For each candidate gene, we bi-directionally re-sequenced all exons (including exons of known alternative transcripts), 5′ and 3′ untranslated regions (UTRs), all intron-exon junctions, 1500 bp upstream (including the core promoter) and selected conserved non-coding sequences (CNS). Our criteria for a CNS was a minimum of 70% conservation over at least 100 bp. Table 2 summarizes amplicon sequencing and variant discovery. Per individual, we sequenced 716 amplicons and ∼360 Kb of DNA. Overall, we generated and analyzed ∼35 million high quality (Phred 20) DNA bases. We detected 935 variants (on average one every 400 bp), of which 550 (59%) are represented in dbSNP (build 126) and 385 (41%) were novel. 87 (9%) are insertions or deletions. The average minor allele frequency (MAF) is 15%. There is a marked difference in the average MAF of markers represented in dbSNP and ones that are not, 21% and 6% respectively. 72% (398/550) of variants that are in dbSNP have a MAF of ≥5%, whereas only 22% (84/385) of novel variants have a MAF of 5% or greater. Despite a MAF of 19% for
