Department: Computer Science & Engineering
Faculty Advisor(s): Vineet Bafna | Pavel A. Pevzner | Chung K. Cheng

Primary Student
Name: Viraj Balkrishna Deshpande
Email: vdeshpan@ucsd.edu
Phone: 979-224-6028
Grad Year: 2017

Gene amplifications are often observed in multiple cancer types, increasing the copy counts of oncogenes like EGFR and MYC. We may also observe multiple oncogenes co-amplifying or viral genomes integrated with amplified oncogenes. These amplicons are often expressed as homogeneous staining regions (HSRs) or extrachromosomal double minutes (DMs). Tumor amplicons can undergo rearrangements during formation and evolution. We develop computational approaches and analyze pan-cancer genome sequencing data for identification and reconstruction of architecture of amplicons. With a better understanding of the amplicon structure we explore important biological questions including what is origin of DMs and HSRs, do amplicons evolve over time, do tumor samples contain a heterogeneous mixture of rearranged amplicons and what are the mechanisms for rearrangements. We revisit the previously proposed episome model for extrachromosomal amplification and study its prevalence and dynamics in various cancer subtypes and oncogenes.

Industry Application Area(s)
Life Sciences/Medical Devices & Instruments | Software, Analytics | Bioinformatics

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Contact:   researchexpo@soe.ucsd.edu   (858) 534-6068