More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.

Angie D Ambers,Harrell Gill-King,Bruce Budowle,Monika Stoljarova,Jonathan L King,Mourad Assidi,Jennifer D Churchill,Muhammad Abu-Elmagd,Abdelbaset Buhmeida

doi:10.1186/s12864-016-3087-2

Abstract

BackgroundAlthough the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample.ResultsUsing MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes.ConclusionsThis study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from the same initial quantities of DNA as that of current CE-based analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3087-2) contains supplementary material, which is available to authorized users.

Highlights

The primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison
The outcome demonstrates that substantially more genetic information can be obtained from the same initial quantities of DNA as that of current capillary electrophoresis (CE)-based analyses
A variety of short tandem repeat (STR) and SNP markers were analyzed via CE and Massively parallel sequencing (MPS)

Summary

Introduction

The primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. In mass disasters, missing persons cases, or cases involving historical/archaeological remains, sometimes there are no clues as to the person’s potential identity and/or there are no associations made with a reference sample or reference pedigree via a database search [1]. In such scenarios, identification can be difficult or impossible using solely autosomal STRs and lineage markers. There are other genetic markers that can extend human identification capabilities, such as analysis of ancestryinformative markers [2,3,4,5,6,7] and phenotype-informative SNPs [7,8,9,10,11]

Methods

Results

Conclusion