Sinergia-CRC (TCGA cohort) Panel - gangstr_crc_hg38 (Manuscript in preparation)

For this reference panel we used statistical framework TRAL to find 1,5 mln STRs in the human reference genome located in the proximity of genes (promoter, exon and intron regions). The Sinergia-CRC repeats have then been genotyped using GangSTR on more than 400 genomes from patients with colorectal cancer available to us through the TCGA consortium. This project is part of a larger effort "Trans-omic approach to colorectal cancer: an integrative computational and clinical perspective" funded by a SNSF Sinergia grant.

Cohort-level summary statistics describing locus-level patterns of genetic variation is stored in the WebSTR database and is publicly available for each STR. The following parameters can be accessed:

• avg_size_diff: the average amount of repeat units difference that was found for this locus between healthy and tumor sample
• total_calls: the total number of patients where the locus was called in both the healthy and tumor sample.
• frac_variable: the fraction of patients where a difference in repeat size was observed between healthy and tumor for this locus. Calculated by dividing the number of patients with variable loci by total_calls

Patient-level length variation data of each STR is controlled and available only upon approval from the TCGA consortium as it can potentially be used to identify the patient.