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

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

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Background: Although 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. Results: Using 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. Conclusions: This 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.

Original languageEnglish
Article number750
JournalBMC Genomics
Volume17
DOIs
StatePublished - 17 Oct 2016

Fingerprint

Forensic Genetics
High-Throughput Nucleotide Sequencing
DNA Sequence Analysis
Genetic Markers
Single Nucleotide Polymorphism
Mitochondrial DNA
Amelogenin
Phenotype
Anthropology
Y Chromosome
DNA
Body Remains
Hair

Keywords

  • Ancestry-informative markers (AIMS)
  • Human skeletal remains
  • Massively parallel sequencing (MPS)
  • Mitochondrial DNA
  • Phenotype-informative SNPs
  • Y-STRs

Cite this

Ambers, Angie D. ; Churchill, Jennifer D. ; King, Jonathan L. ; Stoljarova, Monika ; Gill-King, Harrell ; Assidi, Mourad ; Abu-Elmagd, Muhammad ; Buhmeida, Abdelbaset ; Budowle, Bruce. / More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing. In: BMC Genomics. 2016 ; Vol. 17.
@article{2a6b93c694a341fcb258dda8fa0827c0,
title = "More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing",
abstract = "Background: Although 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. Results: Using 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. Conclusions: This 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.",
keywords = "Ancestry-informative markers (AIMS), Human skeletal remains, Massively parallel sequencing (MPS), Mitochondrial DNA, Phenotype-informative SNPs, Y-STRs",
author = "Ambers, {Angie D.} and Churchill, {Jennifer D.} and King, {Jonathan L.} and Monika Stoljarova and Harrell Gill-King and Mourad Assidi and Muhammad Abu-Elmagd and Abdelbaset Buhmeida and Bruce Budowle",
year = "2016",
month = "10",
day = "17",
doi = "10.1186/s12864-016-3087-2",
language = "English",
volume = "17",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",

}

More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing. / Ambers, Angie D.; Churchill, Jennifer D.; King, Jonathan L.; Stoljarova, Monika; Gill-King, Harrell; Assidi, Mourad; Abu-Elmagd, Muhammad; Buhmeida, Abdelbaset; Budowle, Bruce.

In: BMC Genomics, Vol. 17, 750, 17.10.2016.

Research output: Contribution to journalArticle

TY - JOUR

T1 - More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing

AU - Ambers, Angie D.

AU - Churchill, Jennifer D.

AU - King, Jonathan L.

AU - Stoljarova, Monika

AU - Gill-King, Harrell

AU - Assidi, Mourad

AU - Abu-Elmagd, Muhammad

AU - Buhmeida, Abdelbaset

AU - Budowle, Bruce

PY - 2016/10/17

Y1 - 2016/10/17

N2 - Background: Although 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. Results: Using 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. Conclusions: This 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.

AB - Background: Although 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. Results: Using 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. Conclusions: This 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.

KW - Ancestry-informative markers (AIMS)

KW - Human skeletal remains

KW - Massively parallel sequencing (MPS)

KW - Mitochondrial DNA

KW - Phenotype-informative SNPs

KW - Y-STRs

UR - http://www.scopus.com/inward/record.url?scp=84992061393&partnerID=8YFLogxK

U2 - 10.1186/s12864-016-3087-2

DO - 10.1186/s12864-016-3087-2

M3 - Article

C2 - 27766958

AN - SCOPUS:84992061393

VL - 17

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 750

ER -