Increasing the reference populations for the 55 AISNP panel: the need and benefits

Andrew J Pakstis; Longli Kang; Lijun Liu; Zhiying Zhang; Tianbo Jin; Elena L Grigorenko; Frank R Wendt; Bruce Budowle; Sibte Hadi; Mariam Salam Al Qahtani; Niels Morling; Helle Smidt Mogensen; Goncalo E Themudo; Usha Soundararajan; Haseena Rajeevan; Judith R Kidd; Kenneth K Kidd

doi:10.1007/s00414-016-1524-z

Increasing the reference populations for the 55 AISNP panel: the need and benefits

Int J Legal Med. 2017 Jul;131(4):913-917. doi: 10.1007/s00414-016-1524-z. Epub 2017 Jan 9.

Authors

Andrew J Pakstis¹, Longli Kang^{2

3}, Lijun Liu^{2

3}, Zhiying Zhang^{2

3}, Tianbo Jin^{2

3}, Elena L Grigorenko^{4

5}, Frank R Wendt⁶, Bruce Budowle^{7

8}, Sibte Hadi⁹, Mariam Salam Al Qahtani⁹, Niels Morling¹⁰, Helle Smidt Mogensen¹⁰, Goncalo E Themudo¹⁰, Usha Soundararajan¹¹, Haseena Rajeevan¹¹, Judith R Kidd¹¹, Kenneth K Kidd¹¹

Affiliations

¹ Department of Genetics, Yale University School of Medicine, P.O. Box 208005, 333 Cedar Street, New Haven, CT, 06520-8005, USA. Andrew.Pakstis@yale.edu.
² Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China.
³ Key Laboratory of High Altitude Environment and Genes Related to Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China.
⁴ Department of Psychology, University of Houston, Houston, TX, 77204, USA.
⁵ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
⁶ Institute of Molecular Medicine, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.
⁷ Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.
⁸ Center of Excellence in Genomic Medicine Research, King Abdelaziz University, Jeddah, Saudi Arabia.
⁹ School of Forensic & Applied Sciences, University of Central Lancashire, Preston, UK.
¹⁰ Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, DK-2100, Copenhagen, Denmark.
¹¹ Department of Genetics, Yale University School of Medicine, P.O. Box 208005, 333 Cedar Street, New Haven, CT, 06520-8005, USA.

Abstract

Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.

Keywords: Alfred; Ancestry; FROG-kb; Reference database; SNP.

MeSH terms

Databases, Genetic
Ethnicity / genetics*
Gene Frequency*
Genetics, Population*
Genotype
High-Throughput Nucleotide Sequencing
Humans
Polymorphism, Single Nucleotide*
Racial Groups / genetics*