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Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry

Abstract

Human genetic markers linked with the X chromosome (X-linked) are used in the field of population and medical genetics, as well as for DNA identification of individuals in forensic science and forensic medicine. We proposed an XSNPid panel that consists of 66 unlinked single nucleotide X chromosome markers and developed a protocol for their multiplex genotyping using multilocus PCR and MALDI-TOF mass spectrometry. The XSNPid panel is genotyped within two multiplexes (36 and 30 markers). The developed protocol provides an efficient genotype reading; the fraction of determined genotypes is 98.29%. The high level of gene diversity (0.461) for the X-linked SNPs included in the panel is characteristic of the Russian population. A total of 63 out of 66 markers that provide a high efficiency of genotyping and independent inheritance are suitable for DNA identification purposes. The XSNPid panel is characterized by a very high discriminating ability when studying the Russian population. The probability of genotype coincidence in two unrelated individuals is 9 × 10–27 for women and 2 × 10–18 for men. Also, the XSNPid panel has a greater multiplex capacity in addition to a higher discriminating ability compared to the other closest analogues of the X chromosome SNP sets, which makes it more cost effective and less time consuming. The XSNPid panel is a convenient tool, not only for individual DNA identification, but also for population genetic studies.

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Abbreviations

MALDI-TOF:

matrix assisted laser desorption/ionisation-time of flight

SNP:

single nucleotide polymorphism

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Correspondence to V. A. Stepanov.

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Original Russian Text © V.A. Stepanov, K.V. Vagaitseva, V.N. Kharkov, A.A. Cherednichenko, A.V. Bocharova, 2016, published in Molekulyarnaya Biologiya, 2016, Vol. 50, No. 3, pp. 445–456.

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Stepanov, V.A., Vagaitseva, K.V., Kharkov, V.N. et al. Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry. Mol Biol 50, 387–397 (2016). https://doi.org/10.1134/S0026893316030158

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Keywords

  • single nucleotide polymorphic markers (SNPs)
  • X chromosome
  • MALDI-TOF mass spectrometry
  • multiplex genotyping
  • DNA identification
  • population genetics
  • genetic diversity
  • human populations