Med. 2019 09; 25(9):1328.
Li H, Bullock K, Gurjao C, Braun D, Shukla SA, Bossé D, Lalani AA, Gopal S, Jin C, Horak C, Wind-Rotolo M, Signoretti S, McDermott DF, Freeman GJ, Van Allen EM, Schreiber SL, Stephen Hodi F, Sellers WR, Garraway LA, Clish CB, Choueiri TK, Giannakis M
Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Nat Commun. 2019 09 25; 10(1):4346.
Metabolomic adaptations and correlates of survival to immune checkpoint blockade.
Taylor-Weiner A, Aguet F, Haradhvala NJ, Gosai S, Anand S, Kim J, Ardlie K, Van Allen EM, Getz G
Scaling computational genomics to millions of individuals with GPUs. Genome Biol. 2019 11 01; 20(1):228.
Scaling computational genomics to millions of individuals with GPUs.
McGregor BA, McKay RR, Braun DA, Werner L, Gray K, Flaifel A, Signoretti S, Hirsch MS, Steinharter JA, Bakouny Z, Flippot R, Wei XX, Choudhury A, Kilbridge K, Freeman GJ, Van Allen EM, Harshman LC, McDermott DF, Vaishampayan U, Choueiri TK
Results of a Multicenter Phase II Study of Atezolizumab and Bevacizumab for Patients With Metastatic Renal Cell Carcinoma With Variant Histology and/or Sarcomatoid Features. J Clin Oncol. 2020 01 01; 38(1):63-70.
Results of a Multicenter Phase II Study of Atezolizumab and Bevacizumab for Patients With Metastatic Renal Cell Carcinoma With Variant Histology and/or Sarcomatoid Features.
Hwang JH, Seo JH, Beshiri ML, Wankowicz S, Liu D, Cheung A, Li J, Qiu X, Hong AL, Botta G, Golumb L, Richter C, So J, Sandoval GJ, Giacomelli AO, Ly SH, Han C, Dai C, Pakula H, Sheahan A, Piccioni F, Gjoerup O, Loda M, Sowalsky AG, Ellis L, Long H, Root DE, Kelly K, Van Allen EM, Freedman ML, Choudhury AD, Hahn WC
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Rep. 2019 11 19; 29(8):2355-2370.e6.
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer.
Liu D, Schilling B, Liu D, Sucker A, Livingstone E, Jerby-Arnon L, Zimmer L, Gutzmer R, Satzger I, Loquai C, Grabbe S, Vokes N, Margolis CA, Conway J, He MX, Elmarakeby H, Dietlein F, Miao D, Tracy A, Gogas H, Goldinger SM, Utikal J, Blank CU, Rauschenberg R, von Bubnoff D, Krackhardt A, Weide B, Haferkamp S, Kiecker F, Izar B, Garraway L, Regev A, Flaherty K, Paschen A, Van Allen EM, Schadendorf D
Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019 12; 25(12):1916-1927.
Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma.
Nassar AH, Abou Alaiwi S, AlDubayan SH, Moore N, Mouw KW, Kwiatkowski DJ, Choueiri TK, Curran C, Berchuck JE, Harshman LC, Nuzzo PV, Chanza NM, Van Allen E, Esplin ED, Yang S, Callis T, Garber JE, Rana HQ, Sonpavde G
Genetics in medicine : official journal of the American College of Medical Genetics
Prevalence of pathogenic germline cancer risk variants in high-risk urothelial carcinoma. Genet Med. 2020 04; 22(4):709-718.
Prevalence of pathogenic germline cancer risk variants in high-risk urothelial carcinoma.
Vokes NI, Liu D, Ricciuti B, Jimenez-Aguilar E, Rizvi H, Dietlein F, He MX, Margolis CA, Elmarakeby HA, Girshman J, Adeni A, Sanchez-Vega F, Schultz N, Dahlberg S, Zehir A, Jänne PA, Nishino M, Umeton R, Sholl LM, Van Allen EM, Hellmann MD, Awad MM
Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer. JCO Precis Oncol. 2019; 3.
Harmonization of Tumor Mutational Burden Quantification and Association With Response to Immune Checkpoint Blockade in Non-Small-Cell Lung Cancer.
Nassar AH, Mouw KW, Jegede O, Shinagare AB, Kim J, Liu CJ, Pomerantz M, Harshman LC, Van Allen EM, Wei XX, McGregor B, Choudhury AD, Preston MA, Dong F, Signoretti S, Lindeman NI, Bellmunt J, Choueiri TK, Sonpavde G, Kwiatkowski DJ
A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma. Br J Cancer. 2020 02; 122(4):555-563.
A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma.
Dietlein F, Weghorn D, Taylor-Weiner A, Richters A, Reardon B, Liu D, Lander ES, Van Allen EM, Sunyaev SR
Identification of cancer driver genes based on nucleotide context. Nat Genet. 2020 02; 52(2):208-218.
Identification of cancer driver genes based on nucleotide context.
Rassy E, Bakouny Z, Choueiri TK, Van Allen EM, Fizazi K, Greco FA, Pavlidis N
European journal of cancer (Oxford, England : 1990)
The role of site-specific therapy for cancers of unknown of primary: A meta-analysis. Eur J Cancer. 2020 03; 127:118-122.
The role of site-specific therapy for cancers of unknown of primary: A meta-analysis.
Barroso-Sousa R, Keenan TE, Pernas S, Exman P, Jain E, Garrido-Castro AC, Hughes M, Bychkovsky B, Umeton R, Files JL, Lindeman NI, MacConaill LE, Hodi FS, Krop IE, Dillon D, Winer EP, Wagle N, Lin NU, Mittendorf EA, Van Allen EM, Tolaney SM
Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2020 06 01; 26(11):2565-2572.
Tumor Mutational Burden and PTEN Alterations as Molecular Correlates of Response to PD-1/L1 Blockade in Metastatic Triple-Negative Breast Cancer.
Rafiei S, Fitzpatrick K, Liu D, Cai MY, Elmarakeby HA, Park J, Ricker C, Kochupurakkal BS, Choudhury AD, Hahn WC, Balk SP, Hwang JH, Van Allen EM, Mouw KW
ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer. Cancer Res. 2020 06 01; 80(11):2094-2100.
ATM Loss Confers Greater Sensitivity to ATR Inhibition Than PARP Inhibition in Prostate Cancer.
Shahamatdar S, He MX, Reyna MA, Gusev A, AlDubayan SH, Van Allen EM, Ramachandran S
Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Rep. 2020 03 03; 30(9):2900-2908.e4.
Germline Features Associated with Immune Infiltration in Solid Tumors.
Abou Alaiwi S, Nassar AH, Xie W, Bakouny Z, Berchuck JE, Braun DA, Baca SC, Nuzzo PV, Flippot R, Mouhieddine TH, Spurr LF, Li YY, Li T, Flaifel A, Steinharter JA, Margolis CA, Vokes NI, Du H, Shukla SA, Cherniack AD, Sonpavde G, Haddad RI, Awad MM, Giannakis M, Hodi FS, Liu XS, Signoretti S, Kadoch C, Freedman ML, Kwiatkowski DJ, Van Allen EM, Choueiri TK
Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors. Cancer Immunol Res. 2020 08; 8(8):1075-1084.
Mammalian SWI/SNF Complex Genomic Alterations and Immune Checkpoint Blockade in Solid Tumors.
Derks S, de Klerk LK, Xu X, Fleitas T, Liu KX, Liu Y, Dietlein F, Margolis C, Chiaravalli AM, Da Silva AC, Ogino S, Akarca FG, Freeman GJ, Rodig SJ, Hornick JL, van Allen E, Li B, Liu SX, Thorsson V, Bass AJ
Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas. Ann Oncol. 2020 08; 31(8):1011-1020.
Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas.
Gstalder C, Liu D, Miao D, Lutterbach B, DeVine AL, Lin C, Shettigar M, Pancholi P, Buchbinder EI, Carter SL, Manos MP, Rojas-Rudilla V, Brennick R, Gjini E, Chen PH, Lako A, Rodig S, Yoon CH, Freeman GJ, Barbie DA, Hodi FS, Miles W, Van Allen EM, Haq R
Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade. Cancer Discov. 2020 09; 10(9):1296-1311.
Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade.
Bustoros M, Sklavenitis-Pistofidis R, Park J, Redd R, Zhitomirsky B, Dunford AJ, Salem K, Tai YT, Anand S, Mouhieddine TH, Chavda SJ, Boehner C, Elagina L, Neuse CJ, Cha J, Rahmat M, Taylor-Weiner A, Van Allen E, Kumar S, Kastritis E, Leshchiner I, Morgan EA, Laubach J, Casneuf T, Richardson P, Munshi NC, Anderson KC, Trippa L, Aguet F, Stewart C, Dimopoulos MA, Yong K, Bergsagel PL, Manier S, Getz G, Ghobrial IM
Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression. J Clin Oncol. 2020 07 20; 38(21):2380-2389.
Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression.
Such L, Zhao F, Liu D, Thier B, Le-Trilling VTK, Sucker A, Coch C, Pieper N, Howe S, Bhat H, Kalkavan H, Ritter C, Brinkhaus R, Ugurel S, Köster J, Seifert U, Dittmer U, Schuler M, Lang KS, Kufer TA, Hartmann G, Becker JC, Horn S, Ferrone S, Liu D, Van Allen EM, Schadendorf D, Griewank K, Trilling M, Paschen A
Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy. J Clin Invest. 2020 08 03; 130(8):4266-4281.
Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy.
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant' Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon JC, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med. 2020 06; 26(6):909-918.
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.
Crowdis J, He MX, Reardon B, Van Allen EM
CoMut: visualizing integrated molecular information with comutation plots. Bioinformatics. 2020 08 01; 36(15):4348-4349.
CoMut: visualizing integrated molecular information with comutation plots.
Mouhieddine TH, Sperling AS, Redd R, Park J, Leventhal M, Gibson CJ, Manier S, Nassar AH, Capelletti M, Huynh D, Bustoros M, Sklavenitis-Pistofidis R, Tahri S, Hornburg K, Dumke H, Itani MM, Boehner CJ, Liu CJ, AlDubayan SH, Reardon B, Van Allen EM, Keats JJ, Stewart C, Mehr S, Auclair D, Schlossman RL, Munshi NC, Anderson KC, Steensma DP, Laubach JP, Richardson PG, Ritz J, Ebert BL, Soiffer RJ, Trippa L, Getz G, Neuberg DS, Ghobrial IM
Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant. Nat Commun. 2020 06 12; 11(1):2996.
Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant.
Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2020 Jul; 26(7):1147.
Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma.
Annapragada A, Sikora A, Bollard C, Conejo-Garcia J, Cruz CR, Demehri S, Demetriou M, Demirdjian L, Fong L, Horowitz M, Hutson A, Kadash-Edmondson K, Kufe D, Lipkin S, Liu S, McCarthy C, Morgan M, Morris Z, Pan Y, Pasquini M, Schoenberger S, Van Allen E, Vilar E, Xing Y, Zha W, Odunsi A
Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer. J Immunother Cancer. 2020 06; 8(1).
Cancer Moonshot Immuno-Oncology Translational Network (IOTN): accelerating the clinical translation of basic discoveries for improving immunotherapy and immunoprevention of cancer.
Font-Tello A, Kesten N, Xie Y, Taing L, Varešlija D, Young LS, Hamid AA, Van Allen EM, Sweeney CJ, Gjini E, Lako A, Hodi FS, Bellmunt J, Brown M, Cejas P, Long HW
FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues. Nat Protoc. 2020 08; 15(8):2503-2518.
FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues.
Kehl KL, Xu W, Lepisto E, Elmarakeby H, Hassett MJ, Van Allen EM, Johnson BE, Schrag D
Natural Language Processing to Ascertain Cancer Outcomes From Medical Oncologist Notes. JCO Clin Cancer Inform. 2020 08; 4:680-690.
Natural Language Processing to Ascertain Cancer Outcomes From Medical Oncologist Notes.
McPherson V, Reardon B, Bhayankara A, Scott SN, Boyd ME, Garcia-Grossman IR, Regazzi AM, McCoy AS, Kim PH, Al-Ahmadie H, Ostrovnaya I, Roth AJ, Farooki A, Berger MF, Rosenberg JE, Solit DB, Van Allen E, Milowsky MI, Bajorin DF, Iyer G
A phase 2 trial of buparlisib in patients with platinum-resistant metastatic urothelial carcinoma. Cancer. 2020 10 15; 126(20):4532-4544.
A phase 2 trial of buparlisib in patients with platinum-resistant metastatic urothelial carcinoma.
Methods in molecular biology (Clifton, N.J.)
Integrated Analysis of Germ Cell Tumors. Methods Mol Biol. 2021; 2195:181-187.
Integrated Analysis of Germ Cell Tumors.
Bellmunt J, Kim J, Reardon B, Perera-Bel J, Orsola A, Rodriguez-Vida A, Wankowicz SA, Bowden M, Barletta JA, Morote J, de Torres I, Juanpere N, Lloreta-Trull J, Hernandez S, Mouw KW, Taplin ME, Cejas P, Long HW, Van Allen EM, Getz G, Kwiatkowski DJ
Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer. Cancer Res. 2020 10 15; 80(20):4476-4486.
Genomic Predictors of Good Outcome, Recurrence, or Progression in High-Grade T1 Non-Muscle-Invasive Bladder Cancer.
Tolaney SM, Barroso-Sousa R, Keenan T, Li T, Trippa L, Vaz-Luis I, Wulf G, Spring L, Sinclair NF, Andrews C, Pittenger J, Richardson ET, Dillon D, Lin NU, Overmoyer B, Partridge AH, Van Allen E, Mittendorf EA, Winer EP, Krop IE
Effect of Eribulin With or Without Pembrolizumab on Progression-Free Survival for Patients With Hormone Receptor-Positive, ERBB2-Negative Metastatic Breast Cancer: A Randomized Clinical Trial. JAMA Oncol. 2020 10 01; 6(10):1598-1605.
Effect of Eribulin With or Without Pembrolizumab on Progression-Free Survival for Patients With Hormone Receptor-Positive, ERBB2-Negative Metastatic Breast Cancer: A Randomized Clinical Trial.
Solomon IB, McGraw S, Shen J, Albayrak A, Alterovitz G, Davies M, Del Vecchio Fitz C, Freedman RA, Lopez LN, Sholl LM, Van Allen E, Mortimer J, Fakih M, Pal S, Reckamp KL, Yuan Y, Gray SW
Engaging Patients in Precision Oncology: Development and Usability of a Web-Based Patient-Facing Genomic Sequencing Report. JCO Precis Oncol. 2020; 4.
Engaging Patients in Precision Oncology: Development and Usability of a Web-Based Patient-Facing Genomic Sequencing Report.
Han GC, Hwang J, Wankowicz SAM, Zhang Z, Liu D, Cibulskis C, Gaviola GC, Ghazikhanian V, McKay RR, Bubley GJ, Carter SL, Balk SP, Hahn WC, Taplin ME, Van Allen EM
Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol. 2017; 1.
Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer.
Rusert JM, Juarez EF, Brabetz S, Jensen J, Garancher A, Chau LQ, Tacheva-Grigorova SK, Wahab S, Udaka YT, Finlay D, Seker-Cin H, Reardon B, Gröbner S, Serrano J, Ecker J, Qi L, Kogiso M, Du Y, Baxter PA, Henderson JJ, Berens ME, Vuori K, Milde T, Cho YJ, Li XN, Olson JM, Reyes I, Snuderl M, Wong TC, Dimmock DP, Nahas SA, Malicki D, Crawford JR, Levy ML, Van Allen EM, Pfister SM, Tamayo P, Kool M, Mesirov JP, Wechsler-Reya RJ
Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res. 2020 12 01; 80(23):5393-5407.
Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma.
AlDubayan SH, Conway JR, Camp SY, Witkowski L, Kofman E, Reardon B, Han S, Moore N, Elmarakeby H, Salari K, Choudhry H, Al-Rubaish AM, Al-Sulaiman AA, Al-Ali AK, Taylor-Weiner A, Van Allen EM
Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma. JAMA. 2020 11 17; 324(19):1957-1969.
Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma.
Börcsök J, Sztupinszki Z, Bekele R, Gao SP, Diossy M, Samant AS, Dillon KM, Tisza V, Spisák S, Rusz O, Csabai I, Pappot H, Frazier ZJ, Konieczkowski DJ, Liu D, Vasani N, Rodrigues JA, Solit DB, Hoffman-Censits JH, Plimack ER, Rosenberg JE, Lazaro JB, Taplin ME, Iyer G, Brunak S, Lozsa R, Van Allen EM, Szüts D, Mouw KW, Szallasi Z
Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer. Clin Cancer Res. 2021 04 01; 27(7):2011-2022.
Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer.
Conway JR, Dietlein F, Taylor-Weiner A, AlDubayan S, Vokes N, Keenan T, Reardon B, He MX, Margolis CA, Weirather JL, Haq R, Schilling B, Stephen Hodi F, Schadendorf D, Liu D, Van Allen EM
Integrated molecular drivers coordinate biological and clinical states in melanoma. Nat Genet. 2020 12; 52(12):1373-1383.
Integrated molecular drivers coordinate biological and clinical states in melanoma.
Iyer G, Bochner BH, Van Allen EM, Solit DB, Rosenberg JE
Re: Russell E.N. Becker, Alexa R. Meyer, Aaron Brant, et al. Clinical Restaging and Tumor Sequencing are Inaccurate Indicators of Response to Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.07.016. Eur Urol. 2021 02; 79(2):e56-e57.
Re: Russell E.N. Becker, Alexa R. Meyer, Aaron Brant, et al. Clinical Restaging and Tumor Sequencing are Inaccurate Indicators of Response to Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2020.07.016.
Cheng ML, Donoghue MTA, Audenet F, Wong NC, Pietzak EJ, Bielski CM, Isharwal S, Iyer G, Funt S, Bagrodia A, Bajorin DF, Reuter VE, Eng J, Joseph G, Bourque C, Bromberg M, Ling L, Selcuklu SD, Arcila ME, Tsui DWY, Zehir A, Viale A, Berger MF, Bosl GJ, Sheinfeld J, Van Allen E, Taylor BS, Al-Ahmadie H, Solit DB, Feldman DR
Germ Cell Tumor Molecular Heterogeneity Revealed Through Analysis of Primary and Metastasis Pairs. JCO Precis Oncol. 2020; 4.
Germ Cell Tumor Molecular Heterogeneity Revealed Through Analysis of Primary and Metastasis Pairs.
Keenan TE, Li T, Vallius T, Guerriero JL, Tayob N, Kochupurakkal B, Davis J, Pastorello R, Tahara RK, Anderson L, Conway J, He MX, Shannon E, Godin RE, Sorger PK, D'Andrea A, Overmoyer B, Winer EP, Mittendorf EA, Van Allen EM, Shapiro GI, Tolaney SM
Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2021 02 15; 27(4):983-991.
Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer.
Dissecting the immunogenomic biology of cancer for biomarker development. Nat Rev Clin Oncol. 2021 03; 18(3):133-134.
Dissecting the immunogenomic biology of cancer for biomarker development.
Current opinion in genetics & development
Predicting immunotherapy response through genomics. Curr Opin Genet Dev. 2021 02; 66:1-9.
Predicting immunotherapy response through genomics.
Zavidij O, Haradhvala NJ, Mouhieddine TH, Sklavenitis-Pistofidis R, Cai S, Reidy M, Rahmat M, Flaifel A, Ferland B, Su NK, Agius MP, Park J, Manier S, Bustoros M, Huynh D, Capelletti M, Berrios B, Liu CJ, He MX, Braggio E, Fonseca R, Maruvka YE, Guerriero JL, Goldman M, Van Allen EM, McCarroll SA, Azzi J, Getz G, Ghobrial IM
Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma. Nat Cancer. 2020 05; 1(5):493-506.
Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma.
Braun DA, Bakouny Z, Hirsch L, Flippot R, Van Allen EM, Wu CJ, Choueiri TK
Beyond conventional immune-checkpoint inhibition - novel immunotherapies for renal cell carcinoma. Nat Rev Clin Oncol. 2021 04; 18(4):199-214.
Beyond conventional immune-checkpoint inhibition - novel immunotherapies for renal cell carcinoma.
Count Me In: Partnering with patients to define the clinical and genomic landscape of rare aggressive sarcomas in children and adults
Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Abou Alaiwi S, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, Sant'Angelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Lee GM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. Nat Commun. 2021 02 05; 12(1):808.
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma.
Camp SY, Kofman E, Reardon B, Moore ND, Al-Rubaish AM, Aljumaan M, Al-Ali AK, Van Allen EM, Taylor-Weiner A, AlDubayan SH
Evaluating the molecular diagnostic yield of joint genotyping-based approach for detecting rare germline pathogenic and putative loss-of-function variants. Genet Med. 2021 05; 23(5):918-926.
Evaluating the molecular diagnostic yield of joint genotyping-based approach for detecting rare germline pathogenic and putative loss-of-function variants.
Eid FE, Elmarakeby HA, Chan YA, Fornelos N, ElHefnawi M, Van Allen EM, Heath LS, Lage K
Systematic auditing is essential to debiasing machine learning in biology. Commun Biol. 2021 02 10; 4(1):183.
Systematic auditing is essential to debiasing machine learning in biology.
Nassar AH, Lundgren K, Pomerantz M, Van Allen E, Harshman L, Choudhury AD, Preston MA, Steele GS, Mouw KW, Wei XX, McGregor BA, Choueiri TK, Bellmunt J, Kwiatkowski DJ, Sonpavde GP
Enrichment of FGFR3-TACC3 Fusions in Patients With Bladder Cancer Who Are Young, Asian, or Have Never Smoked. JCO Precis Oncol. 2018; 2.
Enrichment of FGFR3-TACC3 Fusions in Patients With Bladder Cancer Who Are Young, Asian, or Have Never Smoked.
He MX, Cuoco MS, Crowdis J, Bosma-Moody A, Zhang Z, Bi K, Kanodia A, Su MJ, Ku SY, Garcia MM, Sweet AR, Rodman C, DelloStritto L, Silver R, Steinharter J, Shah P, Izar B, Walk NC, Burke KP, Bakouny Z, Tewari AK, Liu D, Camp SY, Vokes NI, Salari K, Park J, Vigneau S, Fong L, Russo JW, Yuan X, Balk SP, Beltran H, Rozenblatt-Rosen O, Regev A, Rotem A, Taplin ME, Van Allen EM
Transcriptional mediators of treatment resistance in lethal prostate cancer. Nat Med. 2021 03; 27(3):426-433.
Transcriptional mediators of treatment resistance in lethal prostate cancer.
Bi K, He MX, Bakouny Z, Kanodia A, Napolitano S, Wu J, Grimaldi G, Braun DA, Cuoco MS, Mayorga A, DelloStritto L, Bouchard G, Steinharter J, Tewari AK, Vokes NI, Shannon E, Sun M, Park J, Chang SL, McGregor BA, Haq R, Denize T, Signoretti S, Guerriero JL, Vigneau S, Rozenblatt-Rosen O, Rotem A, Regev A, Choueiri TK, Van Allen EM
Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Cancer Cell. 2021 05 10; 39(5):649-661.e5.
Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
Mahadevan NR, Knelson EH, Wolff JO, Vajdi A, Saigí M, Campisi M, Hong D, Thai TC, Piel B, Han S, Reinhold BB, Duke-Cohan JS, Poitras MJ, Taus LJ, Lizotte PH, Portell A, Quadros V, Santucci AD, Murayama T, Cañadas I, Kitajima S, Akitsu A, Fridrikh M, Watanabe H, Reardon B, Gokhale PC, Paweletz CP, Awad MM, Van Allen EM, Lako A, Wang XT, Chen B, Hong F, Sholl LM, Tolstorukov MY, Pfaff K, Jänne PA, Gjini E, Edwards R, Rodig S, Reinherz EL, Oser MG, Barbie DA
Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity. Cancer Discov. 2021 08; 11(8):1952-1969.
Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity.
McKay RR, Kwak L, Crowdis JP, Sperger JM, Zhao SG, Xie W, Werner L, Lis RT, Zhang Z, Wei XX, Lang JM, Van Allen EM, Bhatt RS, Yu EY, Nelson PS, Bubley GJ, Montgomery RB, Taplin ME
Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance. Clin Cancer Res. 2021 07 01; 27(13):3610-3619.
Phase II Multicenter Study of Enzalutamide in Metastatic Castration-Resistant Prostate Cancer to Identify Mechanisms Driving Resistance.
Berchuck JE, Zhang Z, Silver R, Kwak L, Xie W, Lee GM, Freedman ML, Kibel AS, Van Allen EM, McKay RR, Taplin ME
Impact of Pathogenic Germline DNA Damage Repair alterations on Response to Intense Neoadjuvant Androgen Deprivation Therapy in High-risk Localized Prostate Cancer. Eur Urol. 2021 09; 80(3):295-303.
Impact of Pathogenic Germline DNA Damage Repair alterations on Response to Intense Neoadjuvant Androgen Deprivation Therapy in High-risk Localized Prostate Cancer.
Liu D, Lin JR, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu A, Mei S, Miao B, Sharova T, Alvarez-Breckenridge C, Stocking JH, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Nowak MA, Brastianos PK, Lian CG, Ruppin E, Izar B, Herlyn M, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM
Evolution of delayed resistance to immunotherapy in a melanoma responder. Nat Med. 2021 06; 27(6):985-992.
Evolution of delayed resistance to immunotherapy in a melanoma responder.
Gillani R, Seong BKA, Crowdis J, Conway JR, Dharia NV, Alimohamed S, Haas BJ, Han K, Park J, Dietlein F, He MX, Imamovic A, Ma C, Bassik MC, Boehm JS, Vazquez F, Gusev A, Liu D, Janeway KA, McFarland JM, Stegmaier K, Van Allen EM
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer Res. 2021 08 01; 81(15):3971-3984.
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival.
Kehl KL, Groha S, Lepisto EM, Elmarakeby H, Lindsay J, Gusev A, Van Allen EM, Hassett MJ, Schrag D
Clinical Inflection Point Detection on the Basis of EHR Data to Identify Clinical Trial-Ready Patients With Cancer. JCO Clin Cancer Inform. 2021 06; 5:622-630.
Clinical Inflection Point Detection on the Basis of EHR Data to Identify Clinical Trial-Ready Patients With Cancer.
Gurjao C, Zhong R, Haruki K, Li YY, Spurr LF, Lee-Six H, Reardon B, Ugai T, Zhang X, Cherniack AD, Song M, Van Allen EM, Meyerhardt JA, Nowak JA, Giovannucci EL, Fuchs CS, Wu K, Ogino S, Giannakis M
Discovery and Features of an Alkylating Signature in Colorectal Cancer. Cancer Discov. 2021 10; 11(10):2446-2455.
Discovery and Features of an Alkylating Signature in Colorectal Cancer.
Hamid AA, Huang HC, Wang V, Chen YH, Feng F, Den R, Attard G, Van Allen EM, Tran PT, Spratt DE, Dittamore R, Davicioni E, Liu G, DiPaola R, Carducci MA, Sweeney CJ
Transcriptional profiling of primary prostate tumor in metastatic hormone-sensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED trial. Ann Oncol. 2021 09; 32(9):1157-1166.
Transcriptional profiling of primary prostate tumor in metastatic hormone-sensitive prostate cancer and association with clinical outcomes: correlative analysis of the E3805 CHAARTED trial.
Mateo J, McKay R, Abida W, Aggarwal R, Alumkal J, Alva A, Feng F, Gao X, Graff J, Hussain M, Karzai F, Montgomery B, Oh W, Patel V, Rathkopf D, Rettig M, Schultz N, Smith M, Solit D, Sternberg C, Van Allen E, VanderWeele D, Vinson J, Soule HR, Chinnaiyan A, Small E, Simons JW, Dahut W, Miyahira AK, Beltran H
Accelerating precision medicine in metastatic prostate cancer. Nat Cancer. 2020 11; 1(11):1041-1053.
Accelerating precision medicine in metastatic prostate cancer.
Barroso-Sousa R, Keenan TE, Li T, Tayob N, Trippa L, Pastorello RG, Richardson Iii ET, Dillon D, Amoozgar Z, Overmoyer B, Schnitt SJ, Winer EP, Mittendorf EA, Van Allen E, Duda DG, Tolaney SM
Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: a phase II and biomarker study. NPJ Breast Cancer. 2021 Aug 25; 7(1):110.
Nivolumab in combination with cabozantinib for metastatic triple-negative breast cancer: a phase II and biomarker study.
Tewari AK, Cheung ATM, Crowdis J, Conway JR, Camp SY, Wankowicz SA, Livitz DG, Park J, Lis RT, Bosma-Moody A, He MX, AlDubayan SH, Zhang Z, McKay RR, Leshchiner I, Brown M, Balk SP, Getz G, Taplin ME, Van Allen EM
Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer. Cell Rep. 2021 09 07; 36(10):109665.
Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer.
Elmarakeby HA, Hwang J, Arafeh R, Crowdis J, Gang S, Liu D, AlDubayan SH, Salari K, Kregel S, Richter C, Arnoff TE, Park J, Hahn WC, Van Allen EM
Biologically informed deep neural network for prostate cancer discovery. Nature. 2021 10; 598(7880):348-352.
Biologically informed deep neural network for prostate cancer discovery.
Keenan TE, Guerriero JL, Barroso-Sousa R, Li T, O'Meara T, Giobbie-Hurder A, Tayob N, Hu J, Severgnini M, Agudo J, Vaz-Luis I, Anderson L, Attaya V, Park J, Conway J, He MX, Reardon B, Shannon E, Wulf G, Spring LM, Jeselsohn R, Krop I, Lin NU, Partridge A, Winer EP, Mittendorf EA, Liu D, Van Allen EM, Tolaney SM
Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer. Nat Commun. 2021 09 21; 12(1):5563.
Molecular correlates of response to eribulin and pembrolizumab in hormone receptor-positive metastatic breast cancer.
Bekele RT, Samant AS, Nassar AH, So J, Garcia EP, Curran CR, Hwang JH, Mayhew DL, Nag A, Thorner AR, Börcsök J, Sztupinszki Z, Pan CX, Bellmunt J, Kwiatkowski DJ, Sonpavde GP, Van Allen EM, Mouw KW
RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics. J Clin Invest. 2021 11 15; 131(22).
RAF1 amplification drives a subset of bladder tumors and confers sensitivity to MAPK-directed therapeutics.
Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK, Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens L, Dreijerink KMA, Ellis L, Alaiwi SA, Seo JH, Baca S, Beltran H, Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM, Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N, Drapkin B, Liu XS, Freedman M, Haffner MC, Corey E, Brown M, Long HW
Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. Nat Commun. 2021 10 01; 12(1):5775.
Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer.
Aldrighetti CM, Niemierko A, Van Allen E, Willers H, Kamran SC
Racial and Ethnic Disparities Among Participants in Precision Oncology Clinical Studies. JAMA Netw Open. 2021 11 01; 4(11):e2133205.
Racial and Ethnic Disparities Among Participants in Precision Oncology Clinical Studies.
Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda M
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology. Mol Cancer Res. 2022 02; 20(2):202-206.
Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology.
