Department of Breast and Molecular Oncology

Dr. Sohrab Shah

Contact:
rm 3427 600 W10th Ave,
BC Cancer Agency Vancouver BC
V5T4E6
+1 604-877-6000 x2589
email: sshah [at] bccrc.ca
[Full CV]
computational biology website: http://compbio.bccrc.ca
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:

• inference of single nucleotide variants from next generation sequencing data (with Ana Crisan MSc student)
• extension and application of hidden Markov models to infer copy number alterations from high density genotyping arrays (with Gavin Ha MSc student)
• inference of gene fusions from paired-end RNAseq data (with Andrew McPherson MSc student)

Current cancer genomics projects:

• 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 Publications

Sohrab P. Shah, Ryan D. Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh,
Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Giuliany, Janine Senz,
Christian Steidl, Robert A. Holt, Steven Jones, Mark Sun, Gillian Leung,
Richard Moore, Tesa Severson, Greg A. Taylor, Andrew E. Teschendorff, Kane Tse,
Gulisa Turashvili, Richard Varhol, Rene L. Warren, Peter Watson, Yongjun Zhao, C
arlos Caldas, David Huntsman, Martin Hirst, Marco A. Marra and Samuel Aparicio
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution Nature. vol461, 809-813. (2009) [PDF]

Sohrab P. Shah, Ph.D., Martin Kobel, M.D., Janine Senz, B.Sc., Ryan D. Morin, M.Sc., Blaise A. Clarke, M.B., B.Ch., Kimberly C. Wiegand, B.Sc., Gillian Leung, B.Sc., Abdalnasser Zayed, B.Sc., Erika Mehl, B.M.L.Sc., Steve E. Kalloger, B.Sc., Mark Sun, B.Sc., Ryan Giuliany, Erika Yorida, B.M.L.Sc., Steven Jones, Ph.D., Richard Varhol, M.Sc., Kenneth D. Swenerton, M.D., Dianne Miller, M.D., Philip B. Clement, M.D., Colleen Crane, B.Tech., Jason Madore, M.Sc., Diane Provencher, M.D., Peter Leung, Ph.D., Anna DeFazio, Ph.D., Jaswinder Khattra, M.Sc., Gulisa Turashvili, M.D., Ph.D., Yongjun Zhao, M.Sc., D.V.M., Thomas Zeng, M.Sc., J.N. Mark Glover, Ph.D., Barbara Vanderhyden, Ph.D., Chengquan Zhao, M.D., Christine A. Parkinson, Ph.D., M.R.C.P., Mercedes Jimenez-Linan, Ph.D., David D.L. Bowtell, Ph.D., Anne-Marie Mes-Masson, Ph.D., James D. Brenton, M.D., F.R.C.P., Samuel A. Aparicio, B.M., B.Ch., Niki Boyd, Ph.D., Martin Hirst, Ph.D., C. Blake Gilks, M.D., Marco Marra, Ph.D., and David G. Huntsman, M.D.
Mutation of FOXL2 in Granulosa-Cell Tumors of the Ovary New England Journal of Medicine. June 10, 2009 [FULLTEXT]

News:

Telegraph, UK | Forbes.com | Vancouver Sun

Editorial:

Cancer Genomes on a Shoestring Budget. Shedure and Stewart

Sohrab P. Shah, K-John Cheung, Jr, Nathalie A. Johnson, Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng and Kevin P. Murphy. Model-based clustering of array CGH data Bioinformatics 2009 25(12):i30-i38 [PDF] [SOFTWARE]

Shah SP. Computational methods for identification of recurrent copy number alteration patterns by array CGH. Cytogenetic and Genome Research 2009.

Cheung KJ*, Shah SP*, Steidl C, Johnson N, Relander T, Telenius A, Lai B, Murphy KP, Lam W, Al-Tourah AJ, Connors JM, Ng RT, Gascoyne RD, Horsman DE. Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances.Blood. 2008 Aug 14. (* – Contributed equally)

S P Shah, W L Lam, R T Ng, K P Murphy. Modeling recurrent DNA copy number alterations in array CGH data Bioinformatics 2007 Jul 1;23(13):i450-8
[Software] [PDF] [Talk slides from ISMB 2007]

S Shah, X Xuang, R DeLeeuw, M Khojasteh, W Lam, R Ng, K Murphy Integrating copy number polymorphisms into array CGH analysis using a robust HMM Bioinformatics 2006 Jul 15;22(14):e431-9 [Software] [PDF]

Kemmer D, Huang Y, Shah SP, Lim J, Brumm J, Yuen MM, Ling J, Xu T, Wasserman WW, Ouellette BF Ulysses – an application for the projection of molecular interactions across species. Genome Biol. 2005; 6(12): R106 [PDF][Web server]

Shah SP. Detecting common secondary structure elements in RNA sequences. MSc Thesis. May 2005 [PDF]

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF. Atlas – a data warehouse for integrative bioinformatics.BMC Bioinformatics. 2005 Feb 21;6(1):34
[Software]

Shah SP, He DY, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GX, Xu T, Ouellette BF.
Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 5(1):40. (2004). [Software]

Shah SP,McVicker GP,Mackworth AK,Rogic S,Ouellette BF. GeneComber: combining outputs of gene prediction programs for improved results. Bioinformatics 19(10):1296-7. (2003).