Sohrab P Shah

Summary

Affiliation: British Columbia
Country: Canada

Publications

  1. pmc Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling
    Ali Bashashati
    Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
    J Pathol 231:21-34. 2013
  2. pmc deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data
    Andrew McPherson
    Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1001138. 2011
  3. pmc SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors
    Rodrigo Goya
    Department of Molecular Oncology Breast Cancer Research Program, British Columbia Cancer Research Centre, Vancouver, BC, Canada
    Bioinformatics 26:730-6. 2010
  4. pmc JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
    Andrew Roth
    Department of Molecular Oncology, BC Cancer Agency, BC, Canada
    Bioinformatics 28:907-13. 2012
  5. pmc Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors
    Anamaria Crisan
    Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
    PLoS ONE 7:e41551. 2012
  6. pmc The clonal and mutational evolution spectrum of primary triple-negative breast cancers
    Sohrab P Shah
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
    Nature 486:395-9. 2012
  7. pmc Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
    Steven Jm Jones
    Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
    Genome Biol 11:R82. 2010
  8. doi request reprint Computational methods for identification of recurrent copy number alteration patterns by array CGH
    S P Shah
    Department of Computer Science, University of British Columbia, British Columbia Cancer Agency, Vancouver, BC, Canada
    Cytogenet Genome Res 123:343-51. 2008
  9. pmc Model-based clustering of array CGH data
    Sohrab P Shah
    Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 25:i30-8. 2009
  10. pmc Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data
    Jiarui Ding
    Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
    Bioinformatics 28:167-75. 2012