Maxwell KN, Cheng HH, Powers J, Gulati R, Ledet EM, Morrison C, Le A, Hausler R, Stopfer J, Hyman S, Kohlmann W, Naumer A, Vagher J, Greenberg SE, Naylor L, Laurino M, Konnick EQ, Shirts BH, AlDubayan SH, Van Allen EM, Nguyen B, Vijai J, Abida W, Carlo MI, Dubard-Gault M, Lee DJ, Maese LD, Mandelker D, Montgomery B, Morris MJ, Nicolosi P, Nussbaum RL, Schwartz LE, Stadler Z, Garber JE, Offit K, Schiffman JD, Nelson PS, Sartor O, Walsh MF, Pritchard CC
Inherited TP53 Variants and Risk of Prostate Cancer. Eur Urol. 2022 Mar; 81(3):243-250.
Inherited TP53 Variants and Risk of Prostate Cancer.
De Sarkar N, Dasgupta S, Chatterjee P, Coleman I, Ha G, Ang LS, Kohlbrenner EA, Frank SB, Nunez TA, Salipante SJ, Corey E, Morrissey C, Van Allen E, Schweizer MT, Haffner MC, Patel R, Hanratty B, Lucas JM, Dumpit RF, Pritchard CC, Montgomery RB, Nelson PS
Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer. JCI Insight. 2021 12 08; 6(23).
Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer.
Kehl KL, Xu W, Gusev A, Bakouny Z, Choueiri TK, Riaz IB, Elmarakeby H, Van Allen EM, Schrag D
Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset. Nat Commun. 2021 12 15; 12(1):7304.
Artificial intelligence-aided clinical annotation of a large multi-cancer genomic dataset.
Bakouny Z, Sadagopan A, Ravi P, Metaferia NY, Li J, AbuHammad S, Tang S, Denize T, Garner ER, Gao X, Braun DA, Hirsch L, Steinharter JA, Bouchard G, Walton E, West D, Labaki C, Dudani S, Gan CL, Sethunath V, Carvalho FLF, Imamovic A, Ricker C, Vokes NI, Nyman J, Berchuck JE, Park J, Hirsch MS, Haq R, Mary Lee GS, McGregor BA, Chang SL, Feldman AS, Wu CJ, McDermott DF, Heng DYC, Signoretti S, Van Allen EM, Choueiri TK, Viswanathan SR
Integrative clinical and molecular characterization of translocation renal cell carcinoma. Cell Rep. 2022 01 04; 38(1):110190.
Integrative clinical and molecular characterization of translocation renal cell carcinoma.
Kamran SC, Xie J, Cheung ATM, Mavura MY, Song H, Palapattu EL, Madej J, Gusev A, Van Allen EM, Huang FW
Tumor Mutations Across Racial Groups in a Real-World Data Registry. JCO Precis Oncol. 2021 11; 5:1654-1658.
Tumor Mutations Across Racial Groups in a Real-World Data Registry.
Mossanen M, Carvalho FLF, Muralidhar V, Preston MA, Reardon B, Conway JR, Curran C, Freeman D, Sha S, Sonpavde G, Hirsch M, Kibel AS, Van Allen EM, Mouw KW
Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol. 2022 05; 81(5):466-473.
Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy.
Stover EH, Oh C, Keskula P, Choudhury AD, Tseng YY, Adalsteinsson VA, Lohr JG, Thorner AR, Ducar M, Kryukov GV, Ha G, Rosenberg M, Freeman SS, Zhang Z, Wu X, Van Allen EM, Takeda DY, Loda M, Wu CL, Taplin ME, Garraway LA, Boehm JS, Huang FW
Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate. 2022 04; 82(5):584-597.
Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples.
Reardon B, Moore ND, Moore NS, Kofman E, AlDubayan SH, Cheung ATM, Conway J, Elmarakeby H, Imamovic A, Kamran SC, Keenan T, Keliher D, Konieczkowski DJ, Liu D, Mouw KW, Park J, Vokes NI, Dietlein F, Van Allen EM
Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat Cancer. 2021 10; 2(10):1102-1112.
Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology.
Labaki C, Bakouny Z, Sonpavde G, Choueiri TK, Van Allen EM
Towards a Better Understanding of Antibody-Drug Conjugates in Urothelial Carcinoma. Eur Urol Oncol. 2022 12; 5(6):719-721.
Towards a Better Understanding of Antibody-Drug Conjugates in Urothelial Carcinoma.
Ma F, Arai S, Wang K, Calagua C, Yuan AR, Poluben L, Gu Z, Russo JW, Einstein DJ, Ye H, He MX, Liu Y, Van Allen E, Sowalsky AG, Bhasin MK, Yuan X, Balk SP
Autocrine Canonical Wnt Signaling Primes Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer. Cancer Res. 2022 04 15; 82(8):1518-1533.
Autocrine Canonical Wnt Signaling Primes Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer.
Linking a Trio of Molecular Features in Clear-Cell Renal Cell Carcinoma. Cancer Immunol Res. 2022 03 01; 10(3):274.
Linking a Trio of Molecular Features in Clear-Cell Renal Cell Carcinoma.
Vokes NI, Chambers E, Nguyen T, Coolidge A, Lydon CA, Le X, Sholl L, Heymach JV, Nishino M, Van Allen EM, Jänne PA
Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer
Concurrent TP53 Mutations Facilitate Resistance Evolution in EGFR-Mutant Lung Adenocarcinoma. J Thorac Oncol. 2022 06; 17(6):779-792.
Concurrent TP53 Mutations Facilitate Resistance Evolution in EGFR-Mutant Lung Adenocarcinoma.
Park HJ, Qin L, Bakouny Z, Krajewski KM, Van Allen EM, Choueiri TK, Shinagare AB
Computed Tomography Texture Analysis for Predicting Clinical Outcomes in Patients With Metastatic Renal Cell Carcinoma Treated With Immune Checkpoint Inhibitors. Oncologist. 2022 05 06; 27(5):389-397.
Computed Tomography Texture Analysis for Predicting Clinical Outcomes in Patients With Metastatic Renal Cell Carcinoma Treated With Immune Checkpoint Inhibitors.
Gillani R, Camp SY, Han S, Jones JK, Chu H, O'Brien S, Young EL, Hayes L, Mitchell G, Fowler T, Gusev A, Kamihara J, Janeway KA, Schiffman JD, Crompton BD, AlDubayan SH, Van Allen EM
Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes. Am J Hum Genet. 2022 06 02; 109(6):1026-1037.
Germline predisposition to pediatric Ewing sarcoma is characterized by inherited pathogenic variants in DNA damage repair genes.
Dietlein F, Wang AB, Fagre C, Tang A, Besselink NJM, Cuppen E, Li C, Sunyaev SR, Neal JT, Van Allen EM
Genome-wide analysis of somatic noncoding mutation patterns in cancer. Science. 2022 04 08; 376(6589):eabg5601.
Genome-wide analysis of somatic noncoding mutation patterns in cancer.
Gil Del Alcazar CR, Trinh A, Aleckovic M, Rojas Jimenez E, Harper NW, Oliphant MUJ, Xie S, Krop ED, Lulseged B, Murphy KC, Keenan TE, Van Allen EM, Tolaney SM, Freeman GJ, Dillon DA, Muthuswamy SK, Polyak K
Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer. Cancer Immunol Res. 2022 06 03; 10(6):680-697.
Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer.
Hwang JH, Arafeh R, Seo JH, Baca SC, Ludwig M, Arnoff TE, Sawyer L, Richter C, Tape S, Bergom HE, McSweeney S, Rennhack JP, Klingenberg SA, Cheung ATM, Kwon J, So J, Kregel S, Van Allen EM, Drake JM, Freedman ML, Hahn WC
CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies. Elife. 2022 05 12; 11.
CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies.
Ricciuti B, Wang X, Alessi JV, Rizvi H, Mahadevan NR, Li YY, Polio A, Lindsay J, Umeton R, Sinha R, Vokes NI, Recondo G, Lamberti G, Lawrence M, Vaz VR, Leonardi GC, Plodkowski AJ, Gupta H, Cherniack AD, Tolstorukov MY, Sharma B, Felt KD, Gainor JF, Ravi A, Getz G, Schalper KA, Henick B, Forde P, Anagnostou V, Jänne PA, Van Allen EM, Nishino M, Sholl LM, Christiani DC, Lin X, Rodig SJ, Hellmann MD, Awad MM
Association of High Tumor Mutation Burden in Non-Small Cell Lung Cancers With Increased Immune Infiltration and Improved Clinical Outcomes of PD-L1 Blockade Across PD-L1 Expression Levels. JAMA Oncol. 2022 08 01; 8(8):1160-1168.
Association of High Tumor Mutation Burden in Non-Small Cell Lung Cancers With Increased Immune Infiltration and Improved Clinical Outcomes of PD-L1 Blockade Across PD-L1 Expression Levels.
Church AJ, Corson LB, Kao PC, Imamovic-Tuco A, Reidy D, Doan D, Kang W, Pinto N, Maese L, Laetsch TW, Kim A, Colace SI, Macy ME, Applebaum MA, Bagatell R, Sabnis AJ, Weiser DA, Glade-Bender JL, Homans AC, Hipps J, Harris H, Manning D, Al-Ibraheemi A, Li Y, Gupta H, Cherniack AD, Lo YC, Strand GR, Lee LA, Pinches RS, Lazo De La Vega L, Harden MV, Lennon NJ, Choi S, Comeau H, Harris MH, Forrest SJ, Clinton CM, Crompton BD, Kamihara J, MacConaill LE, Volchenboum SL, Lindeman NI, Van Allen E, DuBois SG, London WB, Janeway KA
Molecular profiling identifies targeted therapy opportunities in pediatric solid cancer. Nat Med. 2022 08; 28(8):1581-1589.
Molecular profiling identifies targeted therapy opportunities in pediatric solid cancer.
Hantel A, Clancy DD, Kehl KL, Marron JM, Van Allen EM, Abel GA
A Process Framework for Ethically Deploying Artificial Intelligence in Oncology. J Clin Oncol. 2022 12 01; 40(34):3907-3911.
A Process Framework for Ethically Deploying Artificial Intelligence in Oncology.
Luoma AM, Suo S, Wang Y, Gunasti L, Porter CBM, Nabilsi N, Tadros J, Ferretti AP, Liao S, Gurer C, Chen YH, Criscitiello S, Ricker CA, Dionne D, Rozenblatt-Rosen O, Uppaluri R, Haddad RI, Ashenberg O, Regev A, Van Allen EM, MacBeath G, Schoenfeld JD, Wucherpfennig KW
Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy. Cell. 2022 08 04; 185(16):2918-2935.e29.
Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy.
Barroso-Sousa R, Forman J, Collier K, Weber ZT, Jammihal TR, Kao KZ, Richardson ET, Keenan T, Cohen O, Manos MP, Brennick RC, Ott PA, Hodi FS, Dillon DA, Attaya V, O'Meara T, Lin NU, Van Allen EM, Rodig S, Winer EP, Mittendorf EA, Wu CJ, Wagle N, Stover DG, Shukla SA, Tolaney SM
Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit. JCO Precis Oncol. 2022 07; 6:e2100413.
Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit.
Zhou M, Ko M, Hoge AC, Luu K, Liu Y, Russell ML, Hannon WW, Zhang Z, Carrot-Zhang J, Beroukhim R, Van Allen EM, Choudhury AD, Nelson PS, Freedman ML, Taplin ME, Meyerson M, Viswanathan SR, Ha G
Patterns of structural variation define prostate cancer across disease states. JCI Insight. 2022 09 08; 7(17).
Patterns of structural variation define prostate cancer across disease states.
Kim JW, McKay RR, Radke MR, Zhao S, Taplin ME, Davis NB, Monk P, Appleman LJ, Lara PN, Vaishampayan UN, Zhang J, Paul AK, Bubley G, Van Allen EM, Unlu S, Huang Y, Loda M, Shapiro GI, Glazer PM, LoRusso PM, Ivy SP, Shyr Y, Swisher EM, Petrylak DP
Randomized Trial of Olaparib With or Without Cediranib for Metastatic Castration-Resistant Prostate Cancer: The Results From National Cancer Institute 9984. J Clin Oncol. 2023 02 01; 41(4):871-880.
Randomized Trial of Olaparib With or Without Cediranib for Metastatic Castration-Resistant Prostate Cancer: The Results From National Cancer Institute 9984.
Waks AG, Keenan TE, Li T, Tayob N, Wulf GM, Richardson ET, Attaya V, Anderson L, Mittendorf EA, Overmoyer B, Winer EP, Krop IE, Agudo J, Van Allen EM, Tolaney SM
Phase Ib study of pembrolizumab in combination with trastuzumab emtansine for metastatic HER2-positive breast cancer. J Immunother Cancer. 2022 10; 10(10).
Phase Ib study of pembrolizumab in combination with trastuzumab emtansine for metastatic HER2-positive breast cancer.
Carvalho FLF, Mossanen M, Van Allen EM, Mouw KW
Reply to Yuxuan Song, Yiqing Du, and Tao Xu's Letter to the Editor re: Matthew Mossanen, Filipe L.F. Carvalho, Vinayak Muralidhar, et al. Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2022;81:466-73. Eur Urol. 2022 11; 82(5):e141-e142.
Reply to Yuxuan Song, Yiqing Du, and Tao Xu's Letter to the Editor re: Matthew Mossanen, Filipe L.F. Carvalho, Vinayak Muralidhar, et al. Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2022;81:466-73.
Schiantarelli J, Pappa T, Conway J, Crowdis J, Reardon B, Dietlein F, Huang J, Stanizzi D, Carey E, Bosma-Moody A, Imamovic A, Han S, Camp S, Kofman E, Shannon E, Barletta JA, He MX, Liu D, Park J, Lorch JH, Van Allen EM
Mutational Footprint of Platinum Chemotherapy in a Secondary Thyroid Cancer. JCO Precis Oncol. 2022 08; 6:e2200183.
Mutational Footprint of Platinum Chemotherapy in a Secondary Thyroid Cancer.
Berchuck JE, Boiarsky D, Silver R, Sunkara R, McClure HM, Tsai HK, Siegmund S, Tewari AK, Nowak JA, Lindeman NI, Rana HQ, Choudhury AD, Pomerantz MM, Freedman ML, Van Allen EM, Taplin ME
Addition of Germline Testing to Tumor-Only Sequencing Improves Detection of Pathogenic Germline Variants in Men With Advanced Prostate Cancer. JCO Precis Oncol. 2022 Aug; 6:e2200329.
Addition of Germline Testing to Tumor-Only Sequencing Improves Detection of Pathogenic Germline Variants in Men With Advanced Prostate Cancer.
Crowdis J, Balch S, Sterlin L, Thomas BS, Camp SY, Dunphy M, Anastasio E, Shah S, Damon AL, Ramos R, Sosa DM, Small IK, Tomson BN, Nguyen CM, McGillicuddy M, Chastain PS, He MX, Cheung ATM, Wankowicz S, Tewari AK, Kim D, AlDubayan SH, Dowdye A, Zola B, Nowak J, Manarite J, Gunn IH, Olson B, Lander ES, Painter CA, Wagle N, Van Allen EM
A patient-driven clinicogenomic partnership for metastatic prostate cancer. Cell Genom. 2022 Sep 14; 2(9).
A patient-driven clinicogenomic partnership for metastatic prostate cancer.
Riaz IB, Islam M, Ikram W, Naqvi SAA, Maqsood H, Saleem Y, Riaz A, Ravi P, Wang Z, Hussain SA, Warner JL, Odedina FT, Duma N, Singh P, Kehl KL, Kamran SC, Murad MH, Landman A, Van Allen E, Bryce AH
Disparities in the Inclusion of Racial and Ethnic Minority Groups and Older Adults in Prostate Cancer Clinical Trials: A Meta-analysis. JAMA Oncol. 2023 02 01; 9(2):180-187.
