Complex kinship analysis with a combination of STRs, SNPs, and indels

Complex kinship analysis has been widely applied in disaster victim identification and criminal investigations. A larger number of genetic markers is required to improve the discrimination power of the system in complex kinship analysis compared to that in paternity testing, as distant relatives share fewer genetic segments. Genetic markers, including short tandem repeats (STRs), single-nucleotide polymorphisms (SNPs), and insertions-deletions (indels), play complementary roles in kinship analysis. Few studies have systematically analyzed the system discrimination power of a new combination of different types of genetic markers before using these markers in practice. Here, we tested the ability of a set of 56 STRs available in commercial panels on complex kinship analysis. We next introduced a combination marker set of STRs, indels, and SNPs and evaluated the system discrimination power of 72 indels + 52 SNPs to improve the weight of 56 STRs. Statistical analysis of complex kinship within third-degree kinship testing was performed to compare 56 STRs or 72 indels + 52 SNPs alone. True samples were assessed, including 99 full siblings, 112 uncle/aunt-nephew/niece, 43 grandfather/ grandmother-grandson/granddaughter, 63 first cousins, and 5931 unrelated pairs. Simulation was also performed using 10,000 pairs of relatives and 10,000 unrelated individuals. The effectiveness of the three marker sets in kinship testing was ranked as follows: 56 STRs + 72 indels + 52 SNPs > 56 STRs > 72 indels + 52 SNPs. All three marker sets were powerful in first-degree kinship testing; 56 STRs and 56 STRs + 72 indels + 52 SNPs could distinguish most second-degree relatives from unrelated pairs. However, only a portion of third-degree relatives was correctly determined from unrelated individuals using 56 STRs + 72 indels + 52 SNPs. In relationship testing, 56 STRs and 56 STRs + 72 indels + 52 SNPs were powerful enough to distinguish first-degree relatives from second-degree or third-degree relatives. Our results provide a strategy and guidance applicable in forensic practice for complex kinship analysis by combining STRs, SNPs, and indels.