Francisco Sanchez-Vega

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Francisco Sanchez-Vega

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Francisco Sanchez-Vega is an Assistant Attending Computational Oncologist in the Colorectal Cancer Service of the Department of Surgery with a secondary appointment in the Computational Oncology Service. 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. In April 2019, he joined the Colorectal Cancer Research Center at MSK, where he leads several research projects that aim to characterize the genomic landscape of somatic and transcriptomic alterations in colorectal cancer, including both patients with early and advanced metastatic disease. His current work also involves the identification of genomic determinants of response to total neoadjuvant therapy in patients with locally advanced rectal cancer, as well as novel applications of circulating tumor DNA analyses for detection of minimal residual disease.


  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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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Francisco Sanchez-Vega discloses the following relationships and financial interests:

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