Francisco Sanchez-Vega is an Assistant Attending Computational Oncologist in the Colorectal Cancer Service of the Department of Surgery, and is affiliated with Computational Oncology in the Department of Epidemiology and Biostatistics. His research focuses on translational applications of machine learning, statistical modeling and computational methods to the field of cancer genomics and precision oncology. Dr. Sanchez-Vega’s doctoral research work addressed the challenge of learning graphical models to efficiently describe high-dimensional, multivariate probability distributions within the context of small-sample regimes. During his postdoctoral experience at the National Human Genome Research Institute, he investigated patterns of aberrant DNA methylation in cancer and identified novel epigenetic biomarkers that could be used for early detection through non-invasive screening tests. Since his arrival at MSK in 2015, he has worked in a wide variety of translational genomic projects. Notable examples include the analysis of molecular determinants of response to anti-HER2 targeted therapies in patients with ERBB2 positive esophagogastric adenocarcinomas, understanding the interplay between mutational burden and response to immune checkpoint inhibitors in lung adenocarcinoma and characterizing the genomic bases of organ-specific metastasis. Dr. Sanchez-Vega was also actively involved and played leadership roles in several of the final marker papers from The Cancer Genome Atlas (TCGA) and the TCGA Pan-Cancer Atlas initiative, where he was one of the driving forces behind the flagship study that characterized somatic alterations in 10 canonical oncogenic signaling pathways in 9,125 tumors from 33 different cancer types.
Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS Open. 2023 Oct 18;16:9-16. doi: 10.1016/j.xjon.2023.10.016. PMID: 38204702; PMCID: PMC10775106.
Ligero M, Serna G, El Nahhas OSM, Sansano I, Mauchanski S, Viaplana C, Calderaro J, Toledo RA, Dienstmann R, Vanguri RS, Sauter JL, Sanchez-Vega F, Shah SP, Ramón Y Cajal S, Garralda E, Nuciforo P, Perez-Lopez R, Kather JN. Weakly Supervised Deep Learning Predicts Immunotherapy Response in Solid Tumors Based on PD-L1 Expression. Cancer Res Commun. 2024 Jan 11;4(1):92-102. doi: 10.1158/2767-9764.CRC-23-0287. PMID: 38126740; PMCID: PMC10782919.
Omer DM, Thompson HM, Verheij FS, Yuval JB, Rosen R, Beets NRA, Luthra A, Romesser PB, Paty PB, Garcia-Aguilar J, Sanchez-Vega F. Rectal Cancer after Prostate Radiation: A Complex and Controversial Disease. Cancers (Basel). 2023 Apr 9;15(8):2214. doi: 10.3390/cancers15082214. PMID: 37190143; PMCID: PMC10136617.
Liu Y, Chudgar N, Mastrogiacomo B, He D, Lankadasari MB, Bapat S, Jones GD, Sanchez-Vega F, Tan KS, Schultz N, Mukherjee S, Offit K, Bao Y, Bott MJ, Rekhtman N, Adusumilli PS, Li BT, Mayo MW, Jones DR. A germline SNP in BRMS1 predisposes patients with lung adenocarcinoma to metastasis and can be ameliorated by targeting c-fos. Sci Transl Med. 2022 Oct 5;14(665):eabo1050. doi: 10.1126/scitranslmed.abo1050. Epub 2022 Oct 5. PMID: 36197962; PMCID: PMC9926934.
Romesser PB, Sanchez-Vega F, Joshua Smith J. A methylation-based prognostic signature in stage II colorectal patients: Considerations for clinical adoption. J Natl Cancer Inst. 2023 Jan 10;115(1):8-11. doi: 10.1093/jnci/djac184. PMID: 36171662; PMCID: PMC9830476.
Chatila WK, Kim JK, Walch H, Marco MR, Chen CT, Wu F, Omer DM, Khalil DN, Ganesh K, Qu X, Luthra A, Choi SH, Ho YJ, Kundra R, Groves KI, Chow OS, Cercek A, Weiser MR, Widmar M, Wei IH, Pappou EP, Nash GM, Paty PB, Shi Q, Vakiani E, Duygu Selcuklu S, Donoghue MTA, Solit DB, Berger MF, Shia J, Pelossof R, Romesser PB, Yaeger R, Smith JJ, Schultz N, Sanchez-Vega F, Garcia-Aguilar J. Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer. Nat Med. 2022 Aug;28(8):1646-1655. doi: 10.1038/s41591-022-01930-z. Epub 2022 Aug 15. PMID: 35970919.
