Publications
Prognostic and Predictive Value of Immune-Related Gene Expression Signatures vs Tumor-Infiltrating Lymphocytes in Early-Stage ERBB2/HER2-Positive Breast Cancer: A Correlative Analysis of the CALGB 40601 and PAMELA Trials.
Landscape of Genetic Alterations Underlying Hallmark Signature Changes in Cancer Reveals TP53 Aneuploidy-driven Metabolic Reprogramming.
Diffsig: Associating Risk Factors With Mutational Signatures.
Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.
Incorporating RNA-based Risk Scores for Genomic Instability to Predict Breast Cancer Recurrence and Immunogenicity in a Diverse Population.
RNA-Based Classification of Homologous Recombination Deficiency in Racially Diverse Patients with Breast Cancer.
Collaborative study from the Bladder Cancer Advocacy Network for the genomic analysis of metastatic urothelial cancer.
Race and Ancestry in Immune Response to Breast Cancer
A multi-omics longitudinal study of the murine retinal response to chronic low-dose irradiation and simulated microgravity.
Kothiyal P, Eley G, Ilangovan H, Hoadley KA, Elgart SR, Mao XW, Eslami P.Sci Rep. 2022 Oct 7;12(1):1-4. 16825. doi:10-1038/s41598-022-19360-9. PMID: 36207342
RNA-based classification of homologous recombination deficiency in racially-diverse patients with breast cancer.
Walens A, Van Alsten SC, Olsson LT, Smith MA, Lockhart A, Gao X, Hamilton AM, Kirk EL, Love MI, Gupta GP, Perou CM, Vaziri C, Hoadley KA, Troester MA. Cancer Epidemiol Biomarkers Prev. 2022 Sep 21:EPI-22-0590. doi:10.1158/1055-9965.EPI-22-0590. PMID: 36129803.
DNA damage repair classifier defines distinct groups in hepatocellular carcinoma.
Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, and Hoadley KA. Cancers. 2022 Sep 1;14(17):4282. doi: 10.3390/cancers14174282. PMID: 36077818
Analysis of germline-driven ancestry-associated gene expression in cancers.
Chambwe N, Sayaman RW, Hu D, Huntsman S; Cancer Genome Analysis Network, Kemal A, Caesar-Johnson S, Zenklusen JC, Ziv E, Beroukhim R, Cherniack AD. STAR Protoc. 2022 Jul 31;3(3):101586. doi: 10.1016/j.xpro.2022.101586. eCollection 2022 Sep 16. PMID: 35942349
The landscape of immune microenvironments in racially-diverse breast cancer patients.
Hamilton AM, Hurson AN, Olsson
LT, Walens A, Nsonwu-Farley J, Kirk EL, Abdou Y, Downs-Canner SM, Serody JS, Perou CM, Calhoun BC, Troester MA, Hoadley KA. Cancer Epidemiol Biomarkers Prev. 2022 Jul 1;31(7):1341-1350. Epub 2022 Apr 18. doi: 10.1158/1055-9965.EPI-21-1312. PMID: 35437570
Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study.
Gadd S, Huff V, Skol AD, Renfro LA, Fernandez CV, Mullen EA, Jones CD, Hoadley KA, Yap KL, Ramirez NC, Aris S, Phung QH, Perlman EJ. Cell Rep Med. 2022 June 21;3(6):100644. doi: 10.1016/j.xcrm.2022/100644. Epub 2022 May 25. PMID: 35617957
A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data.
Samorodnitsky S, Hoadley KA, Lock EF. BMC Bioinformatics. 2022 June 17;23(1):235. doi: 10.1186/s12859-022-04770-3. PMID: 35710340
Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases. NPJ breast cancer.
Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. 2022 Jun 14;8(1):74. doi:10.1038/s41523-022-00437-7. PMID: 35701440
Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression
Fassler DJ, Torre-Healy LA, Gupta R, Hamilton AM, Kobayashi S, Van Alsten SC, Zhang Y, Kurc T, Moffitt RA, Troester MA, Hoadley KA, Saltz J. . Cancers. 2022 Apr 26;14(9):2148. doi: 10.3390/cancers14092148. PMID: 35565277
CALGB 40603 (Alliance): Long-Term Outcomes and Genomic Correlates of Response and Survival After Neoadjuvant Chemotherapy With or Without Carboplatin and Bevacizumab in Triple-Negative Breast Cancer.
