Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits

Abstract

Multiplex DNA typing methods using massively parallel sequencing can be used to predict externally visible characteristics (EVCs) in forensic DNA phenotyping through the analysis of single‐nucleotide polymorphisms. The focus of EVC determination has focused on hair color, eye color, and skin tone as well as visible biogeographical ancestry features. In this study, we researched off‐label applications beyond what is currently marketed by the manufacturer of the Verogen ForenSeq kit primer set B and Imagen primer set E SNP loci. We investigated additional EVC predictions by examining published genome wide sequencing studies and reported allele‐specific gene expression and predictive values. We have identified 15 SNPs included in the ForenSeq kit panel and Imagen kits that have additional EVC prediction capabilities beyond what is published in the Verogen manuals. The additional EVCs that can be predicted include hair graying, ephelides hyperpigmented spots, dermatoheliosis, facial pigmented spots, standing height, pattern balding, helix‐rolling ear morphology, hair shape, hair thickness, facial morphology, eyebrow thickness, sarcoidosis, obesity, vitiligo, and tanning propensity. The loci can be used to augment and refine phenotype predictions with software such as MetaHuman for missing persons, cold case, and historic case investigations.

Commentary on: Elkins KM, Garloff AT, Zeller CB. Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits. J Forensic Sci. 2023;68(2):608–13. https://doi.org/10.1111/1556‐4029.15215

“…It is unsurprising once again that nearly all of the tested loci are enriched for association with dermatological traits. For example, the SNP rs3827760 indeed influences dermatological traits (enrichment = 134.3-fold, p = 2.82 × 10 −13 ); however, the cited trait associations by Elkins et al [1] do not support a genome-wide significant finding and certainly is not reflective of the large number of associations for this SNP. The GWAS Atlas [7] shows seven genome-wide significant associations (p < 5 × 10 −8 ) with this SNP involving curly versus strait hair, excessive hairiness, and male balding patterns.…”

“…The second major shortcoming of Elkins et al [1] is the language orienting their findings as "predictive." While the authors are transparent about the fact that SNP associations are not causal, they proceed to demonstrate how phenotypic prediction may be performed using genetic information in MetaHuman.…”

“…Frank R. Wendt PhD 1,2,3,4,5 F I G U R E 1 SNP associations from the GWAS Atlas [7]. In panel (A), Elkins et al [1] SNPs are actually associated with over 200 diverse phenotypes, many of which could be considered outwardly visible.…”

“…Elkins et al [1] also report a short-listed selection of traits deemed outwardly visible. For rs12203592, they report three traits, yet the GWAS Atlas [7] shows 43 associations at the level of genomewide significance-26 of which could be considered outwardly visible: cheese intake (p = 3.58 x 10 −10 ), belonging to a religious group (p = 1.46 × 10 −15 ), number of vehicles owned by members of the household (p = 3.55 x 10 −9 ), etc.…”

Authors' response

“…See Original Article here See Commentary on here Editor, Several issues were raised with our recently published [1] Technical Note, "Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits. "…”