52 additional reference population samples for the 55 AISNP panel

Andrew J Pakstis; Eva Haigh; Lotfi Cherni; Amel Ben Ammar ElGaaied; Alison Barton; Baigalmaa Evsanaa; Ariunaa Togtokh; Jane Brissenden; Janet Roscoe; Ozlem Bulbul; Gonul Filoglu; Cemal Gurkan; Kelly A Meiklejohn; James M Robertson; Cai-Xia Li; Yi-Liang Wei; Hui Li; Usha Soundararajan; Haseena Rajeevan; Judith R Kidd; Kenneth K Kidd

doi:10.1016/j.fsigen.2015.08.003

52 additional reference population samples for the 55 AISNP panel

Forensic Sci Int Genet. 2015 Nov:19:269-271. doi: 10.1016/j.fsigen.2015.08.003. Epub 2015 Aug 14.

Authors

Andrew J Pakstis¹, Eva Haigh², Lotfi Cherni³, Amel Ben Ammar ElGaaied⁴, Alison Barton², Baigalmaa Evsanaa⁵, Ariunaa Togtokh⁶, Jane Brissenden⁷, Janet Roscoe⁸, Ozlem Bulbul⁹, Gonul Filoglu¹⁰, Cemal Gurkan¹¹, Kelly A Meiklejohn¹², James M Robertson¹³, Cai-Xia Li¹⁴, Yi-Liang Wei¹⁵, Hui Li¹⁶, Usha Soundararajan², Haseena Rajeevan², Judith R Kidd², Kenneth K Kidd²

Affiliations

¹ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA. Electronic address: Andrew.Pakstis@yale.edu.
² Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
³ Laboratory of Molecular Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University El Manar, 2092 Tunis, Tunisia; High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia.
⁴ Laboratory of Molecular Genetics, Immunology and Human Pathology, Science Faculty of Tunis, University El Manar, 2092 Tunis, Tunisia.
⁵ Department of Medicine, University of Toronto, Toronto, ON M5S, Canada; Department of Nephrology, Health Sciences University of Mongolia, Khoroo 1, Ulaanbataar, Mongolia.
⁶ Department of Nephrology, Health Sciences University of Mongolia, Khoroo 1, Ulaanbataar, Mongolia.
⁷ Department of Medicine, University of Toronto, Toronto, ON M5S, Canada.
⁸ Department of Medicine, University of Toronto, Toronto, ON M5S, Canada; Department of Medicine, The Scarborough Hospital, Toronto, ON M1P 2V5, Canada.
⁹ Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Institute of Forensic Science, Istanbul University, Istanbul, Turkey.
¹⁰ Institute of Forensic Science, Istanbul University, Istanbul, Turkey.
¹¹ Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus, Cyprus.
¹² Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
¹³ Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
¹⁴ Research Centre of Applied Forensic Science Technologies, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China.
¹⁵ Research Centre of Applied Forensic Science Technologies, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, PR China; Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, Tianjin 300070, PR China.
¹⁶ MOE State Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, PR China.

PMID: 26355664
DOI: 10.1016/j.fsigen.2015.08.003

Abstract

Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.

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

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA / genetics
Databases, Genetic
Genetics, Population*
Humans
Polymorphism, Single Nucleotide

Substances

DNA