Ekta Khurana, Ph.D.

Assistant Professor of Physiology and Biophysics

  • Assistant Professor of Computational Genomics in Computational Biomedicine in the Institute for Computational Biomedicine

646-962-6374

1305 York Avenue, Room Y-13.06
New York, NY 10021


Techniques

Research Areas


Research Summary:

The research interests of the lab fall under the broad categories of genomics, computational biology and systems biology. We participate in multiple international genomics consortia and collaborate with scientists at Weill Cornell to develop novel approaches to understand the role of sequence variants in human disease. The decreasing costs of genome sequencing are leading to a growing repertoire of personal genomes. However, we are lagging behind in understanding the functional consequences of the millions of variants obtained from sequencing. This is also the case for somatic variants in cancer. An average cancer genome contains thousands of somatic variants – but the functional implications of these variants on cancer progression and growth are not clear. We develop integrative computational models to understand the relationship between genomic sequence variation and disease. The impact of sequence variants in non-protein-coding regions of the genome is especially less-well-understood. We have developed muliple computational approaches (for example, FunSeq and RegNetDriver) that integrate large-scale data from multiple resources to identify the DNA point mutations and rearrangements in protein-coding genes and non-coding regulatory regions leading to human disease, in particular cancer.

Recent Publications:

  1. Liu, EM, Martinez-Fundichely, A, Diaz, BJ, Aronson, B, Cuykendall, T, MacKay, M et al.. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Cell Syst. 2019;8 (5):446-455.e8. doi: 10.1016/j.cels.2019.04.001. PubMed PMID:31078526 .
  2. Bailey, MH, Tokheim, C, Porta-Pardo, E, Sengupta, S, Bertrand, D, Weerasinghe, A et al.. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018;174 (4):1034-1035. doi: 10.1016/j.cell.2018.07.034. PubMed PMID:30096302 .
  3. Backenroth, D, He, Z, Kiryluk, K, Boeva, V, Pethukova, L, Khurana, E et al.. FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications. Am. J. Hum. Genet. 2018;102 (5):920-942. doi: 10.1016/j.ajhg.2018.03.026. PubMed PMID:29727691 PubMed Central PMC5986983.
  4. Bailey, MH, Tokheim, C, Porta-Pardo, E, Sengupta, S, Bertrand, D, Weerasinghe, A et al.. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018;173 (2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. PubMed PMID:29625053 PubMed Central PMC6029450.
  5. Kim, J, Geyer, FC, Martelotto, LG, Ng, CK, Lim, RS, Selenica, P et al.. MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene. J. Pathol. 2018;244 (2):143-150. doi: 10.1002/path.5006. PubMed PMID:29149504 PubMed Central PMC5839480.
  6. Dhingra, P, Martinez-Fundichely, A, Berger, A, Huang, FW, Forbes, AN, Liu, EM et al.. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol. 2017;18 (1):141. doi: 10.1186/s13059-017-1266-3. PubMed PMID:28750683 PubMed Central PMC5530464.
  7. Romanel, A, Garritano, S, Stringa, B, Blattner, M, Dalfovo, D, Chakravarty, D et al.. Inherited determinants of early recurrent somatic mutations in prostate cancer. Nat Commun. 2017;8 (1):48. doi: 10.1038/s41467-017-00046-0. PubMed PMID:28663546 PubMed Central PMC5491529.
  8. Feigin, ME, Garvin, T, Bailey, P, Waddell, N, Chang, DK, Kelley, DR et al.. Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nat. Genet. 2017;49 (6):825-833. doi: 10.1038/ng.3861. PubMed PMID:28481342 PubMed Central PMC5659388.
  9. Dhingra, P, Fu, Y, Gerstein, M, Khurana, E. Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization. Curr Protoc Bioinformatics. 2017;57 :15.11.1-15.11.17. doi: 10.1002/cpbi.23. PubMed PMID:28463398 .
  10. Cuykendall, TN, Rubin, MA, Khurana, E. Non-coding genetic variation in cancer. Curr Opin Syst Biol. 2017;1 :9-15. doi: 10.1016/j.coisb.2016.12.017. PubMed PMID:30370373 PubMed Central PMC6203332.
  11. Khurana, E. Cancer genomics: Hard-to-reach repairs. Nature. 2016;532 (7598):181-2. doi: 10.1038/532181a. PubMed PMID:27075092 .
  12. Khurana, E, Fu, Y, Chakravarty, D, Demichelis, F, Rubin, MA, Gerstein, M et al.. Role of non-coding sequence variants in cancer. Nat. Rev. Genet. 2016;17 (2):93-108. doi: 10.1038/nrg.2015.17. PubMed PMID:26781813 .
  13. Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015;163 (4):1011-25. doi: 10.1016/j.cell.2015.10.025. PubMed PMID:26544944 PubMed Central PMC4695400.
  14. 1000 Genomes Project Consortium, Auton, A, Brooks, LD, Durbin, RM, Garrison, EP, Kang, HM et al.. A global reference for human genetic variation. Nature. 2015;526 (7571):68-74. doi: 10.1038/nature15393. PubMed PMID:26432245 PubMed Central PMC4750478.
  15. Lochovsky, L, Zhang, J, Fu, Y, Khurana, E, Gerstein, M. LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic Acids Res. 2015;43 (17):8123-34. doi: 10.1093/nar/gkv803. PubMed PMID:26304545 PubMed Central PMC4787796.
  16. Delaneau, O, Marchini, J, 1000 Genomes Project Consortium, 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun. 2014;5 :3934. doi: 10.1038/ncomms4934. PubMed PMID:25653097 PubMed Central PMC4338501.
  17. Fu, Y, Liu, Z, Lou, S, Bedford, J, Mu, XJ, Yip, KY et al.. FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol. 2014;15 (10):480. doi: 10.1186/s13059-014-0480-5. PubMed PMID:25273974 PubMed Central PMC4203974.
  18. Colonna, V, Ayub, Q, Chen, Y, Pagani, L, Luisi, P, Pybus, M et al.. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 2014;15 (6):R88. doi: 10.1186/gb-2014-15-6-r88. PubMed PMID:24980144 PubMed Central PMC4197830.
  19. Talbert-Slagle, K, Atkins, KE, Yan, KK, Khurana, E, Gerstein, M, Bradley, EH et al.. Cellular superspreaders: an epidemiological perspective on HIV infection inside the body. PLoS Pathog. 2014;10 (5):e1004092. doi: 10.1371/journal.ppat.1004092. PubMed PMID:24811311 PubMed Central PMC4014458.
  20. Khurana, E. Learning to swim in a sea of genomic data. Genome Biol. 2013;14 (12):315. doi: 10.1186/gb4144. PubMed PMID:24314026 PubMed Central PMC4053704.
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