Germline genetics within the SJLIFE cohort has been conducted using DNA extracted from blood samples for survivors and cancer-free controls, which include the following:
- SNP genotyping for 2,622 survivors using Affymetrix array 6.0.
- Whole-genome sequencing (WGS) with 30X coverage was performed at the HudsonAlpha Institute for 4422 survivors and 447 non-cancer controls (3026 survivors and 341 controls using Illumina HiSeq X Ten sequencers; 1,396 survivors and 106 controls using Illumina NovaSeq).
- Whole-exome sequencing (WES) with 100X coverage was performed at SJCRH for the 4422 survivors and 447 non-cancer controls using Illumina HiSeq 4000 platform and the Illumina NovaSeq.
- Primary sequencing data analysis including quality control, mapping and variant calling is being carried through an automated pipeline by the bioinformatics team in the Department of Computation Biology at St. Jude Children's Research Hospital, resulting in a WGS/WES clean data set accessible via the St. Jude Cloud.
Genomics characterization, genome-wide epigenetic profiling was done, as a pilot study, for a subset of 300 survivors using Illumina MethylationEPIC BeadChip.