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Cancer Program

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration.
McFarland JM, Ho ZV, Kugener G, et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat Commun. 2018;9(1):4610. doi:10.1038/s41467-018-06916-5.
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
Sievers QL, Petzold G, Bunker RD, et al. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science. 2018;362(6414). doi:10.1126/science.aat0572.
Tumor fraction in cell-free DNA as a biomarker in prostate cancer.
Choudhury AD, Werner L, Francini E, et al. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight. 2018;3(21). doi:10.1172/jci.insight.122109.
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Jerby-Arnon L, Shah P, Cuoco MS, et al. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018;175(4):984-997.e24. doi:10.1016/j.cell.2018.09.006.
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Sade-Feldman M, Yizhak K, Bjorgaard SL, et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell. 2018;175(4):998-1013.e20. doi:10.1016/j.cell.2018.10.038.
Mutational processes shape the landscape of TP53 mutations in human cancer.
Giacomelli AO, Yang X, Lintner RE, et al. Mutational processes shape the landscape of TP53 mutations in human cancer. Nat Genet. 2018. doi:10.1038/s41588-018-0204-y.
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors.
Miao D, Margolis CA, Vokes NI, et al. Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat Genet. 2018;50(9):1271-1281. doi:10.1038/s41588-018-0200-2.
Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry.
Durbin AD, Zimmerman MW, Dharia NV, et al. Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. Nat Genet. 2018. doi:10.1038/s41588-018-0191-z.
Intron retention is a source of neoepitopes in cancer.
Smart AC, Margolis CA, Pimentel H, et al. Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018. doi:10.1038/nbt.4239.
Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma.
Gopal RK, Kübler K, Calvo SE, et al. Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma. Cancer Cell. 2018;34(2):242-255.e5. doi:10.1016/j.ccell.2018.06.013.
Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition.
Wong GS, Zhou J, Bin Liu J, et al. Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018. doi:10.1038/s41591-018-0168-6.
Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in wild-type Ewing sarcoma.
Stolte B, Iniguez ABalboni, Dharia NV, et al. Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in wild-type Ewing sarcoma. J Exp Med. 2018;215(8):2137-2155. doi:10.1084/jem.20171066.
Genetic and transcriptional evolution alters cancer cell line drug response.
Ben-David U, Siranosian B, Ha G, et al. Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018;560(7718):325-330. doi:10.1038/s41586-018-0409-3.
Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice.
Fink EC, McConkey M, Adams DN, et al. Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice. Blood. 2018. doi:10.1182/blood-2018-05-852798.
Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 activity.
Sievers QL, Gasser JA, Cowley GS, Fischer ES, Ebert BL. Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 activity. Blood. 2018. doi:10.1182/blood-2018-01-821769.
Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.
Viswanathan SR, Nogueira MF, Buss CG, et al. Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. Nat Genet. 2018;50(7):937-943. doi:10.1038/s41588-018-0155-3.
PPM1D truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells.
Kahn JD, Miller PG, Silver AJ, et al. PPM1D truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells. Blood. 2018. doi:10.1182/blood-2018-05-850339.
DeTiN: overcoming tumor-in-normal contamination.
Taylor-Weiner A, Stewart C, Giordano T, et al. DeTiN: overcoming tumor-in-normal contamination. Nat Methods. 2018. doi:10.1038/s41592-018-0036-9.
GeNets: a unified web platform for network-based genomic analyses.
Li T, Kim A, Rosenbluh J, et al. GeNets: a unified web platform for network-based genomic analyses. Nat Methods. 2018. doi:10.1038/s41592-018-0039-6.
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.
Viswanathan SR, Ha G, Hoff AM, et al. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018. doi:10.1016/j.cell.2018.05.036.
A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer.
Takeda DY, Spisák S, Seo J-H, et al. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell. 2018. doi:10.1016/j.cell.2018.05.037.
Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition.
Wong GS, Zhou J, Bin Liu J, et al. Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018. doi:10.1038/s41591-018-0022-x.
Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens.
Pan J, Meyers RM, Michel BC, et al. Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. Cell Syst. 2018;6(5):555-568.e7. doi:10.1016/j.cels.2018.04.011.
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models.
