Progress toward an efficient panel of SNPs for ancestry inference

Kídd, Kenneth K.; Speed, William C.; Pakstis, Andrew J.; Furtado, Manohar R.; Fang, Rixun; Madbouly, Abeer; Maiers, Martin; Middha, Mridu; Friedlaender, Françoise R.; Kidd, Judith R.

doi:10.1016/j.fsigen.2014.01.002

Cited by 224 publications

(234 citation statements)

References 36 publications

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“…A fair amount of Ancestry Information Markers (AIMs) have been proposed for various purposes including detecting stratification in biomedical studies12 and determining an individual’s ancestry from a forensic context34567891011121314. In the genotype-phenotype studies, such as the popular genome-wide association studies (GWAS), the presence of uncontrolled population structure may lead to false-positive or false-negative results1516171819.…”

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confidence: 99%

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.

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confidence: 99%

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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“…One special advantage of the SNPs is the very short length of the fragments, which is very important in particular for the analysis of degraded DNA and another special advantage of the SNPs is the use for inferring biogeographical ancestry (BGA) [4] and externally visible characteristics (EVCs). However forensic workers have to find a way to make up for the low discrimination power of the SNPs.…”

Section: Resultsmentioning

confidence: 99%

A novel system for forensic SNP analysis through PCR–ligase detection reaction

Mao

Feng

et al. 2015

Forensic Science International: Genetics Supplement Series

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A B S T R A C TWith the advantages of lower mutation rates and improved analysis of the degraded or aged samples, single nucleotide polymorphism (SNP) markers has been considered as supplementary to the STRs. Consequently, a robust, simple and cost effective technique for SNP typing is essential to analyze a large number of SNPs. Ligase detection reaction (LDR) could detect a SNP on CE platform through the ability of DNA ligase which can seal the nick junction formed by oligonucleotides hybridized to the flank region of target SNP. Here we purposed a prestudy to set up a 8 Y-SNPs (M9, M74, M35, M95, M110, M89, M13, M20) multiplex panel for forensic application through PCR-ligase detection reaction (LDR) system. Primers of 8 loci were designed for multiplexed PCR. According to the sequence around the SNP site, three LDR probes were designed for each SNP including one common fluorescent labeled probe and two allele specific probes different in size with mismatching bases at the 3' end. PCR-LDR products were profiled through ABI3130 Genetic Analyzer. A set of 8 Y-SNP could be profiled through two multiplexed PCR and two multiplexed LDR. Even though the number of markers in the current system is limited, when fully developed, it can easily be multiplied more SNPs and yield a greater power of discrimination. Our study indicated that the PCR-LDR could provide a robust, simple and cost effective multiplexed SNP typing method for forensic cases in the future.

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“…When attempting to differentiate Mediterranean from Middle East individuals, this probability threshold could be increased further to reduce classification error but the use of 87 SNPs still does not provide a reliable framework for securely differentiating these two population groups. Recent published candidate SNPs could be incorporated in further research to provide additional information on differences among these population groups [31,32].…”

Section: Discussionmentioning

confidence: 99%

Inference of biogeographical ancestry across central regions of Eurasia

et al. 2015

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The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

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Progress toward an efficient panel of SNPs for ancestry inference

Cited by 224 publications

References 36 publications

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

A novel system for forensic SNP analysis through PCR–ligase detection reaction

Inference of biogeographical ancestry across central regions of Eurasia

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