Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool.
1000 Genomes
Human Origins SNP array
SNPs
ancestry informative markers
bio-geographical ancestry
massively parallel sequencing
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
22 08 2021
22 08 2021
Historique:
received:
21
07
2021
revised:
18
08
2021
accepted:
18
08
2021
entrez:
27
8
2021
pubmed:
28
8
2021
medline:
4
2
2022
Statut:
epublish
Résumé
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the
Identifiants
pubmed: 34440458
pii: genes12081284
doi: 10.3390/genes12081284
pmc: PMC8391248
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Références
Forensic Sci Int Genet. 2019 Nov;43:102152
pubmed: 31518964
Forensic Sci Int Genet. 2020 Sep;48:102344
pubmed: 32615397
Am J Hum Genet. 2007 Jun;80(6):1171-8
pubmed: 17503334
Mol Ecol. 2005 Jul;14(8):2611-20
pubmed: 15969739
Forensic Sci Int Genet. 2015 Sep;18:49-65
pubmed: 26013312
Forensic Sci Int Genet. 2014 Jul;11:13-25
pubmed: 24631693
Forensic Sci Int Genet. 2020 Jan;44:102200
pubmed: 31760353
Nature. 2016 Oct 13;538(7624):238-242
pubmed: 27654910
Mol Ecol Resour. 2015 Sep;15(5):1179-91
pubmed: 25684545
Bioinformatics. 2010 Feb 1;26(3):419-20
pubmed: 20080509
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Forensic Sci Int Genet. 2020 May;46:102232
pubmed: 31986343
Forensic Sci Int Genet. 2014 May;10:23-32
pubmed: 24508742
Forensic Sci Int Genet. 2013 Jan;7(1):98-115
pubmed: 22917817
Hum Genet. 2017 Jul;136(7):847-863
pubmed: 28500464
Forensic Sci Int Genet. 2019 Sep;42:260-267
pubmed: 31404905
Int J Legal Med. 2017 Jul;131(4):901-912
pubmed: 27995319
Nat Commun. 2014 Dec 02;5:5631
pubmed: 25463651
Forensic Sci Int Genet. 2020 Sep;48:102336
pubmed: 32619960
Science. 2020 Mar 20;367(6484):
pubmed: 32193295
Forensic Sci Int Genet. 2019 Nov;43:102141
pubmed: 31442930
Forensic Sci Rev. 2017 Jul;29(2):121-144
pubmed: 28691915
Forensic Sci Int Genet. 2011 Jun;5(3):170-80
pubmed: 20457092
Nature. 2016 Oct 13;538(7624):201-206
pubmed: 27654912
Forensic Sci Int Genet. 2016 Jan;20:71-80
pubmed: 26517174
PLoS Genet. 2012;8(3):e1002554
pubmed: 22412386
Forensic Sci Int Genet. 2013 May;7(3):359-66
pubmed: 23537756
Forensic Sci Int Genet. 2019 Sep;42:213-226
pubmed: 31377479
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Genes (Basel). 2020 Jun 26;11(6):
pubmed: 32604780
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Int J Legal Med. 2018 Nov;132(6):1581-1594
pubmed: 29556719
Forensic Sci Int Genet. 2015 Sep;18:33-48
pubmed: 25716572