Shepherd JH, Ballman K, Polley MC, Campbell JD, Fan C, Selitsky S, Fernandez-Martinez A, Parker JS, Hoadley KA, Hu Z, Li Y, Soloway MG, Spears PA, Singh B, Tolaney SM, Somlo G, Port ER, Ma C, Kuzma C, Mamounas E, Golshan M, Bellon JR, Collyar D, Hahn OM, Hudis CA, Winer EP, Partridge A, Hyslop T, Carey LA, Perou CM, Sikov WM. J Clin Oncol. 2022 Apr 20;40(12):1323-1334. doi: 10.1200/JCO.21.01506. Epub 2022 Jan 19. PMID: 35044810
Racial differences in breast cancer outcomes by hepatocyte growth factor pathway expression
Jones GS, Hoadley KA, Benefield H, Olsson LT, Hamilton AM, Bhattacharya A, Kirk EL, Tipaldos HJ, Fleming JM, Williams KP, Love MI, Nichols HB, Olshan AF, Troester MA. Breast Cancer Res Treat. 2022 Apr;192(2):447-455. doi: 10.1007/s10549-021-06497-w. Epub 2022 Jan 16. PMID: 35034243
BIODIMENSIONAL LINKED MATRIX FACTORIZATION FOR PAN-OMICS PAN-CANCER ANALYSIS.
Lock EF, Park JY, and Hoadley KA. Ann Appl Stat. 2022 Mar;16(1):193-215. doi: 10.1214/21-AOAS1495. Epub 2022 Mar 28. PMID: 35505906
TP53 Pathway Function, Estrogen Receptor Status, and Breast Cancer Risk Factors in the Carolina Breast Cancer Study.
Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. T Cancer Epidemiol Biomarkers Prev. 2022 Jan;31(1):124-131. doi: 10.1158/1055-9965.EPI-21-0661. Epub 2021 Nov 4. PMID: 34737209
Analytical protocol to identify local ancestry-associated molecular features in cancer.
Carrot-Zhang J, Han S, Zhou W, Damrauer JS, Kemal A; Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R. STAR Protoc. 2021 Sep 20;2(4):100766. doi: 10.1016/j.xpro.2021.100766. eCollection 2021 Dec 17. PMID: 34585150
Molecular analysis of TCGA breast cancer histologic types.
Thennavan A, Beca F, Xia Y, Recio SG, Allison K, Collins LC, Tse GM, Chen YY, Schnitt SJ, Hoadley KA, Beck A, Perou CM. Cell Genom. 2021 Dec 8;1(3):100067. doi: 10.1016/j.xgen.2021.100067. PMID: 35465400
JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES.
Carmichael I, Calhoun BC, Hoadley KA, Troester MA, Geradts J, Couture HD, Olsson L, Perou CM, Niethammer M, Hannig J, Marron JS. Ann Appl Stat. 2021 Dec;15(4):1697-1722. doi: 10.1214/20-aoas1433. Epub 2021 Dec 21. PMID: 35432688
UNMASC: tumor-only variant calling with unmatched normal controls.
Little P, Jo H, Hoyle A, Mazul A, Zhao X, Salazar AH, Farquhar D, Sheth S, Masood M, Hayward MC, Parker JS, Hoadley KA, Zevallos J, Hayes DN. NAR Cancer. 2021 Oct 6;3(4):zcab040. doi: 10.1093/narca/zcab. eCollection 2021 Dec. PMID: 34632388
Genomic characterization of rare molecular subclasses of hepatocellular carcinoma.
Damrauer JS*, Smith MA*, Walter V, Thennavan A, Mose LE, Selitsky SR, Hoadley KA. Commun Biol. 2021 Oct 4;4(1):1150. doi: 10.1038/s42003-021-02674-1. PMID: 34608257
Proteogenomic characterization of pancreatic ductal adenocarcinoma.
Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. PMID: 34534465
Responses to 10 common criticisms of anti-racism action in STEMM
Gosztyla ML, Kwong L, Murray NA, Williams CE, Behnke N, Curry P, Corbett KD, DSouza KN, Gala de Pablo J, Gicobi J, Javidnia M, Lotay N, Prescott SM, Quinn JP, Rivera ZMG, Smith MA, Tang KTY, Venkat A, Yamoah MA. . PLoS Comput Biol. 2021 Jul 15;17(7):e1009141. PMID:34264941
Identification of a novel inflamed tumor microenvironment signature as a predictive biomarker of bacillus Calmette-Guerin immunotherapy in non-muscle invasive bladder cancer.
