All DNA samples used in this sequencing study were whole blood, and were obtained from participants of the MTFS, which is included in the MCTFR. All sequencing was done on Illumina HiSeq technology with 100 or 150 base pair paired-end reads. An introductory overview of sequencing methodology is provide in Appendix 1, with a more complete description in the online supporting information. Sequencing was conducted at two separate institutions, the University of Michigan Sequencing Core and the HudsonAlpha Institute of Technology. After mapping, duplicate read removal, and clipping of overlapping paired-end reads, average depth was 10.47. The variant-calling pipeline, Genomes on the Cloud (GotCloud; Jun, Wing, Abecasis, & Kang, 2014), discovered 27,103,144 autosomal biallelic SNPs in the sample as a whole (see supporting information Table S1 for additional summary information about the genotype calls).