Disparities in the Inclusion of Racial and Ethnic Minority Groups and Older Adults in Prostate Cancer Clinical Trials: A Meta-analysis.
Groha S, Alaiwi SA, Xu W, Naranbhai V, Nassar AH, Bakouny Z, El Zarif T, Saliby RM, Wan G, Rajeh A, Adib E, Nuzzo PV, Schmidt AL, Labaki C, Ricciuti B, Alessi JV, Braun DA, Shukla SA, Keenan TE, Van Allen E, Awad MM, Manos M, Rahma O, Zubiri L, Villani AC, Fairfax B, Hammer C, Khan Z, Reynolds K, Semenov Y, Schrag D, Kehl KL, Freedman ML, Choueiri TK, Gusev A
Germline variants associated with toxicity to immune checkpoint blockade. Nat Med. 2022 12; 28(12):2584-2591.
Germline variants associated with toxicity to immune checkpoint blockade.
Cheung ATM, Palapattu EL, Pompa IR, Aldrighetti CM, Niemierko A, Willers H, Huang F, Vapiwala N, Van Allen E, Kamran SC
Racial and ethnic disparities in a real-world precision oncology data registry. NPJ Precis Oncol. 2023 Jan 19; 7(1):7.
Racial and ethnic disparities in a real-world precision oncology data registry.
Nyman J, Denize T, Bakouny Z, Labaki C, Titchen BM, Bi K, Hari SN, Rosenthal J, Mehta N, Jiang B, Sharma B, Felt K, Umeton R, Braun DA, Rodig S, Choueiri TK, Signoretti S, Van Allen EM
bioRxiv : the preprint server for biology
Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. bioRxiv. 2023 Feb 20.
Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states.
Han S, Camp SY, Chu H, Collins R, Gillani R, Park J, Bakouny Z, Ricker CA, Reardon B, Moore N, Kofman E, Labaki C, Braun D, Choueiri TK, AlDubayan SH, Van Allen EM
medRxiv : the preprint server for health sciences
Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma. medRxiv. 2023 Jan 19.
Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma.
Pan E, Xie W, Ajmera A, Araneta A, Jamieson C, Folefac E, Hussain A, Kyriakopoulos CE, Olson A, Parikh M, Parikh R, Saraiya B, Ivy SP, Van Allen EM, Lindeman NI, Kochupurakkal BS, Shapiro GI, McKay RR
A Phase I Study of Combination Olaparib and Radium-223 in Men with Metastatic Castration-Resistant Prostate Cancer (mCRPC) with Bone Metastases (COMRADE). Mol Cancer Ther. 2023 04 03; 22(4):511-518.
A Phase I Study of Combination Olaparib and Radium-223 in Men with Metastatic Castration-Resistant Prostate Cancer (mCRPC) with Bone Metastases (COMRADE).
Doe-Tetteh SA, Camp SY, Reales D, Crowdis J, Noronha AM, Wolff B, Alano T, Galle J, Selcuklu SD, Viale A, Socci ND, Liu YL, Tew WP, Aghajanian C, Ladanyi M, He MX, AlDubayan SH, Mazor RD, Shpilberg O, Hershkovitz-Rokah O, Riancho JA, Hernandez JL, Gonzalez-Vela MC, Buthorn JJ, Wilson M, Webber AE, Yabe M, Petrova-Drus K, Rosenblum M, Durham BH, Abdel-Wahab O, Berger MF, Donoghue MTA, Kung AL, Glade Bender J, Shukla NN, Funt SA, Dogan A, Soslow RA, Al-Ahmadie H, Feldman DR, Van Allen EM, Diamond EL, Solit DB
Overcoming Barriers to Tumor Genomic Profiling through Direct-to-Patient Outreach. Clin Cancer Res. 2023 07 05; 29(13):2445-2455.
Overcoming Barriers to Tumor Genomic Profiling through Direct-to-Patient Outreach.
Riaz IB, Naqvi SAA, He H, Asghar N, Siddiqi R, Liu H, Singh P, Childs DS, Ravi P, Hussain SA, Murad MH, Boorjian SA, Sweeney C, Van Allen EM, Bryce AH
First-line Systemic Treatment Options for Metastatic Castration-Sensitive Prostate Cancer: A Living Systematic Review and Network Meta-analysis. JAMA Oncol. 2023 05 01; 9(5):635-645.
First-line Systemic Treatment Options for Metastatic Castration-Sensitive Prostate Cancer: A Living Systematic Review and Network Meta-analysis.
Schneider AC, Chandrasekar T, Bowler N, Fogg R, Leong JY, Gusev A, Rodgers LH, McCormick SR, Dahl DM, Efstathiou JA, Blute ML, Zietman AL, Wu CL, Smith MR, Van Allen EM, Feldman AS, Salari K
Impact of an Expanded Definition of Family History on Outcomes of Active Surveillance for Prostate Cancer. J Urol. 2023 06; 209(6):1112-1119.
Impact of an Expanded Definition of Family History on Outcomes of Active Surveillance for Prostate Cancer.
Boiarsky D, Lydon CA, Chambers ES, Sholl LM, Nishino M, Skoulidis F, Heymach JV, Luo J, Awad MM, Janne PA, Van Allen EM, Barbie DA, Vokes NI
Molecular markers of metastatic disease in KRAS-mutant lung adenocarcinoma. Ann Oncol. 2023 07; 34(7):589-604.
Molecular markers of metastatic disease in KRAS-mutant lung adenocarcinoma.
Saliby RM, El Zarif T, Bakouny Z, Shah V, Xie W, Flippot R, Denize T, Kane MH, Madsen KN, Ficial M, Hirsch L, Wei XX, Steinharter JA, Harshman LC, Vaishampayan UN, Severgnini M, McDermott DF, Lee GM, Xu W, Van Allen EM, McGregor BA, Signoretti S, Choueiri TK, McKay RR, Braun DA
Circulating and Intratumoral Immune Determinants of Response to Atezolizumab plus Bevacizumab in Patients with Variant Histology or Sarcomatoid Renal Cell Carcinoma. Cancer Immunol Res. 2023 08 03; 11(8):1114-1124.
Circulating and Intratumoral Immune Determinants of Response to Atezolizumab plus Bevacizumab in Patients with Variant Histology or Sarcomatoid Renal Cell Carcinoma.
Perelli L, Carbone F, Zhang L, Huang JK, Le C, Khan H, Citron F, Del Poggetto E, Gutschner T, Tomihara H, Soeung M, Minelli R, Srinivasan S, Peoples M, Lam TNA, Lundgren S, Xia R, Zhu C, Mohamed AMT, Zhang J, Sircar K, Sgambato A, Gao J, Jonasch E, Draetta GF, Futreal A, Bakouny Z, Van Allen EM, Choueiri T, Signoretti S, Msaouel P, Litchfield K, Turajlic S, Wang L, Chen YB, Di Natale RG, Hakimi AA, Giuliani V, Heffernan TP, Viale A, Bristow CA, Tannir NM, Carugo A, Genovese G
Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. Nat Cancer. 2023 07; 4(7):984-1000.
Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer.
Cotta BH, Choueiri TK, Cieslik M, Ghatalia P, Mehra R, Morgan TM, Palapattu GS, Shuch B, Vaishampayan U, Van Allen E, Ari Hakimi A, Salami SS
Current Landscape of Genomic Biomarkers in Clear Cell Renal Cell Carcinoma. Eur Urol. 2023 08; 84(2):166-175.
Current Landscape of Genomic Biomarkers in Clear Cell Renal Cell Carcinoma.
Konda P, Garinet S, Van Allen EM, Viswanathan SR
Genome-guided discovery of cancer therapeutic targets. Cell Rep. 2023 Aug 29; 42(8):112978.
Genome-guided discovery of cancer therapeutic targets.
Paolino J, Dimitrov B, Apsel Winger B, Sandoval-Perez A, Rangarajan AV, Ocasio-Martinez N, Tsai HK, Li Y, Robichaud AL, Khalid D, Hatton C, Gillani R, Polonen P, Dilig A, Gotti G, Kavanagh J, Adhav AA, Gow S, Tsai J, Li Y, Ebert BL, Van Allen EM, Bledsoe J, Kim AS, Tasian SK, Cooper SL, Cooper TM, Hijiya N, Sulis ML, Shukla NN, Magee JA, Mullighan CG, Burke MJ, Luskin MR, Mar BG, Jacobson MP, Harris MH, Stegmaier K, Place AE, Pikman Y
Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res. 2023 11 14; 29(22):4613-4626.
Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma.
Cheung ATM, Niemierko A, Van Allen E, Vapiwala N, Kamran SC
Reply to: Addressing racial and ethnic disparities in AACR project GENIE. NPJ Precis Oncol. 2023 Aug 31; 7(1):82.
Reply to: Addressing racial and ethnic disparities in AACR project GENIE.
Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states. Cell Rep Med. 2023 09 19; 4(9):101189.
Elmarakeby HA, Trukhanov PS, Arroyo VM, Riaz IB, Schrag D, Van Allen EM, Kehl KL
Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports. BMC Bioinformatics. 2023 Sep 02; 24(1):328.
Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports.
Al-Jumaan M, Chu H, Alsulaiman A, Camp SY, Han S, Gillani R, Al Marzooq Y, Almulhim F, Vatte C, Al Nemer A, Almuhanna A, Van Allen EM, Al-Ali A, AlDubayan SH
Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients. Genome Med. 2023 09 01; 15(1):65.
Interplay of Mendelian and polygenic risk factors in Arab breast cancer patients.
Hoffman SE, Dowrey TW, Villacorta Martin C, Bi K, Titchen B, Johri S, DelloStritto L, Patel M, Mackichan C, Inga S, Chen J, Grimaldi G, Napolitano S, Wakiro I, Wu J, Yeung J, Rotem A, Sicinska E, Shannon E, Clancy T, Wang J, Denning S, Brais L, Besson NR, Pfaff KL, Huang Y, Kao KZ, Rodig S, Hornick JL, Vigneau S, Park J, Kulke MH, Chan J, Van Allen EM, Murphy GJ
Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors. Sci Adv. 2023 09 29; 9(39):eadd9668.
Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors.
Kamran SC, Zhou Y, Otani K, Drumm M, Otani Y, Wu S, Wu CL, Feldman AS, Wszolek M, Lee RJ, Saylor PJ, Lennerz J, Van Allen E, Willers H, Hong TS, Liu Y, Davicioni E, Gibb EA, Shipley WU, Mouw KW, Efstathiou JA, Miyamoto DT
Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. Clin Cancer Res. 2023 12 15; 29(24):5116-5127.
Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer.
Caswell DR, Gui P, Mayekar MK, Law EK, Pich O, Bailey C, Boumelha J, Kerr DL, Blakely CM, Manabe T, Martinez-Ruiz C, Bakker B, De Dios Palomino Villcas J, I Vokes N, Dietzen M, Angelova M, Gini B, Tamaki W, Allegakoen P, Wu W, Humpton TJ, Hill W, Tomaschko M, Lu WT, Haderk F, Al Bakir M, Nagano A, Gimeno-Valiente F, de Carné Trécesson S, Vendramin R, Barbè V, Mugabo M, Weeden CE, Rowan A, McCoach CE, Almeida B, Green M, Gomez C, Nanjo S, Barbosa D, Moore C, Przewrocka J, Black JRM, Grönroos E, Suarez-Bonnet A, Priestnall SL, Zverev C, Lighterness S, Cormack J, Olivas V, Cech L, Andrews T, Rule B, Jiao Y, Zhang X, Ashford P, Durfee C, Venkatesan S, Temiz NA, Tan L, Larson LK, Argyris PP, Brown WL, Yu EA, Rotow JK, Guha U, Roper N, Yu J, Vogel RI, Thomas NJ, Marra A, Selenica P, Yu H, Bakhoum SF, Chew SK, Reis-Filho JS, Jamal-Hanjani M, Vousden KH, McGranahan N, Van Allen EM, Kanu N, Harris RS, Downward J, Bivona TG, Swanton C
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat Genet. 2024 Jan; 56(1):60-73.
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance.
Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer. 2024 01 08; 12(1).
Historical perspective and future directions: computational science in immuno-oncology.
Huffman BM, Singh H, Ali LR, Horick N, Wang SJ, Hoffman MT, Metayer KA, Murray S, Bird A, Abrams TA, Biller LH, Chan JA, Meyerhardt JA, McCleary NJ, Goessling W, Patel AK, Wisch JS, Yurgelun MB, Mouw K, Reardon B, Van Allen EM, Zerillo JA, Clark JW, Parikh A, Mayer RJ, Schlechter B, Ng K, Kumar S, Del Vecchio Fitz C, Kuperwasser C, Hanna GJ, Coveler AL, Rubinson DA, Welsh EL, Pfaff K, Rodig S, Dougan SK, Cleary JM
Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders. J Immunother Cancer. 2024 01 25; 12(1).
Biomarkers of pembrolizumab efficacy in advanced anal squamous cell carcinoma: analysis of a phase II clinical trial and a cohort of long-term responders.
Han SH, Camp SY, Chu H, Collins R, Gillani R, Park J, Bakouny Z, Ricker CA, Reardon B, Moore N, Kofman E, Labaki C, Braun D, Choueiri TK, AlDubayan SH, Van Allen EM
Integrative Analysis of Germline Rare Variants in Clear and Non-clear Cell Renal Cell Carcinoma. Eur Urol Open Sci. 2024 Apr; 62:107-122.
Integrative Analysis of Germline Rare Variants in Clear and Non-clear Cell Renal Cell Carcinoma.
Hantel A, Walsh TP, Marron JM, Kehl KL, Sharp R, Van Allen E, Abel GA
Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care. JAMA Netw Open. 2024 03 04; 7(3):e244077.
Perspectives of Oncologists on the Ethical Implications of Using Artificial Intelligence for Cancer Care.
Choudhury AD, Kwak L, Cheung A, Allaire KM, Marquez J, Yang DD, Tripathi A, Kilar JM, Flynn M, Maynard B, Reichel R, Pace AF, Chen BK, Van Allen EM, Kilbridge K, Wei XX, McGregor BA, Pomerantz MM, Bhatt RS, Sweeney CJ, Bubley GJ, Jacene HA, Taplin ME, Huang FW, Harshman LC, Fong L
Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer. Cancer Immunol Res. 2024 Jun 04; 12(6):704-718.
Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer.
Kamran SC, Otani Y, Qi D, Pompa IR, Dzeng RK, Pittie R, Chung E, Otani K, Wo JY, Zietman AL, Reeves PM, Van Allen EM, Efstathiou JA, Miyamoto DT
Journal of the National Comprehensive Cancer Network : JNCCN
PCO24-175: Immune Cell Dynamics After Radiotherapy for Oligometastatic Prostate Cancer. J Natl Compr Canc Netw. 2024 Apr 05; 22(2.5).
PCO24-175: Immune Cell Dynamics After Radiotherapy for Oligometastatic Prostate Cancer.
Lotter W, Hassett MJ, Schultz N, Kehl KL, Van Allen EM, Cerami E
Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions. Cancer Discov. 2024 May 01; 14(5):711-726.
Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions.
Saliby RM, Labaki C, Jammihal TR, Xie W, Sun M, Shah V, Saad E, Kane MH, Kashima S, Sadak K, El Zarif T, Poduval D, Motzer RJ, Powles T, Rini BI, Albiges L, Pal SK, McGregor BA, McKay RR, Signoretti S, Van Allen EM, Shukla SA, Choueiri TK, Braun DA
Impact of renal cell carcinoma molecular subtypes on immunotherapy and targeted therapy outcomes. Cancer Cell. 2024 May 13; 42(5):732-735.
Impact of renal cell carcinoma molecular subtypes on immunotherapy and targeted therapy outcomes.