Damrauer JS, Roell KR, Smith MA, Sun X, Kirk EL, Hoadley KA, Benefield HC, Iyer G, Solit DB, Milowsky MI, Kim WY, Nielsen ME, Wobker SE, Dalbagni G, Al-Ahmadie HA, Olshan AF, Bochner BH, Furberg H, Troester MA, Pietzak EJ. Clin Cancer Res. 2021 Aug 15;27(16):4599-4609. doi: 10.1158/1078-0432.CCR-21-0205. Epub 2021 Jun 11. PMID: 34117034.
A proteogenomic portrait of
lung squamous cell carcinoma.
Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA; Clinical Proteomic Tumor Analysis Consortium. 2021 Aug 5;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016. PMID: 34358469
Hepatocyte growth factor pathway expression in breast cancer by race and subtype.
Jones GS, Hoadley KA, Olsson LT, Hamilton AM, Bhattacharya A, Kirk EL, Tipaldos HJ, Fleming JM, Love MI, Nichols HB, Olshan AF, Troester MA. Breast Cancer Res. 2021 Aug 3;23(1):80. doi: 10.1186/s13058-021-01460-5. PMID: 34344422
Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer.
Robertson AG, Yau C, Carrot-Zhang J, Damrauer JS, Knijnenburg TA, Chambwe N, Hoadley KA, Kemal A, Zenklusen JC, Cherniack AD, Beroukhim R, Zhou W. STAR Protoc. 2021 Apr 19;2(2):100483. doi:10.1016/j.xpro.2021.100483. eCollection 2021 Jun 18. PMID: 33982016
Protein-based immune profiles of basal-like vs. luminal breast cancers.
Walens A, Olsson LT, Gao X, Hamilton AM, Kirk EL, Cohen SM, Midkiff BR, Xia Y, Sherman ME, Nikolaishvili-Feinberg N, Serody JS, Hoadley KA, Troester MA, Calhoun BC. Lab Invest. 2021 Jun;101(6):785-793. doi: 10.1038/s41374-020-0056-0. Epub 2021 Feb 23. PMID: 33623115
An approach for normalization and quality control for NanoString RNA expression data.
Bhattacharya A*, Hamilton AM*, Furberg H, Pietzak E, Purdue MP, Troester MA, Hoadley KA*, Love MI*. Brief Bioinform. 2020 Aug 13:bbaa163. doi: 10.1093/bib/bbaa163. Online ahead of print. PMID: 32789507
Proteogenomic and metabolomic characterization of human glioblastoma.
Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L; Clinical Proteomic Tumor Analysis Consortium. Cancer Cell. 2021 Apr 12;39(4):509-528.e20. doi: 10.1016/j.ccell.2021.01.006. Epub 2021 Feb 11. PMID: 33577785
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma.
Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieślik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubiński J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW, Zhang H, Zhang B; Clinical Proteomic Tumor Analysis Consortium. Cancer Cell. 2021 Mar 8;39(3):361-379.e16. doi: 10.1016/j.ccell.2020.12.007. Epub 2021 Jan 7. PMID: 33417831
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway
Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network, Meyerson M, Govindan R, Imielinski M. Cell Rep. 2021 Feb 2;34(5):108707. doi: 10.1016/j.celrep.2021.108707. PMID: 33535033
Outcomes of Hormone-Receptor Positive, HER2-Negative Breast Cancers by Race and Tumor Biological Features.
Benefield HC, Reeder-Hayes KE, Nichols HB, Calhoun BC, Love MI, Kirk EL, Geradts J, Hoadley KA, Cole SR, Earp HS, Olshan AF, Carey LA, Perou CM, Troester MA. JNCI Cancer Spectr. 2020 Sep 23;5(1):pkaa072. doi: 10.1093/jncics/pkaa072. eCollection 2021 Feb. PMID: 33442657
SCISSOR: a framework for identifying structural changes in RNA transcripts.
Choi HY, Jo H, Zhao X, Hoadley KA, Newman S, Holt J, Hayward MC, Love MI, Marron JS, Hayes DN. Nat Commun. 2021 Jan 12;12(1):286. doi: 10.1038/s41467-020-20593-3. PMID: 33436599
Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment
Wheeler DA, Takebe N, Hinoue T, Hoadley KAa, Cardenas MF, Hamilton AMb, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, Castro de Moura M, Esteller M, Shen H, Zenklusen JC, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O’Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, Ivy SP, Staudt LM. Cancer Cell. 2021 Jan 11;39(1):38-53.e7. doi: 10.1016/j.ccell.2020.10.015. Epub 2020 Nov 19. PMID: 33217343
Development and validation of a NanoString BASE47 bladder cancer gene classifier.
