GWAS region focused capture-HiC of primary melanocytes from five human donors
Capture-HiC was conducted to map chromatin interactions at all melanoma GWAS identified risk-associated regions across five individual primary human melanocyte cultures. Capture-HiC baits were designed by Arima Genomics (San Diego, CA, 2x tiling, least stringent masking, XTHSBoosting) to obtain an Agilent Sure Select library (Santa Clara, CA) targeting all restriction fragments (recognition sequences: ^GATC, ^GANTC) covering entire regions of association for the 68 independent genome-wide significant signals. Fifteen Capture-HiC libraries were generated from five human primary melanocyte cultures (C56, C140, C205, C24, and C27), with three technical replicates for each culture, except C56 third technical replicate, where the same library was also sequenced in a different batch labeled as rep4. The barcoded Capture-HiC libraries were pooled and sequenced using an Illumina Novaseq. This included one run on an SP flow cell and a second run on an S1 flow cell, resulting in approximately 5.7 billion paired-end reads with a read length of 150 bp. This sequencing yielded a median coverage of about 350 million read pairs per technical replicate and approximately 1.1 billion read pairs per culture.