Dissecting Integrated Cellular Programs Promoting Platinum Resistance and Progression in Bladder Cancer
Dissecting Convergent Somatic and Germline Alterations that Mediate the Origins and Evolution of Kidney Cancer
Conway JR, Gillani R, Crowdis J, Reardon B, Park J, Han S, Titchen B, Benamar M, Haq R, Van Allen EM
Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest. 2024 May 14; 134(13).
Somatic structural variants drive distinct modes of oncogenesis in melanoma.
Gillani R, Collins RL, Crowdis J, Garza A, Jones JK, Walker M, Sanchis-Juan A, Whelan C, Pierce-Hoffman E, Talkowski M, Brand H, Haigis K, LoPiccolo J, AlDubayan SH, Gusev A, Crompton BD, Janeway KA, Van Allen EM
Rare germline structural variants increase risk for pediatric solid tumors. bioRxiv. 2024 Apr 29.
Rare germline structural variants increase risk for pediatric solid tumors.
El Zarif T, Semaan K, Eid M, Seo JH, Garinet S, Davidsohn MP, Sahgal P, Fortunato B, Canniff J, Nassar AH, Abou Alaiwi S, Bakouny Z, Lakshminarayanan G, Savignano H, Lyons K, Matar S, Ali A, Saad E, Saliby RM, Cordeiro P, Zhang Z, El Ahmar N, Laimon YN, Labaki C, Shah V, Freeman D, O'Toole J, Lee GM, Hwang J, Pomerantz M, Signoretti S, Van Allen EM, Xie W, Berchuck JE, Viswanathan SR, Braun DA, Choueiri TK, Freedman ML, Baca SC
Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma. Cell Rep. 2024 06 25; 43(6):114350.
Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma.
Satyal U, Valentine H, Liu D, Slifker M, Lallas CD, Trabulsi EJ, Bukavina L, Szeto L, Hoffman-Censits JH, Mouw KW, Faltas BM, Grivas P, Ibragimova I, Porten SP, Van Allen EM, Geynisman DM, Parker DC, O'Neill JP, Drevik J, Christianson SS, Ginzburg S, Correa AF, Uzzo RG, Ross EA, Zibelman MR, Ghatalia P, Plimack ER, Kutikov A, Abbosh PH
Urine Biopsy as Dynamic Biomarker to Enhance Clinical Staging of Bladder Cancer in Radical Cystectomy Candidates. JCO Precis Oncol. 2024 06; 8:e2300362.
Urine Biopsy as Dynamic Biomarker to Enhance Clinical Staging of Bladder Cancer in Radical Cystectomy Candidates.
Germain RN, Van Allen EM, Trynka G, Tsang JS, Grün D, Kiemen AL, Shi Y, Pugh Bernard A, Nolan GP
Dilly J, Hoffman MT, Abbassi L, Li Z, Paradiso F, Parent BD, Hennessey CJ, Jordan AC, Morgado M, Dasgupta S, Uribe GA, Yang A, Kapner KS, Hambitzer FP, Qiang L, Feng H, Geisberg J, Wang J, Evans KE, Lyu H, Schalck A, Feng N, Lopez AM, Bristow CA, Kim MP, Rajapakshe KI, Bahrambeigi V, Roth JA, Garg K, Guerrero PA, Stanger BZ, Cristea S, Lowe SW, Baslan T, Van Allen EM, Mancias JD, Chan E, Anderson A, Katlinskaya YV, Shalek AK, Hong DS, Pant S, Hallin J, Anderes K, Olson P, Heffernan TP, Chugh S, Christensen JG, Maitra A, Wolpin BM, Raghavan S, Nowak JA, Winter PS, Dougan SK, Aguirre AJ
Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer. Cancer Discov. 2024 Nov 01; 14(11):2135-2161.
Mechanisms of Resistance to Oncogenic KRAS Inhibition in Pancreatic Cancer.
van de Haar J, Roepman P, Andre F, Balmaña J, Castro E, Chakravarty D, Curigliano G, Czarnecka AM, Dienstmann R, Horak P, Italiano A, Marchiò C, Monkhorst K, Pritchard CC, Reardon B, Russnes HEG, Sirohi B, Sosinsky A, Spanic T, Turnbull C, Van Allen E, Westphalen CB, Tamborero D, Mateo J
ESMO Recommendations on clinical reporting of genomic test results for solid cancers. Ann Oncol. 2024 Nov; 35(11):954-967.
ESMO Recommendations on clinical reporting of genomic test results for solid cancers.
Yates J, Mathey-Andrews C, Park J, Garza A, Gagné A, Hoffman S, Bi K, Titchen B, Hennessey C, Remland J, Shannon E, Camp S, Balamurali S, Cavale SK, Li Z, Raghawan AK, Kraft A, Boland G, Aguirre AJ, Sethi NS, Boeva V, Van Allen E
Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma. bioRxiv. 2025 Mar 03.
Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.
Liu Y, Peng C, Brorson IS, O'Mahony DG, Kelly RL, Heng YJ, Baker GM, Grenaker Alnæs GI, Bodelon C, Stover DG, Van Allen EM, Eliassen AH, Kristensen VN, Tamimi RM, Kraft P
Germline polygenic risk scores are associated with immune gene expression signature and immune cell infiltration in breast cancer. Am J Hum Genet. 2024 Oct 03; 111(10):2150-2163.
Germline polygenic risk scores are associated with immune gene expression signature and immune cell infiltration in breast cancer.
Stransky LA, Gao W, Schmidt LS, Bi K, Ricketts CJ, Ramesh V, James A, Difilippantonio S, Ileva L, Kalen JD, Karim B, Jeon A, Morgan T, Warner AC, Turan S, Unite J, Tran B, Choudhari S, Zhao Y, Linn DE, Yun C, Dhandapani S, Parab V, Pinheiro EM, Morris N, He L, Vigeant SM, Pignon JC, Sticco-Ivins M, Signoretti S, Van Allen EM, Linehan WM, Kaelin WG
Toward a CRISPR-based mouse model of Vhl-deficient clear cell kidney cancer: Initial experience and lessons learned. Proc Natl Acad Sci U S A. 2024 Oct 08; 121(41):e2408549121.
Toward a CRISPR-based mouse model of Vhl-deficient clear cell kidney cancer: Initial experience and lessons learned.
Gomez F, Danos AM, Del Fiol G, Madabhushi A, Tiwari P, McMichael JF, Bakas S, Bian J, Davatzikos C, Fertig EJ, Kalpathy-Cramer J, Kenney J, Savova GK, Yetisgen M, Van Allen EM, Warner JL, Prior F, Griffith M, Griffith OL
A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges. Cancer Discov. 2024 Oct 04; 14(10):1774-1778.
A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges.
Sehgal K, Pappa T, Shin KY, Schiantarelli J, Liu M, Ricker C, Besson NR, Jones SM, Welsh EL, Pfaff KL, Barletta JA, Park J, Reardon B, Doherty GM, Alexander EK, Rodig SJ, Barbie DA, O'Neill A, Van Allen E, Haddad RI, Lorch JH
Dual Immune Checkpoint Inhibition in Patients With Aggressive Thyroid Carcinoma: A Phase 2 Nonrandomized Clinical Trial. JAMA Oncol. 2024 12 01; 10(12):1663-1671.
Dual Immune Checkpoint Inhibition in Patients With Aggressive Thyroid Carcinoma: A Phase 2 Nonrandomized Clinical Trial.
Skoulidis F, Araujo HA, Do MT, Qian Y, Sun X, Galan-Cobo A, Le JT, Montesion M, Palmer R, Jahchan N, Juan JM, Min C, Yu Y, Pan X, Arbour KC, Vokes N, Schmidt ST, Molkentine D, Owen DH, Memmott R, Patil PD, Marmarelis ME, Awad MM, Murray JC, Hellyer JA, Gainor JF, Dimou A, Bestvina CM, Shu CA, Riess JW, Blakely CM, Pecot CV, Mezquita L, Tabbó F, Scheffler M, Digumarthy S, Mooradian MJ, Sacher AG, Lau SCM, Saltos AN, Rotow J, Johnson RP, Liu C, Stewart T, Goldberg SB, Killam J, Walther Z, Schalper K, Davies KD, Woodcock MG, Anagnostou V, Marrone KA, Forde PM, Ricciuti B, Venkatraman D, Van Allen EM, Cummings AL, Goldman JW, Shaish H, Kier M, Katz S, Aggarwal C, Ni Y, Azok JT, Segal J, Ritterhouse L, Neal JW, Lacroix L, Elamin YY, Negrao MV, Le X, Lam VK, Lewis WE, Kemp HN, Carter B, Roth JA, Swisher S, Lee R, Zhou T, Poteete A, Kong Y, Takehara T, Paula AG, Parra Cuentas ER, Behrens C, Wistuba II, Zhang J, Blumenschein GR, Gay C, Byers LA, Gibbons DL, Tsao A, Lee JJ, Bivona TG, Camidge DR, Gray JE, Leighl NB, Levy B, Brahmer JR, Garassino MC, Gandara DR, Garon EB, Rizvi NA, Scagliotti GV, Wolf J, Planchard D, Besse B, Herbst RS, Wakelee HA, Pennell NA, Shaw AT, Jänne PA, Carbone DP, Hellmann MD, Rudin CM, Albacker L, Mann H, Zhu Z, Lai Z, Stewart R, Peters S, Johnson ML, Wong KK, Huang A, Winslow MM, Rosen MJ, Winters IP, Papadimitrakopoulou VA, Cascone T, Jewsbury P, Heymach JV
CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors. Nature. 2024 11; 635(8038):462-471.
CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors.
Bao R, Hutson A, Madabhushi A, Jonsson VD, Rosario SR, Barnholtz-Sloan JS, Fertig EJ, Marathe H, Harris L, Altreuter J, Chen Q, Dignam J, Gentles AJ, Gonzalez-Kozlova E, Gnjatic S, Kim E, Long M, Morgan M, Ruppin E, Valen DV, Zhang H, Vokes N, Meerzaman D, Liu S, Van Allen EM, Xing Y
Ten challenges and opportunities in computational immuno-oncology. J Immunother Cancer. 2024 Oct 26; 12(10).
Ten challenges and opportunities in computational immuno-oncology.
Tarantino G, Ricker CA, Wang A, Ge W, Aprati TJ, Huang AY, Madha S, Chen J, Shi Y, Glettig M, Feng CH, Frederick DT, Freeman S, Holovatska MM, Manos MP, Zimmer L, Rösch A, Zaremba A, Livingstone E, Jameson JC, Saghafian S, Lee A, Zhao K, Morris LGT, Reardon B, Park J, Elmarakeby HA, Schilling B, Giobbie-Hurder A, Vokes NI, Buchbinder EI, Flaherty KT, Haq R, Wu CJ, Boland GM, Hodi FS, Van Allen EM, Schadendorf D, Liu D
Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma. Sci Adv. 2024 11 29; 10(48):eadp4670.
Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma.
Camp SY, He MX, Cuoco MS, Saad E, Pimenta E, Meli K, Bakouny Z, Labaki C, Titchen BM, Kang YJ, Horst J, Trowbridge R, Shannon E, Helvie K, Thorner AR, Vigneau S, Mayorga A, Kodali J, Lachmayr H, Bemus M, Park J, Choueiri T, Bi K, Van Allen EM
Single-cell epigenetic profiling reveals an interferon response-high program associated with BAP1 deficiency in kidney cancer. bioRxiv. 2024 Nov 18.
Single-cell epigenetic profiling reveals an interferon response-high program associated with BAP1 deficiency in kidney cancer.
Lyu A, Fan Z, Clark M, Lea A, Luong D, Setayesh A, Starzinski A, Wolters R, Arias-Badia M, Allaire K, Wu K, Gurunathan V, Valderrábano L, Wei XX, Miller RA, Van Allen EM, Fong L
Evolution of myeloid-mediated immunotherapy resistance in prostate cancer. Nature. 2025 01; 637(8048):1207-1217.
Evolution of myeloid-mediated immunotherapy resistance in prostate cancer.
Johri S, Jeong J, Tran BA, Schlessinger DI, Wongvibulsin S, Barnes LA, Zhou HY, Cai ZR, Van Allen EM, Kim D, Daneshjou R, Rajpurkar P
An evaluation framework for clinical use of large language models in patient interaction tasks. Nat Med. 2025 Jan; 31(1):77-86.
An evaluation framework for clinical use of large language models in patient interaction tasks.
Gillani R, Collins RL, Crowdis J, Garza A, Jones JK, Walker M, Sanchis-Juan A, Whelan CW, Pierce-Hoffman E, Talkowski ME, Brand H, Haigis K, LoPiccolo J, AlDubayan SH, Gusev A, Crompton BD, Janeway KA, Van Allen EM
Rare germline structural variants increase risk for pediatric solid tumors. Science. 2025 01 03; 387(6729):eadq0071.
Jammihal T, Saliby RM, Labaki C, Soulati H, Gallegos J, Peris A, McCurry D, Yu C, Shah V, Poduval D, El Zarif T, El Ahmar N, Laimon YN, Eid M, Sheshdeh AB, Krajewski KM, Büttner FA, Schwab M, Heng D, Casellas RC, Rai K, Zacharias Millward NM, Msaouel P, Karam J, Signoretti S, Van Allen E, Choueiri TK, Braun DA, Shukla SA
Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma. Nat Cancer. 2025 Feb; 6(2):372-384.
Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma.
Jiang Q, Braun DA, Clauser KR, Ramesh V, Shirole NH, Duke-Cohan JE, Nabilsi N, Kramer NJ, Forman C, Lippincott IE, Klaeger S, Phulphagar KM, Chea V, Kim N, Vanasse AP, Saad E, Parsons T, Carr-Reynolds M, Carulli I, Pinjusic K, Jiang Y, Li R, Syamala S, Rachimi S, Verzani EK, Stevens JD, Lane WJ, Camp SY, Meli K, Pappalardi MB, Herbert ZT, Qiu X, Cejas P, Long HW, Shukla SA, Van Allen EM, Choueiri TK, Churchman LS, Abelin JG, Gurer C, MacBeath G, Childs RW, Carr SA, Keskin DB, Wu CJ, Kaelin WG
HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy. Cell. 2025 Apr 03; 188(7):1807-1827.e34.
HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy.
Tarczy-Hornoch P, Amendola L, Aronson SJ, Garraway L, Gray S, Grundmeier RW, Hindorff LA, Jarvik G, Karavite D, Lebo M, Plon SE, Van Allen E, Weck KE, White PS, Yang Y
A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record. Genet Med. 2013 Oct; 15(10):824-32.
A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record.
Schiantarelli J, Benamar M, Park J, Sax HE, Oliveira G, Bosma-Moody A, Campbell KM, Liu D, Johnson DB, Rodig S, Wu CJ, Hodi FS, Ribas A, Van Allen E, Haq R
Genomic mediators of acquired resistance to immunotherapy in metastatic melanoma. Cancer Cell. 2025 Feb 10; 43(2):308-316.e6.
Genomic mediators of acquired resistance to immunotherapy in metastatic melanoma.
