Combining results of forensic STR kits: HDplex validation including allelic association and linkage testing with NGM and Identifiler loci

Abstract

The autosomal short tandem repeat (STR) kits that are currently used in forensic science have a high discrimination power. However, this discrimination power is sometimes not sufficient for complex kinship analyses or decreases when alleles are missing due to degradation of the DNA. The Investigator HDplex kit contains nine STRs that are additional to the commonly used forensic markers, and we validated this kit to assist human identification. With the increasing number of markers it becomes inevitable that forensic and kinship analyses include two or more STRs present on the same chromosome. To examine whether such markers can be regarded as independent, we evaluated the 30 STRs present in NGM, Identifiler and HDplex. Among these 30 markers, 17 syntenic STR pairs can be formed. Allelic association between these pairs was examined using 335 Dutch reference samples and no linkage disequilibrium was detected, which makes it possible to use the product rule for profile probability calculations in unrelated individuals. Linkage between syntenic STRs was studied by determining the recombination fraction between them in five three-generation CEPH families. The recombination fractions were compared to the physical and genetic distances between the markers. For most types of pedigrees, the kinship analyses can be performed using the product rule, and for those cases that require an alternative calculation method (Gill et al., Forensic Sci Int Genet 6:477-486, 2011), the recombination fractions as determined in this study can be used. Finally, we calculated the (combined) match probabilities, for the supplementary genotyping results of HDplex, NGM and Identifiler.

Genetic polymorphism of 22 autosomal STR markers in a Han population of Southern China

“…The least informative locus was D10S1435, which had an expected heterozygosity of 0.7358. In kinship analyses, the forensic DNA community is concerned with the genetic linkage and tendency of alleles at two or more syntenic STR markers to be inherited together during meiosis [16,17]. Hence, we present the mapping positions and genetic locations of the 22 STR loci, as well as common forensic loci on the same chromosome, in Table S3.…”

Evaluation of samples comprising minute amounts of DNA

“…Single donor samples and two-and three-person mixtures were prepared using DNA extracts from six different Dutch males that were selected from a large reference set of 2085 samples [26,27]. Donors A, B and C had at least six alleles among the 15 NGM loci with a frequency above 0.3, while donors D, E and F had at least seven alleles with a frequency below 0.08.…”

Evaluation of forensic genetic parameters of 12 STR loci in the Korean population using the InvestigatorⓇ HDplex kit

“…The smallest (6) and largest (39) number of alleles were detected for the D10S2325 and D21S2055 loci, respectively. The mean values of observed heterozygosity (H obs ) and expected heterozygosity (H exp ) were 0.8102 and 0.8105, respectively.…”

“…Forensic genetic studies using the Investigator Ⓡ HDplex kit have been performed in different laboratories [2,[4][5][6][7][8]. To date, the use of the Investigator Ⓡ HDplex kit to calculate the forensic genetic parameters of the Korean population has not been reported.…”

“…Calculations of allele frequencies, observed and expected heterozygosity, the values of Fst, and pairwise p values for the pairwise comparison of genetic distances in Korean and other populations were performed using Arlequin v3.5. Allele frequencies were obtained from published population data including Argentinian [2], North Italian [4], Dutch [6], Japanese [7], and Shanghai Han [8] populations. The population genetics parameters including matching probability (PM), power of discrimination (PD), polymorphism information content (PIC), and power of exclusion (PE) were calculated using PowerStats v1.…”