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Forensic Sci Med Pathol. 2017 Jun;13(2):177-187. doi: 10.1007/s12024-017-9863-8. Epub 2017 Apr 24.

A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians.

Author information

1
Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan.
2
Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan.
3
Department of Medical Genetics, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan.
4
Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan.
5
Institute of Forensic Medicine, Ministry of Justice, No. 123, Min-an St, New Taipei City, 235, Taiwan, Republic of China.
6
Department of Public Health and Institute of Epidemiology and Preventive Medicine, National Taiwan University, No. 17, Xu-Zhou Rd, Taipei, 100, Taiwan.
7
Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan. jimlee@ntu.edu.tw.

Abstract

Ancestry informative single-nucleotide polymorphism (AISNP) panels for differentiating between East and Southeast Asian populations are scarce. This study aimed to identify AISNPs for ancestry assignment of five East and Southeast Asian populations, and Caucasians. We analyzed 145 autosomal SNPs of the 627 DNA samples from individuals of six populations (234 Taiwanese Han, 91 Filipinos, 79 Indonesians, 60 Thais, 71 Vietnamese, and 92 Caucasians) using arrays. The multiple logistic regression model and a multi-tier approach were used for ancestry classification. We observed that 130 AISNPs were effective for classifying the ethnic origins with fair accuracy. Among the 130 AISNPs, 122 were useful for stratification between these five Asian populations and 64 were effective for differentiating between Caucasians and these Asian populations. For differentiation between Caucasians and Asians, an accuracy rate of 100% was achieved in these 627 subjects with 50 optimal AISNPs among the 64 effective SNPs. For classification of the five Asian populations, the accuracy rates of ancestry inference using 20 to 57 SNPs for each of the two Asian populations ranged from 74.1% to 100%. Another 14 degraded DNA samples with incomplete profiling were analyzed, and the ancestry of 12 (85.7%) of those subjects was accurately assigned. We developed a 130-AISNP panel for ethnic origin differentiation between the five East and Southeast Asian populations and Caucasians. This AISNP set may be helpful for individual ancestral assignment of these populations in forensic casework.

KEYWORDS:

Ancestry assignment; Ancestry informative single-nucleotide polymorphism; Array; Ethnic origin differentiation; Forensic genetics

PMID:
28439786
DOI:
10.1007/s12024-017-9863-8
[Indexed for MEDLINE]

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