Principal Investigator: Francisco Sanchez-Vega

MULTIMODAL DATA INTEGRATION

The Sanchez-Vega lab focuses on the use of novel approaches in computational genomics and multimodal data integration for translational applications in cancer research and precision oncology.  Our team works closely with physicians and surgeons at Memorial Sloan Kettering to investigate clinically relevant questions that have the potential to improve outcomes and optimize treatment decisions. We are particularly interested in multifaceted projects in computational oncology where genomic data (obtained from DNA and RNA sequencing) needs to be integrated with orthogonal sources of biological and clinical information.  These include features extracted from diverse imaging modalities (e.g., MRI, CT scans, endoscopies, tissue staining, etc.), other non-invasive approaches for longitudinal monitoring (e.g., liquid biopsies), and comprehensive clinicopathological annotations (e.g., lab results, multiple lines of treatment, detailed clinical outcomes) that are systematically collected for each patient through a combination of manual curation and automatic querying of electronic medical records.  While our research interests span multiple cancer types, we have a strong translational interest in colorectal cancer stablished through a long-standing collaboration with the Colorectal Cancer Research Center.

View available career opportunities in the lab here.

Selected Publications

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, ……., 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 SA, Chakravarty D, Schultz N, Sanchez-Vega F. Computational methods and translational applications for targeted next-generation sequencing platforms. Genes Chromosomes Cancer. 2022 Jun;61(6):322-331. doi: 10.1002/gcc.23023. Epub 2022 Feb 3. PMID: 35066956.

Nguyen B, Fong C, Luthra A, Smith SA, DiNatale RG, Nandakumar S, Walch H, Chatila WK, Madupuri R, Kundra R, Bielski CM, Mastrogiacomo B, Donoghue MTA, Boire A, Chandarlapaty S, Ganesh K, Harding JJ, Iacobuzio-Donahue CA, …….., Gao J, Zehir A, Berger MF, Solit DB, Bakhoum SF, Sanchez-Vega F, Schultz N. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell. 2022 Feb 3;185(3):563-575.e11. doi: 10.1016/j.cell.2022.01.003. PMID: 35120664; PMCID: PMC9147702.

Jones, G.D., Caso, R., Tan, K.S., Mastrogiacomo, B., Sanchez-Vega, F., Liu, Y., Connolly, J.G., Murciano-Goroff, Y.R., Bott, M.J., Adusumilli, P.S., et al. (2021). KRAS G12C Mutation Is Associated with Increased Risk of Recurrence in Surgically Resected Lung Adenocarcinoma. Clinical Cancer Research 27, 2604–2612. 

Jones GD, Caso R, Tan KS, Mastrogiacomo B, Sanchez-Vega F, Liu Y, Connolly JG, Murciano-Goroff YR, Bott MJ, Adusumilli PS, Molena D, Rocco G, Rusch VW, Sihag S, Misale S, Yaeger R, Drilon A, Arbour KC, Riely GJ, Rosen N, Lito P, Zhang H, Lyden DC, Rudin CM, Jones DR, Li BT, Isbell JM. KRASG12C Mutation Is Associated with Increased Risk of Recurrence in Surgically Resected Lung Adenocarcinoma. Clin Cancer Res. 2021 May 1;27(9):2604-2612. doi: 10.1158/1078-0432.CCR-20-4772. Epub 2021 Feb 16. PMID: 33593884; PMCID: PMC8102372.

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 Dec 1;4(12):e2136913. doi: 10.1001/jamanetworkopen.2021.36913. PMID: 34860243; PMCID: PMC8642786.

Nguyen B, Sanchez-Vega F, Fong CJ, Chatila WK, Boroujeni AM, Pareja F, Weigelt B, Sotiriou C, Larsimont D, Reis-Filho JS, Desmedt C, Schultz N. The genomic landscape of carcinomas with mucinous differentiation. Sci Rep. 2021 May 4;11(1):9478. doi: 10.1038/s41598-021-89099-2. PMID: 33947930; PMCID: PMC8097060.

Shoushtari AN, Chatila WK, Arora A, Sanchez-Vega F, Kantheti HS, Rojas Zamalloa JA, Krieger P, Callahan MK, Betof Warner A, Postow MA, Momtaz P, Nair S, Ariyan CE, Barker CA, Brady MS, Coit DG, Rosen N, Chapman PB, Busam KJ, Solit DB, Panageas KS, Wolchok JD, Schultz N. Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas. Clin Cancer Res. 2021 Apr 15;27(8):2226-2235. doi: 10.1158/1078-0432.CCR-20-4189. Epub 2021 Jan 28. PMID: 33509808; PMCID: PMC8046739.

Selected Projects

Molecular determinants of response to neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer – a research project using multimodal integration of clinical, genomic and imaging data in order to optimize patient management and treatment
Genomic characterization of sarcomas – a collaborative effort to draw a comprehensive molecular map of soft tissue and bone sarcomas using targeted sequencing data from patients treated at MSK
Identifying the genomic basis of organ-specific metastasis – a large computational study that aims to characterize recurrent anatomic routes of metastatic spread and unveil associations with individual somatic alterations across a wide variety of cancer types

Please visit Dr. Sanchez-Vega’s faculty page, PubMed or Google Scholar for publications from the team

Team Members

  • Brooke Mastrogiacomo

    Bioinformatics Engineer I

  • Fan Wu

    Bioinformatics Software Engineer I

  • Evan Seffar

    ‪Computational Biologist I

  • Farheen Shah

    ‪Computational Biologist I

  • John Nguyen

    Graduate student

  • Sharafudeen Abubakar

    Postdoctoral Fellow

FORMER LAB MEMBERS

  • Xuan Qu

    Bioinformatics Engineer

  • Shaleigh Smith

    Bioinformatics Software Engineer I

  • Anisha Luthra

    Bioinformatics Software Engineer I