In addition to the primary COGA linkage sample, a subset of the COGA linkage families were selected for additional genotyping as part of GAW14 [Edenberg et al., 2005]. A subset of 1,364 individuals from 143 families was genotyped on an Illumina panel of 4,596 SNPs intended as a linkage SNP panel. Parallel to the full COGA sample, the majority of the sample was Caucasian (83%), with 13% African American, and 4% other. Because linkage disequilibrium can produce spurious inflations in identity-by-descent (IBD) estimates and inflate information content as a result [Huang et al., 2004], we conducted linkage on a thinned panel of 1,717 SNPs, in which all SNPs with r2 ≥ 0.1 with any other SNP within 1 Mb were deleted [Agrawal et al., 2008]. The thinned map provided similar information content across the genome when compared to the full panel of SNPs [Hinrichs et al., 2005].