Skoulidis F, Araujo HA, Do MT, Qian Y, Sun X, Cobo AG, Le JT, Montesion M, Palmer R, Jahchan N, Juan JM, Min C, Yu Y, Pan X, Arbour KC, Vokes N, Schmidt ST, Molkentine D, Owen DH, Memmott R, Patil PD, Marmarelis ME, Awad MM, Murray JC, Hellyer JA, Gainor JF, Dimou A, Bestvina CM, Shu CA, Riess JW, Blakely CM, Pecot CV, Mezquita L, Tabbó F, Scheffler M, Digumarthy S, Mooradian MJ, Sacher AG, Lau SCM, Saltos AN, Rotow J, Johnson RP, Liu C, Stewart T, Goldberg SB, Killam J, Walther Z, Schalper K, Davies KD, Woodcock MG, Anagnostou V, Marrone KA, Forde PM, Ricciuti B, Venkatraman D, Van Allen EM, Cummings AL, Goldman JW, Shaish H, Kier M, Katz S, Aggarwal C, Ni Y, Azok JT, Segal J, Ritterhouse L, Neal JW, Lacroix L, Elamin YY, Negrao MV, Le X, Lam VK, Lewis WE, Kemp HN, Carter B, Roth JA, Swisher S, Lee R, Zhou T, Poteete A, Kong Y, Takehara T, Paula AG, Parra Cuentas ER, Behrens C, Wistuba II, Zhang J, Blumenschein GR, Gay C, Byers LA, Gibbons DL, Tsao A, Lee JJ, Bivona TG, Camidge DR, Gray JE, Leighl NB, Levy B, Brahmer JR, Garassino MC, Gandara DR, Garon EB, Rizvi NA, Scagliotti GV, Wolf J, Planchard D, Besse B, Herbst RS, Wakelee HA, Pennell NA, Shaw AT, Jänne PA, Carbone DP, Hellmann MD, Rudin CM, Albacker L, Mann H, Zhu Z, Lai Z, Stewart R, Peters S, Johnson ML, Wong KK, Huang A, Winslow MM, Rosen MJ, Winters IP, Papadimitrakopoulou VA, Cascone T, Jewsbury P, Heymach JV
Author Correction: CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors. Nature. 2025 Mar; 639(8054):E19.
Author Correction: CTLA4 blockade abrogates KEAP1/STK11-related resistance to PD-(L)1 inhibitors.
Johri S, Bi K, Titchen BM, Fu J, Conway J, Crowdis JP, Vokes NI, Fan Z, Fong L, Park J, Liu D, He MX, Van Allen EM
Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics. Nat Commun. 2025 Mar 01; 16(1):2090.
Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics.
Pimenta EM, Garza AE, Camp SY, Park J, Hoffman SE, Valderrábano L, Fu J, Bi K, Karam J, Titchen BM, Khandekar MJ, Shannon E, Kang YJ, Nag A, Thorner AR, Raut CP, Hornick JL, Merriam P, Solimini NL, George S, Demetri GD, Van Allen EM
Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity. bioRxiv. 2025 Jan 24.
Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity.
Rosenberg JE, Bambury RM, Van Allen EM, Drabkin HA, Lara PN, Harzstark AL, Wagle N, Figlin RA, Smith GW, Garraway LA, Choueiri T, Erlandsson F, Laber DA
A phase II trial of AS1411 (a novel nucleolin-targeted DNA aptamer) in metastatic renal cell carcinoma. Invest New Drugs. 2014 Feb; 32(1):178-87.
A phase II trial of AS1411 (a novel nucleolin-targeted DNA aptamer) in metastatic renal cell carcinoma.
Berg JS, Amendola LM, Eng C, Van Allen E, Gray SW, Wagle N, Rehm HL, DeChene ET, Dulik MC, Hisama FM, Burke W, Spinner NB, Garraway L, Green RC, Plon S, Evans JP, Jarvik GP
Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium. Genet Med. 2013 Nov; 15(11):860-7.
Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
Van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, Place CS, Taylor-Weiner A, Whittaker S, Kryukov GV, Hodis E, Rosenberg M, McKenna A, Cibulskis K, Farlow D, Zimmer L, Hillen U, Gutzmer R, Goldinger SM, Ugurel S, Gogas HJ, Egberts F, Berking C, Trefzer U, Loquai C, Weide B, Hassel JC, Gabriel SB, Carter SL, Getz G, Garraway LA, Schadendorf D
The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 2014 Jan; 4(1):94-109.
The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma.
Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, Rosenberg M, Goetz EM, Sullivan RJ, Farlow DN, Friedrich DC, Anderka K, Perrin D, Johannessen CM, McKenna A, Cibulskis K, Kryukov G, Hodis E, Lawrence DP, Fisher S, Getz G, Gabriel SB, Carter SL, Flaherty KT, Wargo JA, Garraway LA
MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discov. 2014 Jan; 4(1):61-8.
MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition.
New horizons at the interface of artificial intelligence and translational cancer research. Cancer Cell. 2025 Apr 14; 43(4):708-727.
New horizons at the interface of artificial intelligence and translational cancer research.
Van Allen EM, Foye A, Wagle N, Kim W, Carter SL, McKenna A, Simko JP, Garraway LA, Febbo PG
Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy. Prostate Cancer Prostatic Dis. 2014 Mar; 17(1):23-7.
Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy.
Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May; 32(5):479-84.
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.
Waks AG, Fu J, Chu X, Binboga Kurt B, Li T, Kuntz TM, Shen Y, Yang D, Meli K, Reardon B, Park J, Partridge A, Abravanel D, Jeselsohn R, Wrabel E, Alberti J, DiLullo M, Chen S, Mohammed-Abreu A, Sun X, Balko JM, Kleijn M, Audeh W, Morgan XC, Krop IE, Tayob N, Van Allen EM, Mittendorf EA, Tolaney SM
Efficacy, safety, and predictive biomarkers of neoadjuvant nab-paclitaxel and pembrolizumab in hormone receptor-positive breast cancer: A randomized pilot trial. Nat Commun. 2025 Nov 28; 16(1):10705.
Efficacy, safety, and predictive biomarkers of neoadjuvant nab-paclitaxel and pembrolizumab in hormone receptor-positive breast cancer: A randomized pilot trial.
Asada S, Zhu G, Abeykoon JP, Tanaka Y, Nguyen H, Hirohashi Y, Iyer DR, Ashton NW, Mukkavalli S, Velazquez M, Jiang L, Busso MD, Thangaiah JJ, Robinson SI, Parmar K, Van Allen EM, Gillani R, Shapiro GI, D'Andrea AD
Disruption of Microhomology-mediated End-joining in Ewing Sarcoma. bioRxiv. 2025 Sep 18.
Disruption of Microhomology-mediated End-joining in Ewing Sarcoma.
Karam J, Hoffman SE, Garza A, Gui D, Hoffman HI, Titchen BM, Tanaka Y, Pimenta E, Pappa T, Valderrabano L, Bi K, Gillani R, Brais L, Shannon E, Hornick JL, Park J, Chan J, Van Allen EM
Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors. bioRxiv. 2025 Dec 29.
Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors.
Jun H, Tanaka Y, Johri S, Carvalho FL, Jordan AC, Labaki C, Nagy M, O'Meara TA, Pappa T, Pimenta EM, Saad E, Yang DD, Gillani R, Tewari AK, Reardon B, Van Allen E
Implementing a context-augmented large language model to guide precision cancer medicine. medRxiv. 2025 Jul 24.
Implementing a context-augmented large language model to guide precision cancer medicine.
Wagle N, Grabiner BC, Van Allen EM, Hodis E, Jacobus S, Supko JG, Stewart M, Choueiri TK, Gandhi L, Cleary JM, Elfiky AA, Taplin ME, Stack EC, Signoretti S, Loda M, Shapiro GI, Sabatini DM, Lander ES, Gabriel SB, Kantoff PW, Garraway LA, Rosenberg JE
Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov. 2014 May; 4(5):546-53.
Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib.
Van Allen EM, Wagle N, Stojanov P, Perrin DL, Cibulskis K, Marlow S, Jane-Valbuena J, Friedrich DC, Kryukov G, Carter SL, McKenna A, Sivachenko A, Rosenberg M, Kiezun A, Voet D, Lawrence M, Lichtenstein LT, Gentry JG, Huang FW, Fostel J, Farlow D, Barbie D, Gandhi L, Lander ES, Gray SW, Joffe S, Janne P, Garber J, MacConaill L, Lindeman N, Rollins B, Kantoff P, Fisher SA, Gabriel S, Getz G, Garraway LA
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014 Jun; 20(6):682-8.
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Konda P, Weiss CN, Cui Y, Matar S, Wang J, Nabil YL, Deodhar R, Li J, Horst J, Camp SY, Sheshdeh AB, Hecht JL, Einstein DJ, Rustagi Y, Nag A, Thorner AR, Zhang CZ, Van Allen EM, Signoretti S, Choueiri TK, Viswanathan SR
Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma. bioRxiv. 2025 Sep 01.
Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma.
Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Cancer Cell. 2025 Jun 09; 43(6):1177-1179.
Crossnohere NL, Schuster ALR, Blair CK, Bland H, Carpten JD, Claus EB, Colditz GA, Diehl D, Ding L, Drake BF, Fields RC, George S, Janeway K, Kim H, Lenz HJ, Mack JW, Ricker C, Stern MC, Sussman A, Trent J, Van Allen E, Verhaak R, Willman C, Bridges JFP, Mishra SI, Kwan BM
Optimizing participant and community engagement in cancer genomic sequencing research. Genet Med. 2025 Sep; 27(9):101483.
Optimizing participant and community engagement in cancer genomic sequencing research.
Kübler K, Nardone A, Anand S, Gurevich D, Gao J, Droog M, Hermida-Prado F, Akhshi T, Feiglin A, Feit AS, Cohen Feit G, Dackus G, Pun M, Kuang Y, Cha J, Miller M, Gregoricchio S, Lanfermeijer M, Cornelissen S, Gibson WJ, Paweletz CP, Van Allen EM, van Leeuwen FE, Nederlof PM, Nguyen QD, Mourits MJE, Radovich M, Leshchiner I, Stewart C, Matulonis UA, Zwart W, Maruvka YE, Getz G, Jeselsohn R
Tamoxifen induces PI3K activation in uterine cancer. Nat Genet. 2025 Sep; 57(9):2192-2202.
Tamoxifen induces PI3K activation in uterine cancer.
Amiryousefi A, Wala J, Lin JR, Labadie BW, Atmakuri A, Maliga Z, Toye E, Chaudagar K, Torcasso MS, Coy S, Fanelli GN, Kobs B, Socciarelli F, Gagne A, Van Allen EM, Patnaik A, Sorger P
Spatially organized lymphocytic microenvironments in high grade primary prostate tumors. bioRxiv. 2025 Sep 21.
Spatially organized lymphocytic microenvironments in high grade primary prostate tumors.
Shady M, Reardon B, Jiang S, Pimenta E, O'Meara T, Park J, Kehl KL, Elmarakeby HA, Sunyaev SR, Van Allen EM
Learning Patient Similarity from Genomics for Precision Oncology. medRxiv. 2025 Dec 18.
Learning Patient Similarity from Genomics for Precision Oncology.
Shi Y, Maliga Z, Vallius T, Pant SM, Pelletier R, Kobs B, Priyanka S, He Y, Van Allen E, Santagata S, Ott P, Lian CG, Buchbinder EI, Liu D, Sorger PK
Mechanisms of tumor persistence in metastatic melanoma following successful immunotherapy. bioRxiv. 2025 Dec 15.
Mechanisms of tumor persistence in metastatic melanoma following successful immunotherapy.
Pimenta EM, Garza AE, Camp SY, Park J, Hoffman SE, Valderrábano L, Fu J, Bi K, Carson MT, Karam J, Titchen BM, Medjahed S, Khandekar MJ, Shannon E, Kang YJ, Coy S, Lin JR, Nag A, Thorner AR, Gibson WJ, Santagata S, Raut CP, Hornick JL, Merriam P, Solimini NL, George S, Demetri GD, Van Allen EM
Epigenetic dysregulation of metabolic programs mediates liposarcoma cell plasticity. Sci Transl Med. 2026 Jan 21; 18(833):eadw4689.
Camp SY, He MX, Cuoco MS, Garza AE, Xirenayi S, Bakouny Z, Saad E, El Masri J, Pimenta E, Meli K, Labaki C, Titchen BM, Kang YJ, Horst J, Trowbridge R, Shannon E, Helvie K, Thorner AR, Vigneau S, Mayorga A, Kodali J, Lachmayr H, Bemus M, Chen P, Deng H, Park J, Choueiri TK, Bi K, Van Allen EM
Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss. Sci Adv. 2026 Feb 20; 12(8):eadv5457.
Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.
Jun H, Tanaka Y, Johri S, Camp SY, Bao EL, Carvalho FLF, Gui DY, Jordan AC, Labaki C, Martin SD, Nagy M, O'Meara TA, Pappa T, Pimenta EM, Saad E, Yang DD, Gillani R, Tewari AK, Reardon B, Van Allen E
A context-augmented large language model for accurate precision oncology medicine recommendations. Cancer Cell. 2026 Mar 09; 44(3):676-685.e4.
A context-augmented large language model for accurate precision oncology medicine recommendations.
Yang DD, Abdelnaser A, Wala J, Haas AJ, Barney AA, Saad E, Crowdis JP, Ricker CA, Park J, King MT, Nguyen PL, Choueiri TK, Tewari AK, Salari K, Taplin ME, Wu CL, Van Allen EM
Immune Spatial Organization Predicts Metastasis Risk in Aggressive Localized Prostate Cancer. bioRxiv. 2025 May 19.
Immune Spatial Organization Predicts Metastasis Risk in Aggressive Localized Prostate Cancer.
Sun X, Axelrod ML, Waks AG, Fu J, DiLullo M, Van Allen EM, Tolaney SM, Mittendorf EA, Xu Y, Balko JM
Dynamic single-cell systemic immune responses in immunotherapy-treated early-stage HR+ breast cancer patients. NPJ Breast Cancer. 2025 Jul 03; 11(1):65.
Dynamic single-cell systemic immune responses in immunotherapy-treated early-stage HR+ breast cancer patients.
Iyer G, Choi W, Luo B, Carvalho F, Hanlon T, Reis H, Guercio BJ, Fong M, Mountain J, Feng M, Regazzi AM, McCart L, Wen Y, Al-Ahmadie H, Mouw KW, Van Allen EM, Bellmunt J, Dreicer R, Flaig TW, Halabi S, McConkey DJ, Rosenberg JE
Relationship Among DNA Damage Response Gene Alterations, Molecular Subtypes, and Survival Outcomes in Patients With Metastatic Bladder Cancer Treated on CALGB 90601. JCO Precis Oncol. 2025 Jul; 9:e2400938.
Relationship Among DNA Damage Response Gene Alterations, Molecular Subtypes, and Survival Outcomes in Patients With Metastatic Bladder Cancer Treated on CALGB 90601.
Seplyarskiy V, Shady M, Andrianova MA, Chapman MS, Van Allen EM, Sunyaev SR
Segregating DNA lesions point to high selective advantage of tumor initiating cells. bioRxiv. 2025 Oct 04.
Segregating DNA lesions point to high selective advantage of tumor initiating cells.
Miller GA, Roman A, Glettig M, Elmarakeby HA, AlDubayan SH, Park J, Collins RL, Van Allen EM
Simulation and empirical evaluation of biologically-informed neural network performance. bioRxiv. 2025 Nov 14.
Simulation and empirical evaluation of biologically-informed neural network performance.
Xirenayi S, Camp SY, Garza AE, Rustagi Y, Pimenta E, Shannon E, Nag A, Betherman A, Anselmo A, Trowbridge R, Thorner AR, Park J, Bi K, Van Allen EM
Evaluation of single-cell RNA profiling technologies using FFPE, fresh, and frozen ccRCC tumor specimens. bioRxiv. 2025 Nov 28.
Evaluation of single-cell RNA profiling technologies using FFPE, fresh, and frozen ccRCC tumor specimens.
Fu J, Waks AG, Pimenta E, Titchen B, Bi K, Camp S, Pappa T, Keenan T, Shannon E, Vigneau S, Bemus M, Nag A, Thorner AR, Park J, DiLullo M, Wrabel E, Jeselsohn R, Mittendorf EA, Abravanel DL, Tolaney SM, Van Allen EM
Cellular reprogramming during anti-PD-1 and chemotherapy treatment in early-stage primary hormone receptor-positive breast cancer. Nat Commun. 2025 Nov 28; 16(1):10704.
