First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA
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In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshot™ Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500–1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed.
KeywordsY-chromosome SNPs SNaPshot Single base extension Ancient DNA Southern Siberia Y-haplogroup R1a1
We gratefully thank Sarah Romac for her valuable technical help.
- 12.Budowle B (2004) SNP typing strategies. Forensic Sci Int 146(Suppl):S139–S142Google Scholar
- 25.Doi Y, Yamamoto Y, Inagaki S, Shigeta Y, Miyaishi S, Ishizu H (2004) A new method for ABO genotyping using a multiplex single-base primer extension reaction and its application to forensic casework samples. Leg Med (Tokyo) 6:213–223Google Scholar
- 42.Budowle B, Bieber FR, Eisenberg AJ (2005) Forensic aspects of mass disasters: strategic considerations for DNA-based human identification. Leg Med (Tokyo) 7:230–243Google Scholar