Detail Information

Publications36

  1. pmc Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling
    Ali Bashashati
    Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
    J Pathol 231:21-34. 2013
    ....
  2. pmc deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data
    Andrew McPherson
    Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, British Columbia, Canada
    PLoS Comput Biol 7:e1001138. 2011
    ....
  3. pmc SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors
    Rodrigo Goya
    Department of Molecular Oncology Breast Cancer Research Program, British Columbia Cancer Research Centre, Vancouver, BC, Canada
    Bioinformatics 26:730-6. 2010
    ..Although tools exist for SNV discovery from NGS data, none are specifically suited to work with data from tumors, where altered ploidy and tumor cellularity impact the statistical expectations of SNV discovery...
  4. pmc JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
    Andrew Roth
    Department of Molecular Oncology, BC Cancer Agency, BC, Canada
    Bioinformatics 28:907-13. 2012
    ....
  5. pmc Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors
    Anamaria Crisan
    Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
    PLoS ONE 7:e41551. 2012
    ..Our results indicate that in genomically unstable tumors, copy number annotation for SNV detection will be critical to fully characterize the mutational landscape of cancer genomes...
  6. pmc The clonal and mutational evolution spectrum of primary triple-negative breast cancers
    Sohrab P Shah
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
    Nature 486:395-9. 2012
    ..Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes...
  7. pmc Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
    Steven Jm Jones
    Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Avenue, Vancouver, BC, V5Z 4S6, Canada
    Genome Biol 11:R82. 2010
    ..We investigated the utility of massively parallel sequencing to characterize an adenocarcinoma of the tongue, before and after treatment...
  8. doi request reprint Computational methods for identification of recurrent copy number alteration patterns by array CGH
    S P Shah
    Department of Computer Science, University of British Columbia, British Columbia Cancer Agency, Vancouver, BC, Canada
    Cytogenet Genome Res 123:343-51. 2008
    ....
  9. pmc Model-based clustering of array CGH data
    Sohrab P Shah
    Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
    Bioinformatics 25:i30-8. 2009
    ..This can be due to the presence of heterogeneous cancer subtypes within a supposedly homogeneous population...
  10. pmc Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data
    Jiarui Ding
    Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
    Bioinformatics 28:167-75. 2012
    ..As such, the computational problem of accurately inferring somatic mutations from paired tumour/normal NGS data remains an unsolved challenge...
  11. doi request reprint Gene expression profiling of microdissected Hodgkin Reed-Sternberg cells correlates with treatment outcome in classical Hodgkin lymphoma
    Christian Steidl
    Centre for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada
    Blood 120:3530-40. 2012
    ..In summary, our data reveal novel insights into the pathobiology of treatment failure and suggest CSF1R as a drug target of at-risk CHL...
  12. ncbi request reprint High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes
    K John J Cheung
    Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada
    Genes Chromosomes Cancer 49:669-81. 2010
    ....
  13. pmc Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
    Gavin Ha
    Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Genome Res 22:1995-2007. 2012
    ..Finally, we show how inference of LOH can be used to interpret allele frequencies of somatic mutations and postulate on temporal ordering of mutations in the evolutionary history of these tumors...
  14. pmc Atlas - a data warehouse for integrative bioinformatics
    Sohrab P Shah
    UBC Bioinformatics Centre, University of British Columbia, Vancouver, BC, Canada
    BMC Bioinformatics 6:34. 2005
    ..The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development...
  15. ncbi request reprint Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma
    Jay Gunawardana
    1 Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada 2 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    Nat Genet 46:329-35. 2014
    ..Our data establish PTPN1 mutations as new drivers in lymphomagenesis. ..
  16. ncbi request reprint Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers
    Alireza Heravi-Moussavi
    British Columbia Cancer Research Centre, Vancouver, BC, Canada
    N Engl J Med 366:234-42. 2012
    ..Mutation carriers are at risk for nonepithelial ovarian tumors, notably sex cord-stromal tumors...
  17. ncbi request reprint PyClone: statistical inference of clonal population structure in cancer
    Andrew Roth
    1 Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada 2 Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
    Nat Methods 11:396-8. 2014
    ..Single-cell sequencing validation demonstrates PyClone's accuracy. ..
  18. pmc Use of mutation profiles to refine the classification of endometrial carcinomas
    Melissa K McConechy
    Department of Pathology and Laboratory Medicine, University of British Columbia, BC Cancer Agency, Vancouver, BC, Canada
    J Pathol 228:20-30. 2012
    ..If used in practice, it may lead to improved diagnostic reproducibility and may also serve to stratify patients for targeted therapeutics...
  19. ncbi request reprint Genome-wide copy number analysis of Hodgkin Reed-Sternberg cells identifies recurrent imbalances with correlations to treatment outcome
    Christian Steidl
    Department of Pathology and Laboratory Medicine, Centre for Translational and Applied Genomics, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada
    Blood 116:418-27. 2010
    ....
  20. ncbi request reprint Modeling recurrent DNA copy number alterations in array CGH data
    Sohrab P Shah
    Department of Computer Science, University of British Columbia, 201 2366 Main Mall Vancouver, BC V6T 1Z4 Canada
    Bioinformatics 23:i450-8. 2007
    ..In this article we develop statistical models that jointly infer CNA patterns and the discrete labels by borrowing statistical strength across samples...
