SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests?

Abstract

BACKGROUND: Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites-commonly consisting of 12-15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons' identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. METHODS: We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. RESULTS: The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. CONCLUSIONS: There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.

Fig. 1

Six pairwise relationships (individuals A and B) of increasing distance typical of simple (1/4 genetic variation shared) through to challenging (1/32 shared) deficient kinship analyses.

Fig. 2

Identical pedigrees analyzed in two cases with different outcomes. The first case results support the hypothesis H1 - that the tested man was the uncle of the child due to the presence of multiple incompatible genotypes. The second case results supports hypothesis H2 - that the tested man is the father, based on a likelihood that brought a request for extended testing from the court.

Fig. 3

Three simple pairwise relationship tests where the state of the DNA created incomplete STR profiles that required supplementary SNP tests. Cases are ordered from best at the top to worst condition (1 year, 19 and 10 years internment indicated).

Fig. 4

Simple trio kinship analysis with two independent STR incompatibilities (possible step mutations shown). In this case the absence of exclusions in SNPs added to a likelihood ratio that included the STR mutation rates that led to virtual proof of paternity.

Fig. 5

Density distributions of log RI values obtained from 100,000 simulations each of unrelated (black distributions) and related pairs (grey), for four different pairwise relationships. Reference lines of log 9 and log 999 represent doubtful and proven relationship likelihood thresholds respectively. The closest related pairs of grandfather-grandson show almost fully separated distributions with nearly all unrelated pairs less than doubtful and a large majority of related pairs more than proven. This pattern is progressively eroded as the related pairs become more distant, till the second cousin pairs’ distributions are near identical to unrelated pairs showing almost no pairs higher than doubtful.