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.
Department of Biology, San Francisco State University.
bioRxiv. 2023 Mar 9:2023.03.07.531629. doi: 10.1101/2023.03.07.531629.
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.
联合DNA索引系统（CODIS）的20个短串联重复序列（STR）标记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标记仅包含与身份识别相关的信息（就像人类指纹一样），几乎不包含有关祖先或特征的信息。然而，在过去20年中，一个快速发展的领域已经确定了数十万种基因型与特征的关联。在这里，我们对围绕CODIS基因座的此类关联情况与非CODIS STR进行了比较调查。我们发现，与其他随机的常染色体四核苷酸重复STR组相比，CODIS标记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）中被确定为与特征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）。尽管目前尚不清楚CODIS需要传达多少表型信息才会削弱“DNA指纹”的类比，但将CODIS标记作为一个整体来看，它们所在区域的已知表型关联变异异常密集。
