Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification

Abstract

A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10−8. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage.

Genetic Variants Allegedly Linked to Antisocial Behaviour Are Equally Distributed Across Different Populations

“…Genotype and frequency data relating to the African (AFR), American (AMR), East Asian (EAS), European (EUR), Toscani in Italy (TSI), and South Asian (SAS) populations of the 1000 Genomes Project, available on the Ensembl genome browser, were used [17][18][19].…”

“…In this work, we selected 24 polymorphisms in genes related to human behaviour previously associated with criminal behaviour [13][14][15]17]. We considered several genetic variants included in dopaminergic and serotoninergic pathways and other variants involved, for example, in association studies with Alzheimer's disease and in glucocorticoid receptors [13][14][15]17].…”

Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction

“…To further improve the prediction of human eye color, quantitative characterization of eye color phenotypes has been adopted using high-resolution photographic images of the iris in combination with DIAT software analysis, with the aim of increasing understanding of human variability in this character. Advanced machine learning approaches, such as the progress on the implementation of MPS for forensic purposes, i.e., phenotypic trait prediction in ancient DNA analysis, showed a significant increase in sensitivity for color prediction [ 87 , 88 , 89 , 90 ]. Another challenge may be the development of universal genomic predictive methods with the goal of collecting sufficiently large data sets using whole-genome sequencing (WGS) technology and enabling the identification of rare DNA variants implicated in phenotype determination [ 91 ].…”

Forensic DNA Phenotyping: a review on SNP panels, genotyping techniques, and prediction models

“…A great number of genetic techniques have been used to infer BGA or EVCs [13,40,196,242,324]: PCR assays (e.g., PCR-RFLP [171], PCR-REBA [82], and most commonly TaqMan® SNP genotyping assay), microarrays (e.g., GeneChip™ [102,287]), minisequencing (e.g., SNPlex™), MALDI-TOF (matrix-assisted laser desorption/ionization -time-of-ight) together with mass spectrometry (MS) detection (e.g., Sequenom® MassARRAY®) [107,116,120] and high-resolution melting (HRM) [65,196,324]. While some techniques like Sequenom® MassARRAY® or HRM do not reach the sensitivity requirements for forensic samples [107,115,325], others have been developed but discontinued, such as Genomelab™ SNPstream® [66,156,159,214] and Genplex®.…”