Publications
Selected publications from members of our research group.
JointSNVMix paper published: a statistical model for somatic point mutation detection
JointSVNMix paper wordle
MutationSeq paper on feature based classifiers for somatic mutation detection published
Jiarui Ding; Ali Bashashati; Andrew Roth; Arusha Oloumi; Kane Tse; Thomas Zeng; Gholamreza Haffari; Martin Hirst; Marco A. Marra; Anne Condon; Samuel Aparicio; Sohrab P. Shah. “Feature based classifiers for somatic mutation detection in tumour-normal paired sequencing data.”
Discovery of CIITA gene fusions in lymphoid cancers published in Nature.
Today, our discovery that CIITA is a recurrent gene fusion partner in lymphoid cancers appeared in Nature. Here is a link to the article.
CIITA gene fusion in Hodgkin lymphoma cell lines
Full citation:
Christian Steidl*, Sohrab P. Shah*, Bruce Woolcock, Pedro Farinha, Nathalie A. Johnson, Yongjun Zhao, Adele Telenius, Susana Ben Neriah, Arjan Diepstra, Anke van den Berg, Mark Sun, Gillian Leung, Joseph M. Connors, David G. Huntsman, Kerry J. Savage, Lisa Rimsza, Douglas E. Horsman, Marco A. Marra and Randy D. Gascoyne. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature doi:10.1038/nature09754
ARID1A mutations in ovarian cancer published in New England Journal of Medicine
We have discovered recurrent loss of function mutations in ARID1A in endometriosis associated ovarian cancers. Discovered using next generation sequencing of transcriptomes and novel computational methods, our study was published in the New England Journal of Medicine. Here is a link to the article.
ARID1A mutations in endometrioid associated ovarian cancer
Full citation:
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. [PUBMED]
SNVMix Paper in Bioinformatics
Our paper on SNVMix is now published:
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.
Supplemental material for Shah et al Nature (2009)
We have posted an archive of all the supplemental material accompanying the following paper:
“Mutational evolution of a lobular breast cancer profiled at single nucleotide resolution”, Shah et al Nature (2009). Please click here to download.
Mutational evolution in breast cancer study published in Nature
From the Nature website:
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution p809
Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression.
News and Media: [CTV] | [CBC] | [Globe and Mail]
Blogs: Omics! Omics!
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
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, Carlos Caldas, David Huntsman, Martin Hirst, Marco A. Marra and Samuel Aparicio Nature. vol461, 809-813. (2009)
Mutation of FOXL2 in granulosa-cell tumors of the ovary.
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.
Model-based clustering of array CGH data.
Shah SP, Cheung KJ Jr, Johnson NA, Alain G, Gascoyne RD, Horsman DE, Ng RT, Murphy KP. Model-based clustering of array CGH data. Bioinformatics. 2009 Jun 15;25(12):i30-8.