Pathologic Response, and Genomics in CALGB 40601 (Alliance), a Neoadjuvant Phase III Trial of Paclitaxel-Trastuzumab With or Without Lapatinib in HER2-Positive Breast Cancer.
Fernandez-Martinez A, Krop IE, Hillman DW, Polley MY, Parker JS, Huebner L, Hoadley KA, Shepherd J, Tolaney S, Henry NL, Dang C, Harris L, Berry D, Hahn O, Hudis C, Winer E, Partridge A, Perou CM, Carey LA. Survival, J Clin Oncol. 2020 Dec 10;38(35):4184-4193 doi: 10.1200/JCO.20.01276. PMID: 33095682
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y. PMID: 32958763
Sex differences in oncogenic mutational processes.
Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium. Nat Commun. 2020 Aug 28;11(1):4330. doi: 10.1038/s41467-020-17359-2. PMID: 32859912
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.
Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA; Clinical Proteomic Tumor Analysis Consortium. Cell. 2020 Jul 9;182(1):200-225.e35. doi: 10.1016/j.cell.2020.06.013. PMID: 32649874
In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators.
Adaptation and selection shape clonal evolution of tumors during residual disease and recurrence.
Nat Commun. 2020 Oct 6;11(1):5017. doi: 10.1038/s41467-020-18730-z. PMID: 33024122
Ancestry-specific predisposing germline variants in cancer.
Oak N, Cherniack AD, Mashl RJ; TCGA Analysis Network, Hirsch FR, Ding L, Beroukhim R, Gümüş ZH, Plon SE, Huang KL. Genome Med. 2020 May 29;12(1):51. doi: 10.1186/s13073-020-00744-3. PMID: 32471518
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer.
Carrot-Zhang J*, Chambwe N*, Damrauer JS*, Knijnenburg TA*, Robertson AG*, Yau C*, Zhou W*, Berger AC*, Huang KL*, Newberg JY*, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E; Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R. Cancer Cell. 2020 May 11;37(5):639-654.e6. doi: 10.1016/j.ccell.2020.04.012. PMID: 32396860
A Consensus Molecular Classification of Muscle-invasive Bladder Cancer.
Kamoun A, Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F; Bladder Cancer Molecular Taxonomy Group. Eur Urol. 2020 Apr;77(4):420-433. doi: 10.1016/j.eururo.2019.09.006. Epub 2019 Sep 26. PMID: 31563503
Proteogenomic Characterization of Endometrial Carcinoma.
Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D; Clinical Proteomic Tumor Analysis Consortium. Cell. 2020 Feb 20;180(4):729-748.e26. Epub 2020 Feb 13. doi: 10.1016/j.cell.2020.01.026. PMID: 32059776
A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival.
Samorodnitsky S, Hoadley KA, Lock EF. Cancer Inform. 2020 Feb 17;19:1176935120907399. doi: 10.1177/116935120907399. eCollection 2020. PMID: 32116467
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium. Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8. PMID: 32024849
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019. PMID: 32024823
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. Nature. 2020 Feb;578(7793):129-136. Epub 2020 Feb 5. doi:10.1038/s41586-020-1970-0. PMID: 32025019
Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortiuma. Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5. PMID: 32025007
Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer.
Zhang H, Schaefer A, Wang Y, Hodge RG, Blake DR, Diehl JN, Papageorge AG, Stachler MD, Liao J, Zhou J, Wu Z, Akarca FG, de Klerk LK, Derks S, Pierobon M, Hoadley KA, Wang TC, Church G, Wong KK, Petricoin EF, Cox AD, Lowy DR, Der CJ, Bass AJ. Cancer Discov. 2020 Feb; 10(2): 288-305. doi: 10.1158/2159-8290.CD-19-0811. 2019 Nov 26. PMID: 31771969
Virus expression detection reveals RNA-sequencing contamination in TCGA.
Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. BMC Genomics. 2020 Jan 28;21(1):79. doi: 10.1186/s12864-020-683-6. PMID: 31992194
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Cell. 2019 Oct 31;179(4):964-983.e31. doi: 10.1016/j.cell.2019.10.007. PMID: 31675502
Assessment of Long-term Distant Recurrence-Free Survival Associated With Tamoxifen Therapy in Postmenopausal Patients With Luminal A or Luminal B Breast Cancer.
Yu NY, Iftimi A, Yau C, Tobin NP, van ‘t Veer L, Hoadley KA, Benz CC, Nordenskjöld B, Fornander T, Stål O, Czene K, Esserman LJ, Lindström LS.JAMA Oncol. 2019 Sep 1;5(9):1304-1309. doi: 10.1001/jamaoncol.2019.1856. PMID: 31393518
A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival.
