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

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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.

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Acknowledgements

The authors thank the National Center for Genome Medicine at Academia Sinica, Taiwan, for genotyping technical support. This Center was supported by grants from the National Core Facility Program for Biotechnology of National Science Council, Taiwan, R.O.C. We also acknowledge Ms. Pi-Mei Hsu, Ms. Shwu-Fang Li for technical support on DNA extraction. Special thanks are due to the many hundreds of individuals who volunteered to give biological samples for gene frequency studies.

This work was supported by the Ministry of Science and Technology, Taiwan, R.O.C. [grant numbers NSC 100-2320-B-002-013-MY3]; and Institute of Forensic Medicine, Ministry of Justice, Taiwan, R.O.C. [grant numbers 104-1301-05-05-06].

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Authors and Affiliations

  1. Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan

    Hsiao-Lin Hwa, Hsiang-I Yin & James Chun-I Lee

  2. Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan

    Hsiao-Lin Hwa

  3. Department of Medical Genetics, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan

    Hsiao-Lin Hwa & Li-Hui Tseng

  4. Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan

    Chih-Peng Lin & Wei-Hsin Hsieh

  5. Institute of Forensic Medicine, Ministry of Justice, No. 123, Min-an St, New Taipei City, 235, Taiwan, Republic of China

    Tsun-Ying Huang & Chun-Yen Lin

  6. Department of Public Health and Institute of Epidemiology and Preventive Medicine, National Taiwan University, No. 17, Xu-Zhou Rd, Taipei, 100, Taiwan

    Po-Hsiu Kuo

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  1. Hsiao-Lin Hwa
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Correspondence to James Chun-I Lee.

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Hwa, HL., Lin, CP., Huang, TY. et al. A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians. Forensic Sci Med Pathol 13, 177–187 (2017). https://doi.org/10.1007/s12024-017-9863-8

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