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CSHL Biology of Genomes 2009

CSHL Biology of Genomes 2009

A room for coverage of the 2009 Biology of Genomes conference in Cold Spring Harbor
Daniel MacArthur
#cshl Gil McVean mock-annoyed at Tony Kwan's description of the 1000 Genomes Project as a "limited resequencing project"
Boy, that totally came out wrong! What I really meant to say was that for the HapMap populations for the pilot release we had (only Pilot 1 and 2), only a subset of the CEU/YRI individuals were released at very low coverage, so we had access to limited resequencing information for our particular analysis. Maybe I should find Gil ... - Tony Kwan
Hey Tony - I'm pretty sure Gil knew what you meant, and was just messing with you. :-) - Daniel MacArthur
btw, thanks for blogging, even though i'm here! - Tony Kwan
Daniel MacArthur
#cshl David Goode (Stanford) implications: (1) we should use constraint rather than annotation to prioritise functional sites; (2) don't ignore non-coding regions (>90% of functional variation is here); (3) most functional variation is shared between populations; (4) next-gen genotyping platforms should target constrained sites
Daniel MacArthur
#cshl Tony Kwan: combining genetic variation and gene expression data to explore functional effects of disease-associated variants
Daniel MacArthur
#cshl endless irritation with glitchy wireless access
Daniel MacArthur
#cshl Federica Di Palma: 70 genetic regions underlying adaptation of sticklebacks from salt to fresh water; selection on ancient variation
Daniel MacArthur
Philip Awadalla on sequencing of synaptic genes in autism and schizophrenia: (1) de novo mutations explain some cases of both diseases, but many are cell line artifacts; (2) excess of rare mutations in synaptic genes in both disease; (3) same gene can be linked to both diseases
Daniel MacArthur
Peter Donnelly on analysis of CNVs in seven different diseases: (1) most CNVs (especially >10% frequency) are already well-tagged by SNPs; (2) CNV analysis EXTREMELY challenging due to technical artifacts (e.g. systematic diff between blood/cell line DNA); (3) many of these technical artifacts would survive replication; extreme caution required!
Daniel MacArthur
Maria Wilbe on benefits of using the dog for mapping complex traits: (1) same genes and diseases as human; (2) inbred breeds mean very long haplotypes, making genome-wide association easier; (3) much shorter shared haplotypes BETWEEN breeds makes subsequent fine-mapping easier.
Daniel MacArthur
will be posting short, punchy updates on this meeting on Twitter (http://twitter.com/dgmacarthur) - will post more complex issues here for discussion
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