The application of CHISEL to single-cell sequencing using two breast cancer datasets to identify extensive allele-specific copy number aberrations (CNAs) including copy-neutral loss of heterozygosity (LOH), whole-genome duplications (WGDs), and mirrored subclonal CNAs.
The identification of allele-specific CNAs that affect several well-known breast cancer genes, but were invisible to total copy number analysis.
The ability of CHISEL’s allele- and haplotype-specific copy numbers to yield a more refined reconstruction of tumor evolution including: low-frequency clones distinguished by unique CNAs, the timing of allele-specific CNAs before and after WGDs, and evidence of convergent evolution.
Speaker:
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Dr. Ben Raphael Ben Raphael is a Professor of Computer Science at Princeton University. His research focuses on the design and application of novel algorithms for the interpretation of biological data. Recent areas of emphasis include cancer evolution, network/pathway analysis of genetic variants, and structural variation in human and cancer genomes. His group’s algorithms have been used in multiple projects from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). He is the recipient of the Alfred P. Sloan Research Fellowship, the NSF CAREER award, and a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. |
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