Eurasiaplex-2: Shifting the focus to SNPs with high population specificity increases the power of forensic ancestry marker sets. (November 2022)

• Record Type: Journal Article
• Authors: Phillips, C.; de la Puente, M.; Ruiz-Ramirez, J.; Staniewska, A.; Ambroa-Conde, A.; Freire-Aradas, A.; Mosquera-Miguel, A.; Rodriguez, A.; Lareu, M.V.
• Is Part Of: Forensic science international. Volume 61(2022)
• Publication Date: 2022-11
• Subjects: SNPs -- South Asia -- Forensic ancestry analysis -- Population-specific alleles -- 1000 Genomes -- HGDP-CEPH; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2022.102780
• Languages: English
• ISSNs: 1872-4973

Abstract

Abstract: To compile a new South Asian-informative panel of forensic ancestry SNPs, we changed the strategy for selecting the most powerful markers for this purpose by targeting polymorphisms with near absolute specificity – when the South Asian-informative allele identified is absent from all other populations or present at frequencies below 0.001 (one in a thousand). More than 120 candidate SNPs were identified from 1000 Genomes datasets satisfying an allele frequency screen of ≥ 0.1 (10 % or more) allele frequency in South Asians, and ≤ 0.001 (0.1 % or less) in African, East Asian, and European populations. From the candidate pool of markers, a final panel of 36 SNPs, widely distributed across most autosomes, were selected that had allele frequencies in the five 1000 Genomes South Asian populations ranging from 0.4 to 0.15. Slightly lower average allele frequencies, but consistent patterns of informativeness were observed in gnomAD South Asian datasets used to validate the 1000 Genomes variant annotations. We named the panel of 36 South Asian-specific SNPs Eurasiaplex-2, and the informativeness of the panel was evaluated by compiling worldwide population data from 4097 samples in four genome variation databases that largely complement the global sampling of 1000 Genomes. Consistent patterns of allele frequency distribution, which were specific to South Asia, were observed in all populations in, or closely sited to, the Indian sub-continent. Pakistani populations from the HGDP-CEPH panel had markedly lower allele frequencies, highlighting the need to develop a statistical system to evaluate the ancestry inference value of counting the number of population-specific alleles present in an individual. Highlights: New South Asian-informative forensic ancestry marker panel of 36 SNPs compiled called Eurasiaplex-2 . SNPs selected to have zero or near zero South Asian-specific allele frequencies in all other populations located outside Indian sub-continent. Survey of 4097 worldwide samples show average 11–14 South Asian-specific genotypes in South Asians vs. 0.2 in all other population samples. Forensic ancestry markers with near absolute specificity like the SNPs of Eurasiaplex-2 offer potential for highly informative panels differentiating worldwide populations.