Sohrab Shah

Principal Investigator
CV
Google Scholar
Email
sshahobfuscate@bccrc.ca

Dr. Shah received a PhD in computer science from UBC in 2008 and was appointed as a Principal Investigator to The BC Cancer Agency and the University of British Columbia in 2010. He holds the Canada Research Chair in Computational Cancer Genomics, and is the recipient of both a Michael Smith Foundation for Health Research Career Investigator Award and a Terry Fox Research Institute New Investigator Award. His research focuses on understanding how tumours evolve over time through integrative approaches involving genomics and computational modeling. He has made seminal contributions to understanding of clonal evolution in ovarian cancer1,2 and discovered that specific mutational patterns in the genomes of ovarian cancers are prognostic in terms of treatment outcomes3. Dr. Shah has also pioneered computational methods for inference of mutations in cancer genomes as well as deciphering patterns of cancer evolution. He has led development of novel Bayesian statistical models, algorithms, and computational approaches to analyze large, high dimensional genomics and transcriptomic data sets, from both patient tumours and model systems. This includes advancing molecular profiling of cancer cells at single cell resolution4. Dr. Shah has been at the forefront of studying tumor evolution in breast, ovary and lymphoid malignancies. His work has been published in Nature5, Nature Genetics, Nature Methods6, NEJM, Genome Research, Genome Biology, amongst others. Dr. Shah oversees an annual budget of >$1M in competitively awarded funding from philanthropic, government and international bodies.

Other affiliations:
Faculty member, CIHR/MSFHR Bioinformatics Program
Faculty member, UBC Genome Science and Technology Graduate Program
Associate member, UBC Department of Computer Science
Associate member, Michael Smith Genome Sciences Centre
Adjunct Professor, SFU School of Computing Science

View my collection, “My Bibliography” from NCBI

Papers

Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer.

LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers.

The driver landscape of sporadic chordoma.

Prognostic Model to Predict Post-Autologous Stem-Cell Transplantation Outcomes in Classical Hodgkin Lymphoma.

ReMixT: clone-specific genomic structure estimation in cancer.

Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma.

Kronos: a workflow assembler for genome analytics and informatics.

Observing Clonal Dynamics Across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact.

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.

Enhancing knowledge discovery from cancer genomics data with Galaxy.

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.

Scalable whole-genome single-cell library preparation without preamplification.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.

Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer.

densityCut: an efficient and versatile topological approach for automatic clustering of biological data.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

Clonal genotype and population structure inference from single-cell tumor sequencing.

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.

Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer.

Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.

Divergent clonal selection dominates medulloblastoma at recurrence.

The genomic landscape of epithelioid sarcoma cell lines and tumours.

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Cell of origin of transformed follicular lymphoma.

Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.

Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond.

Using Somatic Mutations to Guide Treatment Decisions: Context Matters.

Spatial genomic heterogeneity within localized, multifocal prostate cancer.

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.

Recurrent genomic rearrangements in primary testicular lymphoma.

Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas.

A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.

Mutational context and diverse clonal development in early and late bladder cancer.

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.

PyClone: statistical inference of clonal population structure in cancer.

Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.

Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma.

A robust hidden semi-Markov model with application to aCGH data processing.

Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles.

Type-specific cell line models for type-specific ovarian cancer research.

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.

Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays.

nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.

Gene expression profiling of microdissected Hodgkin Reed-Sternberg cells correlates with treatment outcome in classical Hodgkin lymphoma.

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.

Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

Use of mutation profiles to refine the classification of endometrial carcinomas.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

The clonal and mutational evolution spectrum of primary triple-negative breast cancers.

BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma.

Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.

Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.

Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas.

Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis.

ARID1A mutations in endometriosis-associated ovarian carcinomas.

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.

Genome-wide copy number analysis of Hodgkin Reed-Sternberg cells identifies recurrent imbalances with correlations to treatment outcome.

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.

Tumor-associated macrophages and survival in classic Hodgkin's lymphoma.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.

Mutation of FOXL2 in granulosa-cell tumors of the ovary.

Model-based clustering of array CGH data.

Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances.

Modeling recurrent DNA copy number alterations in array CGH data.

Integrating copy number polymorphisms into array CGH analysis using a robust HMM.

Ulysses - an application for the projection of molecular interactions across species.

Atlas - a data warehouse for integrative bioinformatics.

Pegasys: software for executing and integrating analyses of biological sequences.

GeneComber: combining outputs of gene prediction programs for improved results.