We targeted a 455-kb region (10,943,936–11,399,037 bp [Hg19]) on chromosome 16p13.13 for deep sequencing. This region encompassed the four genes (CIITA, CLEC16A, DEXI,and SOCS1) and all SNPs previously reported to be significantly associated with type 1 diabetes. The region was tiled with ∼10-kb PCR fragments with ∼0.5-kb overlaps. Amplifications were done in 48 pools that each contained DNA from 4 individuals (128 type 1 diabetic patients and 64 control subjects). Amplified PCR fragments were pooled in equimolar amounts to create DNA libraries. DNA libraries were prepared for sequencing using Illumina’s Paired-End Sample Preparation Kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina Genome Analyzer IIx (Illumina) using 63 bp-end reads. Sequencing reads were assembled using the Burrows-Wheeler Aligner tool (34 (link)). Sequence Alignment/Map Tools (35 (link)) was used for conversion, indexing, and aligning of the data using the reference genome (Hg18; National Center for Biotechnology Information ver. 36) (36 (link),37 (link)) as well as for SNP identification.