RT Journal Article
T1 Eurasiaplex-2: Shifting the focus to SNPs with high population specificity increases the power of forensic ancestry marker sets
A1 Phillips, Christopher Paul
A1 Puente, María de la
A1 Ruiz Ramírez, Jorge
A1 Staniewska, Alexandra
A1 Ambroa Conde, Adrián
A1 Freire Aradas, Ana María
A1 Mosquera Miguel, Ana
A1 Rodríguez, Amelia
K1 SNPs
K1 South Asia
K1 Forensic ancestry analysis
K1 Population-specific alleles
K1 1000 Genomes
K1 HGDP-CEPH
AB 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
PB Elsevier
YR 2022
FD 2022
LK http://hdl.handle.net/10347/29484
UL http://hdl.handle.net/10347/29484
LA eng
NO Forensic Science International: Genetics 61 (2022) 102780
NO M.d.l.P. is supported by a post-doctorate grant funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the “Programa de axudas á etapa predoutoral” funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020-039)
DS Minerva
RD 24 abr 2026