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Sharing Genomics: BRCA Exchange and the Human Genome Variation Map

Speaker Name: 
Benedict Paten
Speaker Title: 
Associate Research Scientist and Co-Director of the Computational Genomics Lab
Speaker Organization: 
UCSC
Start Time: 
Tuesday, January 24, 2017 - 12:00pm
End Time: 
Tuesday, January 24, 2017 - 1:15pm
Location: 
Biomed 200

Abstract:

Pathogenic BRCA1 and BRCA2 mutations lead to thousands of breast and ovarian cancer cases yearly, worldwide. Accurate genetic testing can reveal these mutations and give individuals therapeutic choices. However, determining the pathogenicity of BRCA mutation often relies upon having accurate population and case-level information. Previously there was no single source for this information, potentially leading to confusion and inconsistency in test reporting. I will introduce BRCAExchange.org, an attempt to aggregate global knowledge about BRCA1 and BRCA2 mutations into a simple to use portal for patients, clinicians, genetic counsellors and researchers.

BRCA1 and BRCA2 are just two genes of the 19-20,000 protein coding genes in the human genome. In the second part of my talk I will describe the Human Genome Variation Map project. The human reference genome has transformed human genetics by providing a proxy to a universal coordinate system. However, the reference is but one genome, and as such can not contain all the variations present in the population. Analysis relative to it creates a so called reference allele bias. When identifying the variations within a new sample by mapping against the reference it is easy to find alleles within the reference but harder to near impossible to find the alleles not contained within it. Adding additional variations to the reference genome naturally defines a graph structure, a genome graph, with the intersections between additional sequences defining vertices that connect myriad possible human genomes. This subtle extension opens numerous possibilities and forces us to redefine many basic concepts that the field has taken for granted. I will layout our theoretical and empirical investigations of these issues, and show our progress towards a holy grail: comprehensive genome inference conditioned on not a single genome but a population.

Bio:

Benedict Paten is an Associate Research Scientist and Co-Director of the Computational Genomics Lab (cgl.genomics.ucsc.edu) at UCSC. He did his undergraduate at University College London in Neuroscience, then did the computer science diploma at Cambridge University. He did his PhD in Ewan Birney's lab at Cambridge University/EMBL, focusing on genome comparison and cis-regulation. He was a postdoc with David Haussler at UCSC, where he tackled problems in genome assembly, genome rearrangement and comparative genomics. His group is focused on computational genomics, in particular how we connect variations in our genomes with health and disease.