Performance of ancestry-informative SNP and microhaplotype markers

Elaine Y.Y. Cheung, Christopher Phillips, Mayra Eduardoff, Maria Victoria Lareu, Dennis McNevin

Research output: Contribution to journalArticle

Abstract

The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.

Original languageEnglish
Article number102141
Pages (from-to)1-7
Number of pages7
JournalForensic Science International: Genetics
Volume43
DOIs
Publication statusPublished - Nov 2019

Fingerprint

Single Nucleotide Polymorphism
Population
Asian Americans
Population Groups
Gene Frequency
Alleles
Genome
Databases

Cite this

Cheung, E. Y. Y., Phillips, C., Eduardoff, M., Lareu, M. V., & McNevin, D. (2019). Performance of ancestry-informative SNP and microhaplotype markers. Forensic Science International: Genetics, 43, 1-7. [102141]. https://doi.org/10.1016/j.fsigen.2019.102141
Cheung, Elaine Y.Y. ; Phillips, Christopher ; Eduardoff, Mayra ; Lareu, Maria Victoria ; McNevin, Dennis. / Performance of ancestry-informative SNP and microhaplotype markers. In: Forensic Science International: Genetics. 2019 ; Vol. 43. pp. 1-7.
@article{034d41bac1ee4a47b28757b99559bcfd,
title = "Performance of ancestry-informative SNP and microhaplotype markers",
abstract = "The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16{\%}) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4{\%}) for differentiation between the five continental populations.",
keywords = "Allele frequency, Ancestry-informative markers, Biogeographical ancestry, Microhaplotype, Population differentiation potential, Single nucleotide polymorphism (SNP)",
author = "Cheung, {Elaine Y.Y.} and Christopher Phillips and Mayra Eduardoff and Lareu, {Maria Victoria} and Dennis McNevin",
year = "2019",
month = "11",
doi = "10.1016/j.fsigen.2019.102141",
language = "English",
volume = "43",
pages = "1--7",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier Ireland Ltd",

}

Cheung, EYY, Phillips, C, Eduardoff, M, Lareu, MV & McNevin, D 2019, 'Performance of ancestry-informative SNP and microhaplotype markers', Forensic Science International: Genetics, vol. 43, 102141, pp. 1-7. https://doi.org/10.1016/j.fsigen.2019.102141

Performance of ancestry-informative SNP and microhaplotype markers. / Cheung, Elaine Y.Y.; Phillips, Christopher; Eduardoff, Mayra; Lareu, Maria Victoria; McNevin, Dennis.

In: Forensic Science International: Genetics, Vol. 43, 102141, 11.2019, p. 1-7.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Performance of ancestry-informative SNP and microhaplotype markers

AU - Cheung, Elaine Y.Y.

AU - Phillips, Christopher

AU - Eduardoff, Mayra

AU - Lareu, Maria Victoria

AU - McNevin, Dennis

PY - 2019/11

Y1 - 2019/11

N2 - The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.

AB - The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.

KW - Allele frequency

KW - Ancestry-informative markers

KW - Biogeographical ancestry

KW - Microhaplotype

KW - Population differentiation potential

KW - Single nucleotide polymorphism (SNP)

UR - http://www.scopus.com/inward/record.url?scp=85070877099&partnerID=8YFLogxK

U2 - 10.1016/j.fsigen.2019.102141

DO - 10.1016/j.fsigen.2019.102141

M3 - Article

VL - 43

SP - 1

EP - 7

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

M1 - 102141

ER -