Sara Sadeghi
University of British Columbia
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Publication
Featured researches published by Sara Sadeghi.
Cell Reports | 2017
Farshad Farshidfar; Siyuan Zheng; Marie-Claude Gingras; Yulia Newton; Juliann Shih; A. Gordon Robertson; Toshinori Hinoue; Katherine A. Hoadley; Ewan A. Gibb; Jason Roszik; Kyle Covington; Chia Chin Wu; Eve Shinbrot; Nicolas Stransky; Apurva M. Hegde; Ju Dong Yang; Ed Reznik; Sara Sadeghi; Chandra Sekhar Pedamallu; Akinyemi I. Ojesina; Julian Hess; J. Todd Auman; Suhn Kyong Rhie; Reanne Bowlby; Mitesh J. Borad; Andrew X. Zhu; Josh Stuart; Chris Sander; Rehan Akbani; Andrew D. Cherniack
Summary Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.
Bioinformatics | 2014
Justin Chu; Sara Sadeghi; Anthony Raymond; Shaun D. Jackman; Ka Ming Nip; Richard Mar; Hamid Mohamadi; Yaron S N Butterfield; A. Gordon Robertson; Inanc Birol
Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements. Availability and implementaion: www.bcgsc.ca/platform/bioinfo/software/biobloomtools Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