Ng SY, Yoshida N, Christie AL, et al. Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models. Nat Commun. 2018;9(1):2024. doi:10.1038/s41467-018-04356-9.
A Convergence-Based Framework for Cancer Drug Resistance.
Konieczkowski DJ, Johannessen CM, Garraway LA. A Convergence-Based Framework for Cancer Drug Resistance. Cancer Cell. 2018;33(5):801-815. doi:10.1016/j.ccell.2018.03.025.
Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes.
Chapuy B, Stewart C, Dunford AJ, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018;24(5):679-690. doi:10.1038/s41591-018-0016-8.
Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair.
Haradhvala NJ, Kim J, Maruvka YE, et al. Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair. Nat Commun. 2018;9(1):1746. doi:10.1038/s41467-018-04002-4.
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma.
Manier S, Park J, Capelletti M, et al. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun. 2018;9(1):1691. doi:10.1038/s41467-018-04001-5.
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.
Filbin MG, Tirosh I, Hovestadt V, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018;360(6386):331-335. doi:10.1126/science.aao4750.
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.
Shukla SA, Bachireddy P, Schilling B, et al. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell. 2018;173(3):624-633.e8. doi:10.1016/j.cell.2018.03.026.
Genomic and Functional Approaches to Understanding Cancer Aneuploidy.
Taylor AM, Shih J, Ha G, et al. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018;33(4):676-689.e3. doi:10.1016/j.ccell.2018.03.007.
The long tail of oncogenic drivers in prostate cancer.
Armenia J, Wankowicz SAM, Liu D, et al. The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018. doi:10.1038/s41588-018-0078-z.
Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in Colorectal Cancer.
Hazar-Rethinam M, Kleyman M, G Han C, et al. Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in Colorectal Cancer. Cancer Discov. 2018;8(4):417-427. doi:10.1158/2159-8290.CD-17-1227.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Wala JA, Bandopadhayay P, Greenwald NF, et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018;28(4):581-591. doi:10.1101/gr.221028.117.
Landscapes of childhood tumours.
Bandopadhayay P, Meyerson M. Landscapes of childhood tumours. Nature. 2018;555(7696):316-317. doi:10.1038/d41586-018-01648-4.
Pooled in vivo screens for cancer immunotherapy target discovery.
Lane-Reticker SK, Manguso RT, W Haining N. Pooled in vivo screens for cancer immunotherapy target discovery. Immunotherapy. 2018;10(3):167-170. doi:10.2217/imt-2017-0164.
Inherited DNA-Repair Defects in Colorectal Cancer.
AlDubayan SH, Giannakis M, Moore ND, et al. Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018;102(3):401-414. doi:10.1016/j.ajhg.2018.01.018.
Autophosphorylation of the carboxyl-terminal domain is not required for oncogenic transformation by lung-cancer derived EGFR mutants.
Cho J, Kim S, Du J, Meyerson M. Autophosphorylation of the carboxyl-terminal domain is not required for oncogenic transformation by lung-cancer derived EGFR mutants. Int J Cancer. 2018. doi:10.1002/ijc.31332.
EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma.
Iniguez ABalboni, Stolte B, Wang EJue, et al. EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma. Cancer Cell. 2018. doi:10.1016/j.ccell.2017.12.009.
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.
Miao D, Margolis CA, Gao W, et al. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018. doi:10.1126/science.aan5951.
Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer.
Stover DG, Parsons HA, Ha G, et al. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol. 2018:JCO2017760033. doi:10.1200/JCO.2017.76.0033.
NetSig: network-based discovery from cancer genomes.
Horn H, Lawrence MS, Chouinard CR, et al. NetSig: network-based discovery from cancer genomes. Nat Methods. 2018;15(1):61-66. doi:10.1038/nmeth.4514.
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Subramanian A, Narayan R, Corsello SM, et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell. 2017;171(6):1437-1452.e17. doi:10.1016/j.cell.2017.10.049.
Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer.
Bullman S, Pedamallu CS, Sicinska E, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science. 2017. doi:10.1126/science.aal5240.
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
Adalsteinsson VA, Ha G, Freeman SS, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017;8(1):1324. doi:10.1038/s41467-017-00965-y.
Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Meyers RM, Bryan JG, McFarland JM, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017. doi:10.1038/ng.3984.
SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia.
Mar BG, S Chu H, Kahn JD, et al. SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia. Blood. 2017. doi:10.1182/blood-2017-03-775569.
Patient-derived xenografts undergo mouse-specific tumor evolution.
Ben-David U, Ha G, Tseng Y-Y, et al. Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet. 2017. doi:10.1038/ng.3967.
Multiplex CRISPR/Cas9-Based Genome Editing in Human Hematopoietic Stem Cells Models Clonal Hematopoiesis and Myeloid Neoplasia.
Tothova Z, Krill-Burger JM, Popova KD, et al. Multiplex CRISPR/Cas9-Based Genome Editing in Human Hematopoietic Stem Cells Models Clonal Hematopoiesis and Myeloid Neoplasia. Cell Stem Cell. 2017;21(4):547-555.e8. doi:10.1016/j.stem.2017.07.015.
Emerging Opportunities for Target Discovery in Rare Cancers.
Sharifnia T, Hong AL, Painter CA, Boehm JS. Emerging Opportunities for Target Discovery in Rare Cancers. Cell Chem Biol. 2017;24(9):1075-1091. doi:10.1016/j.chembiol.2017.08.002.
Genomic activation of PPARG reveals a candidate therapeutic axis in bladder cancer.
Goldstein JT, Berger AC, Shih J, et al. Genomic activation of PPARG reveals a candidate therapeutic axis in bladder cancer. Cancer Res. 2017. doi:10.1158/0008-5472.CAN-17-1701.
Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway.
Viswanathan VS, Ryan MJ, Dhruv HD, et al. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017;547(7664):453-457. doi:10.1038/nature23007.
In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.
Manguso RT, Pope HW, Zimmer MD, et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 2017;547(7664):413-418. doi:10.1038/nature23270.
Defining a Cancer Dependency Map.
Tsherniak A, Vazquez F, Montgomery PG, et al. Defining a Cancer Dependency Map. Cell. 2017;170(3):564-576.e16. doi:10.1016/j.cell.2017.06.010.
An immunogenic personal neoantigen vaccine for patients with melanoma.
Ott PA, Hu Z, Keskin DB, et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature. 2017;547(7662):217-221. doi:10.1038/nature22991.
Recurrent and functional regulatory mutations in breast cancer.
Rheinbay E, Parasuraman P, Grimsby J, et al. Recurrent and functional regulatory mutations in breast cancer. Nature. 2017;547(7661):55-60. doi:10.1038/nature22992.
Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression.
Rosenbluh J, Xu H, Harrington W, et al. Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression. Nat Commun. 2017;8:15403. doi:10.1038/ncomms15403.
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.
Huang FW, Mosquera JMiguel, Garofalo A, et al. Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017. doi:10.1158/2159-8290.CD-16-0960.
Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer.
Gibson WJ, Ruan DT, Paulson VA, et al. Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer. Clin Cancer Res. 2017;23(9):2367-2373. doi:10.1158/1078-0432.CCR-16-2154-T.
PIK3CA mutant tumors depend on oxoglutarate dehydrogenase.
Ilic N, Birsoy K, Aguirre AJ, et al. PIK3CA mutant tumors depend on oxoglutarate dehydrogenase. Proc Natl Acad Sci U S A. 2017;114(17):E3434-E3443. doi:10.1073/pnas.1617922114.
The Drug Repurposing Hub: a next-generation drug library and information resource.
Corsello SM, Bittker JA, Liu Z, et al. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat Med. 2017;23(4):405-408. doi:10.1038/nm.4306.
Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma.
George S, Miao D, Demetri GD, et al. Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity. 2017;46(2):197-204. doi:10.1016/j.immuni.2017.02.001.
Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.
Paolella BR, Gibson WJ, Urbanski LM, et al. Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Elife. 2017;6. doi:10.7554/eLife.23268.
Insertions and Deletions Target Lineage-Defining Genes in Human Cancers.
Imielinski M, Guo G, Meyerson M. Insertions and Deletions Target Lineage-Defining Genes in Human Cancers. Cell. 2017;168(3):460-472.e14. doi:10.1016/j.cell.2016.12.025.