Happy birthday @jcshott sorry I’m at SFO on my way to #agbt14

First scientific session of #agbt14 first up in this all female session is Aviv Regev discussing single cell analysis.

Now up Valerie Schneider (@dnadiver) to ton nice you all that GRCh38 is great. #agbt14

#agbt14 VS making the case that the GRC had made enough fixes/improvements that it was time to bite the bullet and update- inc 8MB new seq

#agbt14 over 250 regions with alternate loci. Winner is KIR locus with 30 alts. #diversity

#agbt14 more data and stats at <a href="http://genomerefence.org" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://genomerefence.org and @NCBI annotation is out: <a href="http://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/106/" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky">http://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/106/

VS now discussing addition of model centromeres- paper just out from Karen Miga in @genomeresearch #agbt14

VS: discussing addition of human specific sequences to GRCh38. Being very understated about how hard this was. #agbt14

VS shows that GRCh38 has good coverage of the 1000 genomes decoy sequence. #agbt14

@StevenNHart @lexnederbragt I wouldn’t call these decoys. They contain biologically interesting sequences like genes. #agbt14

@StevenNHart @lexnederbragt last I checked EBV is not human. :) and the decoy provided no chromosome context so hard to analyze. #agbt14

VS: making the point that current tool chains not equipped to deal with allelic duplication introduced by alt loci. #agbt14

VS: looking at applying masking to allow current tools to use full reference. #agbt14

Great talk by Valerie on GRCh38. Slides will be available soon. #agbt14

The great Aravinda Chakravarti up first to talk about his work on Hirschsprung disease. #agbt14

Karen Mohlke from UNC discussing GWAS SNPs overlapping regulatory elements in type 2 diabetes #agbt14

KM: Nice gel shift assay showing allelic differences in Tx binding at rs11603334 #agbt14 #ilovegelshifts

Epigenics and transcriptomics session starting in 3 minutes in salons G through J. #agbt14

If anyone had seen Hiro Aburatani please ask him to come to salon g now. Thanks! #agbt14

David Botstein starting the morning session talking about yeast, evolution and cancer. #agbt14

DB: showing examples of yeast genome changes and analogies to changes you see in tumors. #agbt14

Joe DeRisi is up next talking at NGS in the context of critical care illness. #agbt14

JD: doing a great job of expressing the other difficulty of diagnosis- lots of phenotypes and no smoking gun. #agbt14

JD: hasn’t used the term ‘diagnostic odyssey’ yet- may be an understatement in this case. Got an emergency IRB to sequence. #agbt14

JD: bravely showing a live demo of uBiome taxonomy browser with data from sequencing run. #agbt14