Determining the effects of genetic linkage when using a combination of STR and SNP loci for kinship testing

Da Yang; Sheng Xuan Ma; Guo Liang Zhao; Ao Gao; Zhao Kun Xu

doi:10.1016/j.legalmed.2024.102441

Determining the effects of genetic linkage when using a combination of STR and SNP loci for kinship testing

Leg Med (Tokyo). 2024 Apr 4:69:102441. doi: 10.1016/j.legalmed.2024.102441. Online ahead of print.

Authors

Da Yang¹, Sheng Xuan Ma², Guo Liang Zhao², Ao Gao², Zhao Kun Xu²

Affiliations

¹ Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China; Forensic Science Center of Jining Medical University, Shandong province, P. R. China. Electronic address: yangdajnmu@163.com.
² Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China.

PMID: 38599008
DOI: 10.1016/j.legalmed.2024.102441

Abstract

The pedigree likelihood ratio (LR) can be used for determining kinship in the forensic kinship testing. LR can be obtained by analyzing the DNA data of Short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. With the advancement of biotechnology, increasing number of genetic markers have been identified, thereby expanding the pedigree range of kinship testing. Moreover, some of the loci are physically closer to each other and genetic linkage between loci is inevitable. LRs can be calculated by accounting for linkage or ignoring linkage (LR_linkage and LR_ignore, respectively). GeneVisa is a software for kinship testing (www.genevisa.net) and adopts the Lander-Green algorithm to deal with genetic linkage. Herein, we used the simulation program of the software GeneVisa to investigate the effects of genetic linkage on 1st-degree, 2nd-degree, and 3rd-degree kinship testing. We used this software to simulate LR_linkage and LR_ignore values based on 43 STRs and 134 SNPs in commercial kits by using the allele frequency rate and genetic distance data of the European population. The effects of linkage on LR distribution and LRs of routine cases were investigated by comparing the LR_linkage values with the LR_ignore values. Our results revealed that the linkage effect on LR distributions is small, but the effect on LRs of routine cases may be large. Moreover, the results indicated that the discriminatory power of genetic markers for kinship testing can be improved by accounting for linkage.

Keywords: DNA testing; Kinship; Lander-green algorithm; Linkage; Paternity testing; Pedigree likelihood.