Autosomal STR and SNP characterization of populations from the Northeastern Peruvian Andes with the ForenSeq™ DNA Signature Prep Kit

Abstract

Autosomal DNA data from Peru for human identity testing purposes are scarce in the scientific literature, which hinders obtaining an appropriate portrait of the genetic variation of the resident populations. In this study we genetically characterize five populations from the Northeastern Peruvian Andes (Chachapoyas, Awajún, Wampís, Huancas and Cajamarca). Autosomal short tandem repeat (aSTR) and identity informative single nucleotide polymorphism (iiSNP) data from a total of 233 unrelated individuals are provided, and forensic genetic parameters are calculated for each population and for the combined set Northeastern Peruvian Andes. After correction for multiple testing in the whole dataset of the Northeastern Peruvian Andes, the only departure from Hardy-Weinberg equilibrium was observed in locus rs2111980. Twenty one out of 27 aSTR loci exhibited an increased number of alleles due to sequence variation in the repeat motif and flanking regions. For iiSNPs 33% of the loci displayed flanking region variation. The combined random match probability (RMP), assuming independence of all loci (aSTRs and iiSNPs), in the Chachapoyas, the population with the largest samples size (N = 172), was 8.14 × 10 -62 for length-based data while for sequence-based was 4.15 × 10 -67 . In the merged dataset (Northeastern Peruvian Andes; N = 233), the combined RMP when including all markers were 2.96 × 10 -61 (length-based) and 3.21 × 10 -66 (sequence-based). These new data help to fill up some of the gaps in the genetic canvas of South America and provide essential length-and sequence-based background information for other forensic genetic studies in Peru.

Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing

“…This signifies higher polymorphism and discriminatory power of the 90 autosomal SNPs, and they can be used in the identification and kinship analysis for forensic purposes. Combinatorial use of STR and SNP markers has been reported to further increase the combined RMP to 3.21 × 10 -66 in the Northeastern Peruvian Andes populations [21]. Thus, population-specific analysis of autosomal SNP markers will further explore their usefulness in the human identification process.…”

Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application

“…MPS can simultaneously amplify a large number of target forensic genetic markers and allow multiple samples to be processed in a joint sequencing run using sample-tagging DNA barcodes, which is an efficient tool for forensic applications. At present, several commercially available MPS kits have emerged, such as the Precision ID Ancestry Panel (Thermo Fischer Scientific) containing 165 ancestry-informative SNPs [16,21], Precision ID Identity Panel (Thermo Fis-cher Scientific) consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs [6,22], and ForenSeq DNA Signature Prep Kit (Illumina) comprising 27 autosomal STRs, 7 X-chromosomal STRs, 24 Y-chromosomal STRs, and 94 identity-informative SNPs with the option to contain 22 phenotypic-informative SNPs and 56 ancestry-informative SNPs for individual identification, biogeographical ancestry and phenotype inference [23,24]. In addition, Zhang et al presented an MPS multiplex system containing 52 autosomal SNPs, 72 autosomal InDels (A-InDels), and amelogenin loci for complex kinship analysis [25].…”

Accuracy of Eye and Hair Color Prediction in Mexican Mestizos from Monterrey City Based on ForenSeqTM DNA Signature Prep

“…The DPS-A of this forensic MPS system has been analyzed worldwide [13][14][15][16][17][18][19][20]. Conversely, scarce population studies based on DPS-B have been reported; they are limited to the Norwegian population [21], Yavapai ethnic group [22], and the four major ethnic groups from the USA [23].…”