Samorodnitsky S, Hoadley KA, Lock EF. Cancer Inform. 2020 Feb 17;19:1176935120907399. doi: 10.1177/1176935120907399. eCollection 2020. PMID: 32116467
B7-H3-redirected chimeric antigen receptor T cells target glioblastoma and neurospheres.
The immune microenvironment in hormone receptor-positive breast cancer before and after preoperative chemotherapy.
Waks AG, Stover DG, Guerriero JL, Dillon DA, Barry WT, Gjini E, Hartl CA, Lo WT, Savoie J, Brock J, Wesolowski R, Li Z, Damicis A, Philips AV, Wu Y, Yang F, Sullivan A, Danaher P, Brauer HA, Osmani W, Lipschitz M, Hoadley KA, Goldberg MS, Perou CM, Rodig S, Winer EP, Krop I, Mittendorf EA, Tolaney SM. Clin Cancer Res. 2019 Aug 1;25(15):4644-4655. doi: 10.1158/1078-0432.CCR-19-0173. Epub 2019 May 6. PMID: 31061067
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data.
Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z; Genomic Data Analysis Network, Liang H, Noble MS. Cell Syst. 2019 Jul 24;9(1):24-34.e10. doi: 10.1016/j.cels.2019.06.006. PMID: 31344359
Prognostic value of B cells in cutaneous melanoma.
Selitsky SR, Mose LE, Smith CC, Chai S, Hoadley KA, Dittmer DP, Moschos SJ, Parker JS, Vincent BG. Genome Med. 2019 May 28;11(1):36. doi: 10.1186/s13073-019-0647-5. PMID: 31138334
Androgen Receptor mRNA Expression in Urothelial Carcinoma of the Bladder: A Retrospective Analysis of Two Independent Cohorts.
Sikic D, Wirtz RM, Wach S, Dyrskjøt L, Erben P, Bolenz C, Breyer J, Otto W, Hoadley KA, Lerner SP, Eckstein M, Hartmann A, Keck B. Transl Oncol. 2019 Apr;12(4):661-668. doi: 10.1016/j.tranon.2019.01.005. Epub 2019 Mar 2. PMID: 30831560
Intrinsic Subtypes in the Nurses’ Health Study Cohorts
Kensler KH, Sankar VN, Wang J, Zhang X, Rubadue CA, Baker GM, Parker JS, Hoadley KA, Stancu AL, Pyle ME, Collins LC, Hunter DJ, Elissen AH, Hankinson SE, Tamimi RM, Heng YJ. PAM50 Molecular. Cancer Epidemiol Biomarkers Prev. 2019 Apr;28(4):798-806. doi: 10.1158/1055-9965.EPI-18-0863. Epub 2018 Dec 27. PMID: 30591591
CCL5 promotes breast cancer recurrence through macrophage recruitment in residual tumors.
FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer
Arceci A, Bonacci T, Wang X, Stewart K, Damrauer JS, Hoadley KA, Emanuele MJ. F. Cell Rep. 2019 Mar 12;26(11):3076-3086.e6. doi: 10.1016/j.celrep.2019.02.054. PMID: 30865895
The Prognostic Significance of Frequency Somatic Mutations in Metastatic Cutaneous Melanoma
Zhao X, Little P, Hoyle AP, Pegna GJ, Hayward MC, Ivanova A, Parker JS, Marron DL, Soloway MG, Jo H, Salazar AH, Papakonstantinou MP, Bouchard DM, Jefferys SR, Hoadley KA, Ollila DW, Frank JS, Thomas NE, Googe PB, Ezzell AJ, Collichio FA, Lee CB, Earp HS, Sharpless NE, Hugo W, Wilmott JS, Quek C, Waddell N, Johansson PA, Thompson JF, Hayward NK, Mann GJ, Lo RS, Johnson DB, Scolyer RA, Hayes DN, Moschos SJ. Front Oncol. 2019 Jan 4;8:584. doi: 10.3389/fonc.2018.00584. eCollection 2018. PMID: 30662871
Differences in race, molecular and tumor characteristics among women diagnosed with invasive ductal and lobular breast carcinomas.
Williams LA, Hoadley KA, Nichols HB, Geradts J, Perou CM, Love MI, Olshan AF, Troester MA. Cancer Causes Control. 2019 Jan;30(1):31-39. doi: 10.1007/s10552-018-1121-1. Epub 2019 Jan 8. PMID: 30617775