  21. pmc ARID1A mutations in endometriosis-associated ovarian carcinomas
    Kimberly C Wiegand
    British Columbia Cancer Agency, Vancouver, Canada
    N Engl J Med 363:1532-43. 2010
    ..Ovarian clear-cell and endometrioid carcinomas may arise from endometriosis, but the molecular events involved in this transformation have not been described...
  22. pmc Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles
    Melissa K McConechy
    Department of Pathology and Laboratory Medicine, University of British Columbia, BC Cancer Agency, Centre for Translational and Applied Genomics, Vancouver, BC, Canada
    Mod Pathol 27:128-34. 2014
    ..Understanding the distinct mutation patterns found in the PI3K and Wnt pathways of ovarian and endometrial endometrioid carcinomas may provide future opportunities for stratifying patients for targeted therapeutics. ..
  23. doi request reprint Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances
    K John J Cheung
    Center for Lymphoid Cancer, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC, Canada
    Blood 113:137-48. 2009
    ..Two of these 16 regions (1p36.22-p36.33 and 6q21-q24.3) were also predictors of transformation risk and independent of IPI. These prognostic features may be useful to identify high-risk patients as candidates for risk-adapted therapies...
  24. ncbi request reprint Mutation of FOXL2 in granulosa-cell tumors of the ovary
    Sohrab P Shah
    Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada
    N Engl J Med 360:2719-29. 2009
    ..The pathogenesis of these tumors is unknown. Moreover, their histopathological diagnosis can be challenging, and there is no curative treatment beyond surgery...
  25. ncbi request reprint Integrating copy number polymorphisms into array CGH analysis using a robust HMM
    Sohrab P Shah
    Department of Computer Science, University of British Columbia, 201 2366 Main Mall Vancouver, BC V6T 1Z4 Canada
    Bioinformatics 22:e431-9. 2006
    ..Unfortunately, standard HMMs are sensitive to outliers, causing over-segmentation, where segments erroneously span very short regions...
  26. pmc MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
    Christian Steidl
    Department of Pathology and Laboratory Medicine, Centre for Lymphoid Cancers and the Centre for Translational and Applied Genomics, Vancouver, British Columbia, V5Z4E6, Canada
    Nature 471:377-81. 2011
    ..Thus, our findings suggest that recurrent rearrangements of CIITA may represent a novel genetic mechanism underlying tumour-microenvironment interactions across a spectrum of lymphoid cancers...
  27. ncbi request reprint Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
    Sohrab P Shah
    Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
    Nature 461:809-13. 2009
    ..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression...
  28. doi request reprint BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma
    Jessica N McAlpine
    Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, University of British Columbia, Vancouver, BC, Canada
    Mod Pathol 25:740-50. 2012
    ..TP53 abnormalities and increased immune cell infiltrates are significantly more common in high-grade serous with germline and somatic mutations in BRCA1 or BRCA2, compared with tumors lacking BRCA abnormalities...
  29. pmc Pegasys: software for executing and integrating analyses of biological sequences
    Sohrab P Shah
    UBC Bioinformatics Centre, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Bioinformatics 5:40. 2004
    ..We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools...
  30. pmc Type-specific cell line models for type-specific ovarian cancer research
    Michael S Anglesio
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e72162. 2013
    ..Unrelated model systems do offer value for study of biochemical processes but specific cellular context needs to be applied to assess relevant therapeutic strategies...
  31. doi request reprint Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities
    Kasmintan A Schrader
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
    J Pathol 225:12-8. 2011
    ..The diagnosis was confirmed by biochemical studies and both broadens the mucolipidosis type III phenotype and demonstrates the clinical utility of next-generation sequencing to diagnose rare genetic diseases...
  32. pmc Tumor-associated macrophages and survival in classic Hodgkin's lymphoma
    Christian Steidl
    Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, Canada
    N Engl J Med 362:875-85. 2010
    ..Current prognostic models predict the outcome of treatment with imperfect accuracy, and clinically relevant biomarkers have not been established to improve on the International Prognostic Score...
  33. doi request reprint Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas
    Melissa K McConechy
    Department of Pathology and Laboratory Medicine, University of British Columbia, British Columbia Cancer Agency, 3427 600 West 10th Avenue, Vancouver, BC, Canada
    J Pathol 223:567-73. 2011
    ..The finding of frequent PPP2R1A mutations in high-grade serous carcinoma of the endometrium but not in high-grade serous carcinoma of the ovary provides clear genetic evidence that these are distinct diseases...
  34. ncbi request reprint Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis
    K John J Cheung
    Center for Lymphoid Cancer, British Columbia Cancer Agency, Canada
    Cancer Res 70:9166-74. 2010
    ..06-9.57, P=0.039), respectively]. Our findings identify TNFRSF14 as a candidate gene associated with a subset of FL, based on frequent occurrence of acquired mutations and their correlation with inferior clinical outcomes...
  35. ncbi request reprint Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma
    David D W Twa
    Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada and
    Blood 123:2062-5. 2014
    ..Our data suggest that recurrent genomic rearrangement events underlie an immune privilege phenotype in a subset of B-cell lymphomas. ..
  36. ncbi request reprint GeneComber: combining outputs of gene prediction programs for improved results
    Sohrab P Shah
    UBC Bioinformatics Centre, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z4H4 Canada
    Bioinformatics 19:1296-7. 2003
    ..The web interface is written in PHP and is structured so as to be easily modified for viewing data from any database that stores gene structures...