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First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA

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Abstract

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.

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Acknowledgements

We gratefully thank Sarah Romac for her valuable technical help.

Author information

Authors and Affiliations

  1. Institute of Legal Medicine, EA3428, Strasbourg, France

    C. Bouakaze, C. Keyser, S. Amory & B. Ludes

  2. Anthropobiology Laboratory, CNRS, FRE2960, Toulouse, France

    S. Amory, E. Crubézy & B. Ludes

Authors
  1. C. Bouakaze
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  2. C. Keyser
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  3. S. Amory
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  4. E. Crubézy
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  5. B. Ludes
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Corresponding author

Correspondence to C. Bouakaze.

Electronic supplementary material

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Fig. S1

Electropherograms obtained from the typing of 13 Y-SNPs with a modern European sample. These plots, obtained using the Genotyper v.3.7 software, show the RFUs vs measured size (nt) of SBE products relative to GS120 LIZ internal size standard. Various PCR products purification methods were tested to eliminate the background signals between 25 and 32 nt (black rectangle): a treatment with SAP and ExoI (GE Healthcare), b UltraClean PCR Clean-up Kit (MoBio Laboratories), and c Genopure ds™ (Brucker Daltonik). Arrows indicate artifact pull-up peaks (DOC 56 kb)

Table S1

PCR primers for the 2 multiplex PCR amplifications of the 13 Y-SNPs used in this study (DOC 47 kb)

Table S2

Minisequencing primers for the detection of the 13 Y-SNPs used in this study (DOC 48 kb)

Table S3

Quantitation results of aDNA extracts (DOC 71 kb)

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Bouakaze, C., Keyser, C., Amory, S. et al. First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. Int J Legal Med 121, 493–499 (2007). https://doi.org/10.1007/s00414-007-0177-3

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  • DOI: https://doi.org/10.1007/s00414-007-0177-3

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