A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians
- 252 Downloads
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.
KeywordsAncestry assignment Ancestry informative single-nucleotide polymorphism Array Ethnic origin differentiation Forensic genetics
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].
Compliance with ethical standards
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Informed consent was obtained from all individual participants included in the study.
- 2.Butler M. Forensic DNA typing: biology, technology, and genetics of STR markers. 2nd ed. London: Elsevier Academic Press; 2005.Google Scholar
- 6.Myles S, Stoneking M, Timpson N. An assessment of the portability of ancestry informative markers between human populations. BMC Med Genet. 2009;2:45.Google Scholar