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
N1 - Funding Information:
This research was possible with thanks to the 2018 Australia Awards-Endeavour Research Fellowship. EYYC was supported by an Australian Government Research Training Program (RTP) Scholarship. CP received funding from the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the Visible Attributes Through Genomics (VISAGE) Project and Consortium.
Publisher Copyright:
© 2019 Elsevier B.V.
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
AN - SCOPUS:85070877099
SN - 1872-4973
VL - 43
SP - 1
EP - 7
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
M1 - 102141
ER -