Luthra A, Mastrogiacomo B , Smith A , Chakravarty D, Schultz N, Sanchez-Vega F. Computational methods and translational applications for targeted next-generation sequencing platforms. Genes Chromosomes Cancer 2022; doi: 10.1002/gcc.23023. PMID: 35066956
Nguyen, B, Fong, C, Luthra, A et al., Sanchez-Vega F. and Schultz N Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell 2022; 185 (3): 563-575
Alatise OI, Knapp GC, Sharma A, Chatila WK, Arowolo OA, et al., Sanchez-Vega F, Schultz N, Brennan M, Smith JJ, Kingham TP. Molecular and phenotypic profiling of colorectal cancer patients in West Africa reveals biological insights. Nat Commun. 2021;12(1):6821.
Jones GD, Brandt WS, Shen R, Sanchez-Vega F, et al. A Genomic-Pathologic Annotated Risk Model to Predict Recurrence in Early-Stage Lung Adenocarcinoma. JAMA Surg. 2021;156(2):e205601.
Jones GD, Caso R, Tan KS, Mastrogiacomo B, Sanchez-Vega F. et al. KRAS (G12C) Mutation Is Associated with Increased Risk of Recurrence in Surgically Resected Lung Adenocarcinoma. Clin Cancer Res. 2021;27(9):2604-12.
Kim JK, Marco MR, Choi SH, Qu X et al, Sanchez-Vega F, Garcia-Aguilar J. KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix. Mol Oncol. 2021;15(10):2766-81.
Kim JK, Qu X, Chen CT, Smith JJ, Sanchez-Vega F, Garcia-Aguilar J. Identifying Diagnostic MicroRNAs and Investigating Their Biological Implications in Rectal Cancer. JAMA Netw Open. 2021;4(12):e2136913.
Nguyen B, Sanchez-Vega F, Fong CJ, Chatila WK, et al., Schultz N. The genomic landscape of carcinomas with mucinous differentiation. Sci Rep. 2021;11(1):9478.
Shoushtari AN, Chatila WK, Arora A, Sanchez-Vega F, et al. Schultz N. Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas. Clin Cancer Res. 2021;27(8):2226-35.
Sanchez-Vega F, et al. EGFR and MET Amplifications Determine Response to HER2 Inhibition in ERBB2-Amplified Esophagogastric Cancer. Cancer Discov. 2019 Feb;9(2):199-209. doi: 10.1158/2159-8290.CD-18-0598. Epub 2018 Nov 21. PubMed PMID: 30463996; PubMed Central PMCID: PMC6368868.
Hmeljak J, Sanchez-Vega F, et al. Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discov. 2018 Dec;8(12):1548-1565. doi: 10.1158/2159-8290.CD-18-0804. Epub 2018 Oct 15. PubMed PMID: 30322867; PubMed Central PMCID: PMC6310008.
Liu Y, …, Sanchez-Vega F, et al. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell. 2018 Apr 9;33(4):721-735.e8. doi: 10.1016/j.ccell.2018.03.010. Epub 2018 Apr 2. PubMed PMID: 29622466; PubMed Central PMCID: PMC5966039.
Sanchez-Vega F, et al. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035. PubMed PMID: 29625050; PubMed Central PMCID: PMC6070353.
Hoadley KA, …, Sanchez-Vega F, et al. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022. PubMed PMID: 29625048; PubMed Central PMCID: PMC5957518.
Way GP, Sanchez-Vega F, et al. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046. PubMed PMID: 29617658; PubMed Central PMCID: PMC5918694.
Rizvi H, Sanchez-Vega F, et al. Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing. J Clin Oncol. 2018 Mar 1;36(7):633-641. doi: 10.1200/JCO.2017.75.3384. Epub 2018 Jan 16. Erratum in: J Clin Oncol. 2018 Jun 1;36(16):1645. PubMed PMID: 29337640; PubMed Central PMCID: PMC6075848.
Janjigian YY, Sanchez-Vega F, et al. Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer. Cancer Discov. 2018 Jan;8(1):49-58. doi: 10.1158/2159-8290.CD-17-0787. Epub 2017 Nov 9. PubMed PMID: 29122777; PubMed Central PMCID: PMC5813492.
Sánchez-Vega F, et al. Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype. Epigenetics Chromatin. 2015 Apr 17;8:14. doi: 10.1186/s13072-015-0007-7. eCollection 2015. PubMed PMID: 25960768; PubMed Central PMCID: PMC4424513.
Sánchez-Vega F, et al. Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines. Epigenetics. 2013 Dec;8(12):1355-72. doi: 10.4161/epi.26701. Epub 2013 Oct 22. PubMed PMID: 24149212; PubMed Central PMCID: PMC3933495.
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