Cellular reprogramming during anti-PD-1 and chemotherapy treatment in early-stage primary hormone receptor-positive breast cancer.
Riaz IB, Ahmed Naqvi SA, Faisal KS, He H, Rubab Khakwani KZ, Childs DS, Orme JJ, Ravi P, Singh P, Hussain SA, Chi K, Agarwal N, Merseburger AS, Davis ID, Armstrong A, Hussain MH, Smith M, Attard G, Tombal B, Fizazi K, James N, Omlin A, Gillessen S, Murad MH, Van Allen EM, Sweeney CJ, Bryce AH
Comparative Survival in Metastatic Hormone-sensitive Prostate Cancer by Volume of Disease and Timing of Metastasis: A Living Network Meta-analysis. Eur Urol. 2026 Jan; 89(1):31-44.
Comparative Survival in Metastatic Hormone-sensitive Prostate Cancer by Volume of Disease and Timing of Metastasis: A Living Network Meta-analysis.
Elmarakeby H, Roman A, Johri S, Van Allen EM
Empirical Evaluation of Single-Cell Foundation Models for Predicting Cancer Outcomes. bioRxiv. 2025 Nov 03.
Empirical Evaluation of Single-Cell Foundation Models for Predicting Cancer Outcomes.
Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H
Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat Biotechnol. 2014 Jul; 32(7):644-52.
Assessing the clinical utility of cancer genomic and proteomic data across tumor types.
Van Allen EM, Mouw KW, Kim P, Iyer G, Wagle N, Al-Ahmadie H, Zhu C, Ostrovnaya I, Kryukov GV, O'Connor KW, Sfakianos J, Garcia-Grossman I, Kim J, Guancial EA, Bambury R, Bahl S, Gupta N, Farlow D, Qu A, Signoretti S, Barletta JA, Reuter V, Boehm J, Lawrence M, Getz G, Kantoff P, Bochner BH, Choueiri TK, Bajorin DF, Solit DB, Gabriel S, D'Andrea A, Garraway LA, Rosenberg JE
Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov. 2014 Oct; 4(10):1140-53.
Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma.
Wagle N, Grabiner BC, Van Allen EM, Amin-Mansour A, Taylor-Weiner A, Rosenberg M, Gray N, Barletta JA, Guo Y, Swanson SJ, Ruan DT, Hanna GJ, Haddad RI, Getz G, Kwiatkowski DJ, Carter SL, Sabatini DM, Jänne PA, Garraway LA, Lorch JH
Response and acquired resistance to everolimus in anaplastic thyroid cancer. N Engl J Med. 2014 Oct 09; 371(15):1426-33.
Response and acquired resistance to everolimus in anaplastic thyroid cancer.
Giannakis M, Hodis E, Jasmine Mu X, Yamauchi M, Rosenbluh J, Cibulskis K, Saksena G, Lawrence MS, Qian ZR, Nishihara R, Van Allen EM, Hahn WC, Gabriel SB, Lander ES, Getz G, Ogino S, Fuchs CS, Garraway LA
RNF43 is frequently mutated in colorectal and endometrial cancers. Nat Genet. 2014 Dec; 46(12):1264-6.
RNF43 is frequently mutated in colorectal and endometrial cancers.
Bhola NE, Jansen VM, Bafna S, Giltnane JM, Balko JM, Estrada MV, Meszoely I, Mayer I, Abramson V, Ye F, Sanders M, Dugger TC, Allen EV, Arteaga CL
Kinome-wide functional screen identifies role of PLK1 in hormone-independent, ER-positive breast cancer. Cancer Res. 2015 Jan 15; 75(2):405-14.
Kinome-wide functional screen identifies role of PLK1 in hormone-independent, ER-positive breast cancer.
Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, Ambrogio L, Sougnez C, Sivachenko A, Walensky LD, Wagle N, Mora J, de Torres C, Lavarino C, Dos Santos Aguiar S, Yunes JA, Brandalise SR, Mercado-Celis GE, Melendez-Zajgla J, Cárdenas-Cardós R, Velasco-Hidalgo L, Roberts CW, Garraway LA, Rodriguez-Galindo C, Gabriel SB, Lander ES, Golub TR, Orkin SH, Getz G, Janeway KA
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A. 2014 Dec 23; 111(51):E5564-73.
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma.
Wilson FH, Johannessen CM, Piccioni F, Tamayo P, Kim JW, Van Allen EM, Corsello SM, Capelletti M, Calles A, Butaney M, Sharifnia T, Gabriel SB, Mesirov JP, Hahn WC, Engelman JA, Meyerson M, Root DE, Jänne PA, Garraway LA
A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar 09; 27(3):397-408.
A functional landscape of resistance to ALK inhibition in lung cancer.
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM
Integrative clinical genomics of advanced prostate cancer. Cell. 2015 May 21; 161(5):1215-1228.
Integrative clinical genomics of advanced prostate cancer.
Bellmunt J, Werner L, Leow JJ, Mullane SA, Fay AP, Riester M, Van Hummelen P, Taplin ME, Choueiri TK, Van Allen E, Rosenberg J
Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors. PLoS One. 2015; 10(6):e0124711.
Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors.
Hsieh CL, Botta G, Gao S, Li T, Van Allen EM, Treacy DJ, Cai C, He HH, Sweeney CJ, Brown M, Balk SP, Nelson PS, Garraway LA, Kantoff PW
PLZF, a tumor suppressor genetically lost in metastatic castration-resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy. Cancer Res. 2015 May 15; 75(10):1944-8.
PLZF, a tumor suppressor genetically lost in metastatic castration-resistant prostate cancer, is a mediator of resistance to androgen deprivation therapy.
Ahronian LG, Sennott EM, Van Allen EM, Wagle N, Kwak EL, Faris JE, Godfrey JT, Nishimura K, Lynch KD, Mermel CH, Lockerman EL, Kalsy A, Gurski JM, Bahl S, Anderka K, Green LM, Lennon NJ, Huynh TG, Mino-Kenudson M, Getz G, Dias-Santagata D, Iafrate AJ, Engelman JA, Garraway LA, Corcoran RB
Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations. Cancer Discov. 2015 Apr; 5(4):358-67.
Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations.
Re: Floris H. Groenendijk, Jeroen de Jong, Elisabeth E. Fransen van de Putte, et al. ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy. Eur Urol. In press. http://dx.doi.org/10.1016/j.eururo.2015.01.014. Eur Urol. 2015 Aug; 68(2):e31-2.
Re: Floris H. Groenendijk, Jeroen de Jong, Elisabeth E. Fransen van de Putte, et al. ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy. Eur Urol. In press. http://dx.doi.org/10.1016/j.eururo.2015.01.014.
Van Allen EM, Lui VW, Egloff AM, Goetz EM, Li H, Johnson JT, Duvvuri U, Bauman JE, Stransky N, Zeng Y, Gilbert BR, Pendleton KP, Wang L, Chiosea S, Sougnez C, Wagle N, Zhang F, Du Y, Close D, Johnston PA, McKenna A, Carter SL, Golub TR, Getz G, Mills GB, Garraway LA, Grandis JR
Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma. JAMA Oncol. 2015 May; 1(2):238-44.
Genomic Correlate of Exceptional Erlotinib Response in Head and Neck Squamous Cell Carcinoma.
Next-generation sequencing to guide cancer therapy. Genome Med. 2015; 7(1):80.
Next-generation sequencing to guide cancer therapy.
Van Allen EM, Golay HG, Liu Y, Koyama S, Wong K, Taylor-Weiner A, Giannakis M, Harden M, Rojas-Rudilla V, Chevalier A, Thai T, Lydon C, Mach S, Avila AG, Wong JA, Rabin AR, Helmkamp J, Sholl L, Carter SL, Oxnard G, Janne P, Getz G, Lindeman N, Hammerman PS, Garraway LA, Hodi FS, Rodig SJ, Dranoff G, Wong KK, Barbie DA
Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation. Cancer Immunol Res. 2015 Aug; 3(8):855-63.
Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation.
Michaelson MD, McKay RR, Werner L, Atkins MB, Van Allen EM, Olivier KM, Song J, Signoretti S, McDermott DF, Choueiri TK
Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Cancer. 2015 Oct 01; 121(19):3435-43.
Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma.
Tolaney SM, Tan S, Guo H, Barry W, Van Allen E, Wagle N, Brock J, Larrabee K, Paweletz C, Ivanova E, Janne P, Overmoyer B, Wright JJ, Shapiro GI, Winer EP, Krop IE
Phase II study of tivantinib (ARQ 197) in patients with metastatic triple-negative breast cancer. Invest New Drugs. 2015 Oct; 33(5):1108-14.
Phase II study of tivantinib (ARQ 197) in patients with metastatic triple-negative breast cancer.
Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, Dunn IF, Paek SH, Park SH, McKenna A, Chevalier A, Rosenberg M, Barker FG, Gill CM, Van Hummelen P, Thorner AR, Johnson BE, Hoang MP, Choueiri TK, Signoretti S, Sougnez C, Rabin MS, Lin NU, Winer EP, Stemmer-Rachamimov A, Meyerson M, Garraway L, Gabriel S, Lander ES, Beroukhim R, Batchelor TT, Baselga J, Louis DN, Getz G, Hahn WC
Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discov. 2015 Nov; 5(11):1164-1177.
Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets.
Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, Sucker A, Hillen U, Foppen MHG, Goldinger SM, Utikal J, Hassel JC, Weide B, Kaehler KC, Loquai C, Mohr P, Gutzmer R, Dummer R, Gabriel S, Wu CJ, Schadendorf D, Garraway LA
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015 Oct 09; 350(6257):207-211.
Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Shirts BH, Salama JS, Aronson SJ, Chung WK, Gray SW, Hindorff LA, Jarvik GP, Plon SE, Stoffel EM, Tarczy-Hornoch PZ, Van Allen EM, Weck KE, Chute CG, Freimuth RR, Grundmeier RW, Hartzler AL, Li R, Peissig PL, Peterson JF, Rasmussen LV, Starren JB, Williams MS, Overby CL
Journal of the American Medical Informatics Association : JAMIA
CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc. 2015 Nov; 22(6):1231-42.
CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record.
Genomic predictors of response to CTLA4 blockade in metastatic melanoma
Roccaro AM, Sacco A, Shi J, Chiarini M, Perilla-Glen A, Manier S, Glavey S, Aljawai Y, Mishima Y, Kawano Y, Moschetta M, Correll M, Improgo MR, Brown JR, Imberti L, Rossi G, Castillo JJ, Treon SP, Freedman ML, Van Allen EM, Hide W, Hiller E, Rainville I, Ghobrial IM
Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia. Blood. 2016 05 26; 127(21):2598-606.
Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia.
Kwiatkowski DJ, Choueiri TK, Fay AP, Rini BI, Thorner AR, de Velasco G, Tyburczy ME, Hamieh L, Albiges L, Agarwal N, Ho TH, Song J, Pignon JC, Barrios PM, Michaelson MD, Van Allen E, Krajewski KM, Porta C, Pal S, Bellmunt J, McDermott DF, Heng DYC, Gray KP, Signoretti S
Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma. Clin Cancer Res. 2016 05 15; 22(10):2445-2452.
Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma.
Beltran H, Prandi D, Mosquera JM, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BV, Varambally S, Tomlins SA, Nanus DM, Tagawa ST, Van Allen EM, Elemento O, Sboner A, Garraway LA, Rubin MA, Demichelis F
Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med. 2016 Mar; 22(3):298-305.
Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.
McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, Watkins TB, Shafi S, Murugaesu N, Mitter R, Akarca AU, Linares J, Marafioti T, Henry JY, Van Allen EM, Miao D, Schilling B, Schadendorf D, Garraway LA, Makarov V, Rizvi NA, Snyder A, Hellmann MD, Merghoub T, Wolchok JD, Shukla SA, Wu CJ, Peggs KS, Chan TA, Hadrup SR, Quezada SA, Swanton C
Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016 Mar 25; 351(6280):1463-9.
Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.
Precision medicine for advanced prostate cancer. Curr Opin Urol. 2016 May; 26(3):231-9.
Precision medicine for advanced prostate cancer.
Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P
Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 05; 34(5):539-46.
Characterizing genomic alterations in cancer by complementary functional associations.
Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 Apr 08; 352(6282):189-96.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Kryukov GV, Bielski CM, Samocha K, Fromer M, Seepo S, Gentry C, Neale B, Garraway LA, Sweeney CJ, Taplin ME, Van Allen EM
Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors. Clin Cancer Res. 2016 05 01; 22(9):2183-9.
Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors.
Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 Apr 26; 15(4):857-865.
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma.
Kim J, Mouw KW, Polak P, Braunstein LZ, Kamburov A, Kwiatkowski DJ, Rosenberg JE, Van Allen EM, D'Andrea A, Getz G
Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat Genet. 2016 06; 48(6):600-606.
Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.
Fay AP, de Velasco G, Ho TH, Van Allen EM, Murray B, Albiges L, Signoretti S, Hakimi AA, Stanton ML, Bellmunt J, McDermott DF, Atkins MB, Garraway LA, Kwiatkowski DJ, Choueiri TK
Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma. J Natl Compr Canc Netw. 2016 07; 14(7):820-4.
Whole-Exome Sequencing in Two Extreme Phenotypes of Response to VEGF-Targeted Therapies in Patients With Metastatic Clear Cell Renal Cell Carcinoma.
McKay RR, De Velasco G, Werner L, Bellmunt J, Harshman L, Sweeney C, Rosenberg JE, Hirsch M, Signoretti S, Van Allen EM, Walsh M, Vaishampayan U, McDermott DF, Choueiri TK
A phase 1 study of buparlisib and bevacizumab in patients with metastatic renal cell carcinoma progressing on vascular endothelial growth factor-targeted therapies. Cancer. 2016 Aug 01; 122(15):2389-98.
A phase 1 study of buparlisib and bevacizumab in patients with metastatic renal cell carcinoma progressing on vascular endothelial growth factor-targeted therapies.
Garofalo A, Sholl L, Reardon B, Taylor-Weiner A, Amin-Mansour A, Miao D, Liu D, Oliver N, MacConaill L, Ducar M, Rojas-Rudilla V, Giannakis M, Ghazani A, Gray S, Janne P, Garber J, Joffe S, Lindeman N, Wagle N, Garraway LA, Van Allen EM
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016 07 26; 8(1):79.
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.
Pal SK, Choueiri TK, Wang K, Khaira D, Karam JA, Van Allen E, Palma NA, Stein MN, Johnson A, Squillace R, Elvin JA, Chmielecki J, Yelensky R, Yakirevich E, Lipson D, Lin DI, Miller VA, Stephens PJ, Ali SM, Ross JS
Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling. Eur Urol. 2016 09; 70(3):516-21.
Characterization of Clinical Cases of Collecting Duct Carcinoma of the Kidney Assessed by Comprehensive Genomic Profiling.
Liu D, Plimack ER, Hoffman-Censits J, Garraway LA, Bellmunt J, Van Allen E, Rosenberg JE
Clinical Validation of Chemotherapy Response Biomarker ERCC2 in Muscle-Invasive Urothelial Bladder Carcinoma. JAMA Oncol. 2016 Aug 01; 2(8):1094-6.
Clinical Validation of Chemotherapy Response Biomarker ERCC2 in Muscle-Invasive Urothelial Bladder Carcinoma.
