SNP confirmation: Sequencing of PCR amplicons that contained potential biallelic SNPs in HD-B and DM1-A patient cells.

We performed DNA sequencing of potential biallelic SNPs in HD-B and DM1-A patient cell lines. These potential biallelic SNPs were identified in the 4C-seq interaction data. We selected a subset of these SNPs for confirmation by PCR, so we amplified the genomic regions that contained these potential SNPs and performed 2 x 150 bp paired-end sequencing on Illumina MiSeq nano. Overall design: The HD family individuals used were: GM02180 (UN-C, unaffected mother), GM02164 (HD-A, HD father), and GM03620 (HD-B, HD daughter). For the HD family individuals' cell lines, we sequenced 16 genomic regions in a 1 Mb region around the HTT gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.The DM1 family individuals used were: GM04604 (UN-B, unaffected father) and GM06077 (DM1-A, DM1 daughter). For the DM1 family individuals, we sequenced 14 genomic regions in a 1 Mb region around the DMPK gene and 10 genomic regions in a 1 Mb region around the ACTA1 locus.