DNA Extraction and Quality Control. Genomic DNA will be extracted from 
(insert source - blood/saliva/specific tissue) using Gentra Puregene 
system and bar-coded by the UW Center for Clinical Genomics (CCG). All
 isolated DNA is quantitated by pico green, evaluated for quality by 
gel electrophoresis, and the concentrations normalized to 75 ng/ul.  
Extracted samples are tested for genotyping quality with a 48-plex 
custom SNP set. This custom genotyping serves multiple quality control
 purposes: 1) Successful genotyping ensures that the DNA quality is 
high enough for genome wide analysis. Samples that fail in this initial
 test will fail at all subsequent levels.  Typically, only one or two
 samples fail this initial testing and these will be eliminated from
 the subsequent genome wide analysis.  2) This multiplex assay also 
includes markers that determine the sample sex by interrogating an X-Y
 chromosome region, which will be checked against data for the sample 
to insure consistency. In the event of inconsistencies, we will identify
 and attempt to rectify the underlying problems, or re-plate the samples
 from the initial stocks.  Again, these problems are usually minor. 3) 
We will use the genotypes from the 48-plex panel as a genetic 'barcode'
 which at the conclusion of the GWAS can confirm sample consistency 
(i.e., by comparison to genotypes obtained during the genome wide scan).  
The SNPs genotyped in this test panel overlap SNPs found on all high 
density Affymetrix and Illumina genome wide products.