Dr. Sohrab Shah

Dr. Sohrab Shah

Dr. Sohrab Shah

Assistant Professor, Dept of Pathology, UBC
Scientist, Dept of Molecular Oncology, BC Cancer Agency

Contact:
rm 4.108 675 W10th Ave,
BC Cancer Agency Vancouver BC
V5T4E6
+1 604-675-8252
email: sshah [at] bccrc.ca
[Full CV]

Research Interests:

Cancer genomics is dependent on computational biology and bioinformatics to produce new knowledge. My research is devoted to the development and application of statistical models for inferring genomic abnormalities from high dimensional genomic measurements in tumour samples.

Current computational projects:
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  • inference of single nucleotide variants from next generation sequencing data (with Andy Roth, PhD student)
  • extension and application of hidden Markov models to infer copy number alterations from high density genotyping arrays (with Gavin Ha PhD student)
  • inference of gene fusions from paired-end RNAseq data (with Andrew McPherson PhD student

Current cancer genomics projects:
foxl2

  • etiology and evolution of serous ovarian cancer (led by Dr. Sohrab Shah)
  • genome and transcriptome sequencing of triple negative breast cancers (led by Dr. Sam Aparicio)
  • subtype discovery and characterization of 2000 breast tumours through gene expression and copy number analysis (led by Dr. Sam Aparicio and Dr. Carlos Caldas)
  • subtype characterization of 100 ovarian cancers by transcriptome sequencing (led by Dr. David Huntsman)

Selected Recent Publications

1: McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M,
Heravi Moussavi A, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO,
Sahinalp SC, Huntsman D, Shah SP. deFuse: an algorithm for gene fusion discovery
in tumor RNA-Seq data. PLoS Comput Biol. 2011 May;7(5):e1001138. Epub 2011 May
19. PubMed PMID: 21625565; PubMed Central PMCID: PMC3098195.

2: Steidl C*, Shah SP*, Woolcock BW, Rui L, Kawahara M, Farinha P, Johnson NA, Zhao
Y, Telenius A, Neriah SB, McPherson A, Meissner B, Okoye UC, Diepstra A, van den
Berg A, Sun M, Leung G, Jones SJ, Connors JM, Huntsman DG, Savage KJ, Rimsza LM,
Horsman DE, Staudt LM, Steidl U, Marra MA, Gascoyne RD. MHC class II
transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.
Nature. 2011 Mar 17;471(7338):377-81. Epub 2011 Mar 2. PubMed PMID: 21368758.
* – equal contribution

3: Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK,
Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J,
Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S,
McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D,
Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM,
Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A
mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct
14;363(16):1532-43. Epub 2010 Sep 8. PubMed PMID: 20942669; PubMed Central PMCID:
PMC2976679.

4: Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra
MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting
single nucleotide variants from next-generation sequencing of tumors.
Bioinformatics. 2010 Mar 15;26(6):730-6. Epub 2010 Feb 3. PubMed PMID: 20130035;
PubMed Central PMCID: PMC2832826.

5: Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A,
Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones S, Sun M, Leung G, Moore R,
Severson T, Taylor GA, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL,
Watson P, Zhao Y, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational
evolution in a lobular breast tumour profiled at single nucleotide resolution.
Nature. 2009 Oct 8;461(7265):809-13. PubMed PMID: 19812674.

6: Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand KC, Leung G, Zayed A,
Mehl E, Kalloger SE, Sun M, Giuliany R, Yorida E, Jones S, Varhol R, Swenerton
KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A,
Khattra J, Turashvili G, Zhao Y, Zeng T, Glover JN, Vanderhyden B, Zhao C,
Parkinson CA, Jimenez-Linan M, Bowtell DD, Mes-Masson AM, Brenton JD, Aparicio
SA, Boyd N, Hirst M, Gilks CB, Marra M, Huntsman DG. Mutation of FOXL2 in
granulosa-cell tumors of the ovary. N Engl J Med. 2009 Jun 25;360(26):2719-29.
Epub 2009 Jun 10. PubMed PMID: 19516027.