Capturing Short Tandem Repeat Variation to Measure Genome Instability

Genome instability is a hallmark of many cancers and may be a general marker for increased disease susceptibility. To measure genome instability with high resolution, we propose assessing somatic variation in short tandem repeats (STRs). STRs are highly mutable genomic elements that, due to their repetitive nature, are prone to mutation from strand slippage during DNA replication and misalignment during homologous recombination. Accurately genotyping STRs in a high-throughput manner remains challenging for several reasons, one of which is the high level of “amplification” stutter that confounds identification of true, biological variation. Here we present our method MIPSTR to address the technical challenges of genotyping repetitive DNA. Using single molecule DNA barcodes, MIPSTR allows us to accurately genotype somatic STR variation in additional to germline STR variation across many individuals. Applying MIPSTR to Arabidopsis thaliana, we find increased somatic STR variation in msh2 mutants deficient in mismatch repair as well as in HSP90-reduced plants. The increased somatic STR variation in these plants correlates with increased genome instability and increased expressivity of EMS-induced mutations.