Link Vivian, Zavaleta Yuómi Jhony A, Reyes Rochelle-Jan, Ding Linda, Wang Judy, Rohlfs Rori V, Edge Michael D
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Department of Biology, San Francisco State University, San Francisco, CA, USA.
iScience. 2023 Sep 21;26(10):107992. doi: 10.1016/j.isci.2023.107992. eCollection 2023 Oct 20.
The 20 short tandem repeat (STR) loci 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 loci are thought to contain little information about ancestry or traits. However, in the past 20 years, a 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. Although this study cannot establish or quantify associations between CODIS genotypes and phenotypes, we find that the regions around the CODIS loci are enriched for both known pathogenic variants (> 90th percentile) and for trait-associated SNPs identified in genome-wide association studies (GWAS) (≥ 95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs.
联合DNA索引系统（CODIS）的20个短串联重复序列（STR）位点是美国绝大多数法医遗传学的基础。对于CODIS基因型采集采取宽松规则的一个理由是，人们认为CODIS位点几乎不包含有关祖先或性状的信息。然而，在过去20年中，一个不断发展的领域已经确定了数十万种基因型与性状的关联。在这里，我们对围绕CODIS位点的此类关联情况与非CODIS STR进行了调查。尽管本研究无法确定或量化CODIS基因型与表型之间的关联，但我们发现，与其他随机选择的常染色体四核苷酸重复STR相比，CODIS位点周围区域富含已知的致病变异（>第90百分位数）以及在全基因组关联研究（GWAS）中确定的与性状相关的单核苷酸多态性（SNP）（在侧翼10kb和100kb区域中≥第95百分位数）。
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