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Cancer Genomics Webinar, Hanlee Ji
April 26, 2016 @ 9:00 am - 10:00 am PDT
“Illuminating human genetics and cancer genomics with Linked-Reads and phased genome analysis”Hanlee P. Ji Stanford University co-hosted by 10x Genomics and illumina
The human genome is diploid, with each cell containing a copy of both the maternal and paternal chromosomes. A comprehensive understanding of human genetic variation requires identifying the order, structure, and origin of these sets of alleles and their variants across the genome. In addition, phased variant and haplotype information provides opportunities to dramatically improve our understanding of critical features of genetics and genome structural complexity. Despite advances in the next generation sequencing of cancer genomes, analysis of contiguous variant phasing and Megabase (Mb) haplotypes has been extremely limited to a handful of genomes, typically from cell lines. To overcome these issues, we have applied 10X GemCode technology on Illumina instrumentation. This approach enables the routine, efficient analysis of high molecular weight DNA (i.e. as high if not greater than 150 Kb) and generation of extended haplotypes covering Mb segments of the genome. We demonstrates its application for dissecting complex genomic structure of cancer genomes from primary tumors (rather than cell lines), considering Mb haplotypes in Mendelian analysis, generating next generation diploid assemblies that overcome issues of haplotype genome references and enabling analysis of samples that pose challenges for current methods.
During this webinar, we will review:
- Generation of Mb haplotypes from germline and cancer genomes and their application
- Resolving complex structural variation from cancer genomes using linked reads and high molecular weight DNA
- Application of Mb haplotype analysis in Mendelian disorders