Microsatellites used in forensics are located in regions unusually rich in trait-associated variants

Abstract

The 20 short tandem repeat (STR) markers of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS markers are thought to contain information relevant to identification only (such as a human fingerprint would), with little information about ancestry or traits. However, in the past 20 years, a quickly growing field has identified hundreds of thousands of genotype-trait associations. Here we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. We find that the regions around the CODIS markers are enriched for both known pathogenic variants (>90th percentile) and for SNPs identified as trait-associated in genome-wide association studies (GWAS) (>95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs. Although it is not obvious how much phenotypic information CODIS would need to convey to strain the DNA fingerprint analogy, the CODIS markers, considered as a set, are in regions unusually dense with variants with known phenotypic associations.

Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations

“…Historically, the forensic field has favored analyses that target specific loci due to cost, efficacy, and privacy concerns 47 . In the United States, CODIS STRs were selected in part due their being medically uninformative 54,55 , although this has since been called into question 56 . There are currently multiple NGS kits or SNP panels available for forensic analyses (94 -9,959 SNPs 48 ), but most target relatively few SNPs compared to SNP panels in other fields (widely used commercial SNP arrays for medical and population genetic studies contain ~700,000-3.7 millions SNPs [57][58][59] ).…”