Pritchard CC, Mateo J, Walsh MF, De Sarkar N, Abida W, Beltran H, Garofalo A, Gulati R, Carreira S, Eeles R, Elemento O, Rubin MA, Robinson D, Lonigro R, Hussain M, Chinnaiyan A, Vinson J, Filipenko J, Garraway L, Taplin ME, AlDubayan S, Han GC, Beightol M, Morrissey C, Nghiem B, Cheng HH, Montgomery B, Walsh T, Casadei S, Berger M, Zhang L, Zehir A, Vijai J, Scher HI, Sawyers C, Schultz N, Kantoff PW, Solit D, Robson M, Van Allen EM, Offit K, de Bono J, Nelson PS
Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. N Engl J Med. 2016 Aug 04; 375(5):443-53.
Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer.
Genomic determinants of cancer immunotherapy. Curr Opin Immunol. 2016 08; 41:32-38.
Genomic determinants of cancer immunotherapy.
Resistance to Emerging Androgen Deprivation Therapies in Prostate Cancer
The Use of Whole-Exome Sequencing to Guide the Care of Cancer Patients
Gray SW, Park ER, Najita J, Martins Y, Traeger L, Bair E, Gagne J, Garber J, Jänne PA, Lindeman N, Lowenstein C, Oliver N, Sholl L, Van Allen EM, Wagle N, Wood S, Garraway L, Joffe S
Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study. Genet Med. 2016 10; 18(10):1011-9.
Oncologists' and cancer patients' views on whole-exome sequencing and incidental findings: results from the CanSeq study.
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep. 2016 10 18; 17(4):1206.
Genomic Approaches to Understanding Response and Resistance to Immunotherapy. Clin Cancer Res. 2016 Dec 01; 22(23):5642-5650.
Genomic Approaches to Understanding Response and Resistance to Immunotherapy.
de Velasco G, Miao D, Voss MH, Hakimi AA, Hsieh JJ, Tannir NM, Tamboli P, Appleman LJ, Rathmell WK, Van Allen EM, Choueiri TK
Tumor Mutational Load and Immune Parameters across Metastatic Renal Cell Carcinoma Risk Groups. Cancer Immunol Res. 2016 10; 4(10):820-822.
Tumor Mutational Load and Immune Parameters across Metastatic Renal Cell Carcinoma Risk Groups.
Ritter DI, Roychowdhury S, Roy A, Rao S, Landrum MJ, Sonkin D, Shekar M, Davis CF, Hart RK, Micheel C, Weaver M, Van Allen EM, Parsons DW, McLeod HL, Watson MS, Plon SE, Kulkarni S, Madhavan S
Somatic cancer variant curation and harmonization through consensus minimum variant level data. Genome Med. 2016 11 04; 8(1):117.
Somatic cancer variant curation and harmonization through consensus minimum variant level data.
Delivering on the promise of precision cancer medicine. Genome Med. 2016 10 25; 8(1):110.
Delivering on the promise of precision cancer medicine.
Senbabaoglu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2016 11 17; 17(1):231.
Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Van Allen EM, Robinson D, Morrissey C, Pritchard C, Imamovic A, Carter S, Rosenberg M, McKenna A, Wu YM, Cao X, Chinnaiyan A, Garraway L, Nelson PS
A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine. Oncotarget. 2016 Aug 16; 7(33):52888-52899.
A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine.
Mouw KW, Cleary JM, Reardon B, Pike J, Braunstein LZ, Kim J, Amin-Mansour A, Miao D, Damish A, Chin J, Ott PA, Fuchs CS, Martin NE, Getz G, Carter S, Mamon HJ, Hornick JL, Van Allen EM, D'Andrea AD
Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma. Clin Cancer Res. 2017 Jun 15; 23(12):3214-3222.
Genomic Evolution after Chemoradiotherapy in Anal Squamous Cell Carcinoma.
Gibson WJ, Ruan DT, Paulson VA, Barletta JA, Hanna GJ, Kraft S, Calles A, Nehs MA, Moore FD, Taylor-Weiner A, Wala JA, Zack TI, Lee TC, Fennessy FM, Alexander EK, Thomas T, Janne PA, Garraway LA, Carter SL, Beroukhim R, Lorch JH, Van Allen EM
Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017 May 01; 23(9):2367-2373.
Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer.
Nathanson T, Ahuja A, Rubinsteyn A, Aksoy BA, Hellmann MD, Miao D, Van Allen E, Merghoub T, Wolchok JD, Snyder A, Hammerbacher J
Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade. Cancer Immunol Res. 2017 01; 5(1):84-91.
Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade.
Lerner SP, Bajorin DF, Dinney CP, Efstathiou JA, Groshen S, Hahn NM, Hansel D, Kwiatkowski D, O'Donnell M, Rosenberg J, Svatek R, Abrams JS, Al-Ahmadie H, Apolo AB, Bellmunt J, Callahan M, Cha EK, Drake C, Jarow J, Kamat A, Kim W, Knowles M, Mann B, Marchionni L, McConkey D, McShane L, Ramirez N, Sharabi A, Sharpe AH, Solit D, Tangen CM, Amiri AT, Van Allen E, West PJ, Witjes JA, Quale DZ
Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer. Bladder Cancer. 2016 Apr 27; 2(2):165-202.
Summary and Recommendations from the National Cancer Institute's Clinical Trials Planning Meeting on Novel Therapeutics for Non-Muscle Invasive Bladder Cancer.
Taylor-Weiner A, Zack T, O'Donnell E, Guerriero JL, Bernard B, Reddy A, Han GC, AlDubayan S, Amin-Mansour A, Schumacher SE, Litchfield K, Turnbull C, Gabriel S, Beroukhim R, Getz G, Carter SL, Hirsch MS, Letai A, Sweeney C, Van Allen EM
Genomic evolution and chemoresistance in germ-cell tumours. Nature. 2016 11 30; 540(7631):114-118.
Genomic evolution and chemoresistance in germ-cell tumours.
Ghazani AA, Oliver NM, St Pierre JP, Garofalo A, Rainville IR, Hiller E, Treacy DJ, Rojas-Rudilla V, Wood S, Bair E, Parello M, Huang F, Giannakis M, Wilson FH, Stover EH, Corsello SM, Nguyen T, Rana HQ, Church AJ, Lowenstein C, Cibulskis C, Amin-Mansour A, Heng J, Brais L, Santos A, Bauer P, Waldron A, Lo P, Gorman M, Lydon CA, Welch M, McNamara P, Gabriel S, Sholl LM, Lindeman NI, Garber JE, Joffe S, Van Allen EM, Gray SW, Ja Nne PA, Garraway LA, Wagle N
Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study. Genet Med. 2017 07; 19(7):787-795.
Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study.
Jay R, McKay RR, Werner L, Atkins MB, Van Allen EM, Olivier KM, Song J, Signoretti S, McDermott DF, Choueiri TK
Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Michaelson MD, McKay RR, Werner L, Atkins MB, Van Allen EM, Olivier KM, Song J, Signoretti S, McDermott DF, Choueiri TK.Cancer. 2015 Oct 1;121(19):3435-43. [Epub 2015 Jun 8]. doi: 10.1002/cncr.29503. Urol Oncol. 2017 03; 35(3):117-118.
Phase 2 trial of sunitinib and gemcitabine in patients with sarcomatoid and/or poor-risk metastatic renal cell carcinoma. Michaelson MD, McKay RR, Werner L, Atkins MB, Van Allen EM, Olivier KM, Song J, Signoretti S, McDermott DF, Choueiri TK.Cancer. 2015 Oct 1;121(19):3435-43. [Epub 2015 Jun 8]. doi: 10.1002/cncr.29503.
George S, Miao D, Demetri GD, Adeegbe D, Rodig SJ, Shukla S, Lipschitz M, Amin-Mansour A, Raut CP, Carter SL, Hammerman P, Freeman GJ, Wu CJ, Ott PA, Wong KK, Van Allen EM
Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity. 2017 02 21; 46(2):197-204.
Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma.
Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2017 03 01; 18(1):46.
Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.
Mishima Y, Paiva B, Shi J, Park J, Manier S, Takagi S, Massoud M, Perilla-Glen A, Aljawai Y, Huynh D, Roccaro AM, Sacco A, Capelletti M, Detappe A, Alignani D, Anderson KC, Munshi NC, Prosper F, Lohr JG, Ha G, Freeman SS, Van Allen EM, Adalsteinsson VA, Michor F, San Miguel JF, Ghobrial IM
The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell Rep. 2017 04 04; 19(1):218-224.
The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma.
Intron retention as a novel source of tumor neoantigens associated with response to checkpoint inhibitor therapy
Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 09; 7(9):973-983.
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.
Novel secondary hormonal therapy in advanced prostate cancer: an update. Curr Opin Urol. 2009 May; 19(3):315-21.
Novel secondary hormonal therapy in advanced prostate cancer: an update.
Toward Molecularly Driven Precision Medicine in Lung Adenocarcinoma. Cancer Discov. 2017 06; 7(6):555-557.
Toward Molecularly Driven Precision Medicine in Lung Adenocarcinoma.
Johnson CP, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Lane AM, Gragoudas ES, Vazquez F, Nickerson E, Cibulskis K, McKenna A, Gabriel SB, Getz G, Van Allen EM, 't Hoen PAC, Garraway LA, Woodman SE
Systematic genomic and translational efficiency studies of uveal melanoma. PLoS One. 2017; 12(6):e0178189.
Systematic genomic and translational efficiency studies of uveal melanoma.
Moving toward personalized medicine in castration-resistant prostate cancer. Urol Clin North Am. 2012 Nov; 39(4):483-90.
Moving toward personalized medicine in castration-resistant prostate cancer.
Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N, Nickerson E, Chae SS, Boysen G, Auclair D, Onofrio RC, Park K, Kitabayashi N, MacDonald TY, Sheikh K, Vuong T, Guiducci C, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Hussain WM, Ramos AH, Winckler W, Redman MC, Ardlie K, Tewari AK, Mosquera JM, Rupp N, Wild PJ, Moch H, Morrissey C, Nelson PS, Kantoff PW, Gabriel SB, Golub TR, Meyerson M, Lander ES, Getz G, Rubin MA, Garraway LA
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012 May 20; 44(6):685-9.
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.
Comments on the recent clinical guidance statement on HIV screening. Ann Intern Med. 2009 Aug 18; 151(4):286; author reply 287.
Comments on the recent clinical guidance statement on HIV screening.
Van Allen EM, Miyake T, Gunn N, Behler CM, Kohlwes J
Off-label use of rituximab in a multipayer insurance system. J Oncol Pract. 2011 Mar; 7(2):76-9.
Off-label use of rituximab in a multipayer insurance system.
Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 08 23; 5(2):105-118.e9.
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.
Giltnane JM, Hutchinson KE, Stricker TP, Formisano L, Young CD, Estrada MV, Nixon MJ, Du L, Sanchez V, Ericsson PG, Kuba MG, Sanders ME, Mu XJ, Van Allen EM, Wagle N, Mayer IA, Abramson V, G?mez H, Rizzo M, Toy W, Chandarlapaty S, Mayer EL, Christiansen J, Murphy D, Fitzgerald K, Wang K, Ross JS, Miller VA, Stephens PJ, Yelensky R, Garraway L, Shyr Y, Meszoely I, Balko JM, Arteaga CL
Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. Sci Transl Med. 2017 Aug 09; 9(402).
Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance.
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Sboner A, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM
Integrative Clinical Genomics of Advanced Prostate Cancer. Cell. 2015 Jul 16; 162(2):454.
Integrative Clinical Genomics of Advanced Prostate Cancer.
Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, Collins NB, Bi K, LaFleur MW, Juneja VR, Weiss SA, Lo J, Fisher DE, Miao D, Van Allen E, Root DE, Sharpe AH, Doench JG, Haining WN
In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 2017 07 27; 547(7664):413-418.
In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.
The Potential and Challenges of Expanded Germline Testing in Clinical Oncology. JAMA. 2017 09 05; 318(9):801-803.
The Potential and Challenges of Expanded Germline Testing in Clinical Oncology.
McGraw SA, Garber J, Jänne PA, Lindeman N, Oliver N, Sholl LM, Van Allen EM, Wagle N, Garraway LA, Joffe S, Gray SW
The fuzzy world of precision medicine: deliberations of a precision medicine tumor board. Per Med. 2017 Jan; 14(1):37-50.
The fuzzy world of precision medicine: deliberations of a precision medicine tumor board.
Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA
Punctuated evolution of prostate cancer genomes. Cell. 2013 Apr 25; 153(3):666-77.
Punctuated evolution of prostate cancer genomes.
Jenkins RW, Aref AR, Lizotte PH, Ivanova E, Stinson S, Zhou CW, Bowden M, Deng J, Liu H, Miao D, He MX, Walker W, Zhang G, Tian T, Cheng C, Wei Z, Palakurthi S, Bittinger M, Vitzthum H, Kim JW, Merlino A, Quinn M, Venkataramani C, Kaplan JA, Portell A, Gokhale PC, Phillips B, Smart A, Rotem A, Jones RE, Keogh L, Anguiano M, Stapleton L, Jia Z, Barzily-Rokni M, Cañadas I, Thai TC, Hammond MR, Vlahos R, Wang ES, Zhang H, Li S, Hanna GJ, Huang W, Hoang MP, Piris A, Eliane JP, Stemmer-Rachamimov AO, Cameron L, Su MJ, Shah P, Izar B, Thakuria M, LeBoeuf NR, Rabinowits G, Gunda V, Parangi S, Cleary JM, Miller BC, Kitajima S, Thummalapalli R, Miao B, Barbie TU, Sivathanu V, Wong J, Richards WG, Bueno R, Yoon CH, Miret J, Herlyn M, Garraway LA, Van Allen EM, Freeman GJ, Kirschmeier PT, Lorch JH, Ott PA, Hodi FS, Flaherty KT, Kamm RD, Boland GM, Wong KK, Dornan D, Paweletz CP, Barbie DA
Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids. Cancer Discov. 2018 02; 8(2):196-215.
Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids.
Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O'Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017 11 06; 8(1):1324.
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
Tumor Evolution: A Problem of Histocompatibility. Cell. 2017 11 30; 171(6):1252-1253.
Tumor Evolution: A Problem of Histocompatibility.
Whittaker SR, Theurillat JP, Van Allen E, Wagle N, Hsiao J, Cowley GS, Schadendorf D, Root DE, Garraway LA
A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov. 2013 Mar; 3(3):350-62.
A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition.
Liu D, Abbosh P, Keliher D, Reardon B, Miao D, Mouw K, Weiner-Taylor A, Wankowicz S, Han G, Teo MY, Cipolla C, Kim J, Iyer G, Al-Ahmadie H, Dulaimi E, Chen DYT, Alpaugh RK, Hoffman-Censits J, Garraway LA, Getz G, Carter SL, Bellmunt J, Plimack ER, Rosenberg JE, Van Allen EM
Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer. Nat Commun. 2017 12 19; 8(1):2193.
Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer.
Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, Norton C, Bossé D, Wankowicz SM, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder A, Hellmann MD, Ho T, Motzer RJ, Signoretti S, Kaelin WG, Choueiri TK, Van Allen EM
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018 Feb 16; 359(6377):801-806.
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.
Gray SW, Gagan J, Cerami E, Cronin AM, Uno H, Oliver N, Lowenstein C, Lederman R, Revette A, Suarez A, Lee C, Bryan J, Sholl L, Van Allen EM
Interactive or static reports to guide clinical interpretation of cancer genomics. J Am Med Inform Assoc. 2018 05 01; 25(5):458-464.
Interactive or static reports to guide clinical interpretation of cancer genomics.
Lalani AA, Xie W, Martini DJ, Steinharter JA, Norton CK, Krajewski KM, Duquette A, Bossé D, Bellmunt J, Van Allen EM, McGregor BA, Creighton CJ, Harshman LC, Choueiri TK
Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma. J Immunother Cancer. 2018 01 22; 6(1):5.
Change in Neutrophil-to-lymphocyte ratio (NLR) in response to immune checkpoint blockade for metastatic renal cell carcinoma.