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Genotype Committee 10-4-2012

We met on October 4, 2012


Present were:  Jennifer A. Doherty <Jennifer.A.Doherty@dartmouth.edu>; Finn, Andrea (Andrea_Finn@affymetrix.com); Forrest-Hay, Alex (Alex_Forrest-Hay@affymetrix.com); Zhan, Yiping <Yiping_Zhan@affymetrix.com>; Wei Chen; Rayjean Hung; Jeannette Schmidt;  Chris Amos


SNP selection: waiting for IARC to finalize a few SNP names (probably a dozen or so priority 1 and 2 SNPs).  Rayjean has submitted positions using HG19 and will not send flanking sequence.


Gene selection:  Still waiting for a few names from German collaborators to be clarified.   Dr. Amos sent CHRN genes that had been overlooked.


Sample Handling: protocol distributed by Rayjean to contributing sites.   Decision to add some reference samples that have been genotyped by 1000 genomes and also as a part of Tom Sellers project as controls.


Laboratory:  Training on platform in early November.  Genotyping of samples could begin probably 3 rd week of November.  Need to finalize array design so that array can be sent at same time as the lab is ready to perform genotyping.


Analysis:  Integrating SNP arrays was difficult in the past but should be less complex for exome arrays since a great deal of overlapping content (Illumina has about 20K not provided by Affymetrix and Affymetrix has about 90K not provided by Illumina).


Game-On chip.  Willl be discussed next week.  Timing for TRICL is awkward because our results are unlikely to be ready until the end of the year at the earliest. 



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