title: Transplant Outcomes in Aplastic Anemia (TOAA): Sample TOAA_TOAA_Exome_480
design: Exome sequencing data on all 732 patients were generated at the NCI Cancer Genomics Research Laboratory as previously described (ref). In brief, DNA was extracted from pre-HCT peripheral blood mononuclear cells or whole blood using the QIAamp Maxi Kit (Qiagen Inc., Valencia, CA). Exon-enriched libraries were generated via NimbleGen v3 or v3+UTR capture kit. Samples were sequenced (Illumina MiSeq or HiSeq) to an average depth of ~55x and minimum coverage of >80% at 15x.  Reads were aligned to the hg19 reference genome (Novoalign, Picard). GATK Version 3.8 UnifiedGenotyper, HaplotypeCaller, and Freebayes were used to call variants with variants only used if called by at least two of three callers. Variant calling was limited to only the regions in the intersection of both the v3 and v3+UTR capture kit.