Forensic and population genetic characteristics of 62 X chromosome SNPs revealed by multiplex PCR and MALDI-TOF mass spectrometry genotyping in 4 North Eurasian populations

Степанов, В. Г.; Вагайцева, К. В.; Kharkov, V. N.; Cherednichenko, A. A.; Бочарова, А. В.; Berezina, Galina; Svyatova, Gulnara

doi:10.1016/j.legalmed.2015.12.008

Cited by 11 publications

(8 citation statements)

References 18 publications

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“…Although, this method has rarely been previously tested at intraspecific levels (e.g., for population detachments) [ 43 , 44 ], the results of these studies show that its sensitivity may make it suitable for stock identification as well.…”

Section: Introductionmentioning

confidence: 99%

Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

et al. 2020

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Knowledge of intraspecific variability of a certain species is essential for their long-term survival and for the development of conservation plans. Nowadays, molecular/genetic methods are the most frequently used for this purpose. Although, the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has become a promising alternative tool to specify intraspecific variability, there is a lack of information about the limitations of this method, and some methodological issues need to be resolved. Towards this goal, we tested the sensitivity of this method on an intraspecific level, using genetically identified individuals of a cryptic fish species complex collected from five distinct populations. Additionally, some methodologic issues, such as the effect of (1) delayed sample preparation, (2) clove oil anaesthetization, and (3) different tissue types (muscle, and brain) were investigated using the MS analysis results. Our results show that the delayed sample preparation has a fundamental effect on the result of MS analysis, while at the same time the clove oil did not affect the results considerably. Both the brain and muscle samples were usable for cryptic species identification, but in our opinion this method has limited applicability for population-level segregation. The application of MALDI-TOF MS to the exploitable toolkit of phylogenetic and taxonomic researches could be used to broaden conclusions.

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Section: Introductionmentioning

confidence: 99%

Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

et al. 2020

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“…More importantly, the different mutant type targets can still be identified at an abundance of as low as 1% even under the complex conditions, which is better than those reported by some other methods for multiple SNP detection. 45 , 48 , 55 – 57 Therefore, the CuAAC-based assay can be well used for the multiplex detection of SNPs.…”

Section: Resultsmentioning

confidence: 99%

Simultaneous multiple single nucleotide polymorphism detection based on click chemistry combined with DNA-encoded probes

et al. 2018

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“…One of the efficient modern methods of genotyping of panels of markers, consisting of dozens of SNPs, is the method of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF mass spectrometry). Previously, we have developed a number of multiplex panels of SNPs, based on MALDI-TOF, with capacity of 30-70 markers for the purposes of human population genetics, associative genetic research and DNA identification [9,[14][15][16]. Based on this experience, we chose mass spectrometry of DNA molecules in order to develop a method of multiplex genotyping of markers associated with adaptation to cold climate.…”

Section: Development Of a Multiplex Snp Genotyping Methodmentioning

confidence: 99%

Development of Multiplex Genotyping Methodof Polymorphic Markers for Genes Involved in Human Adaptation to Cold Climate

Степанов¹,

Vagajceva²,

Бочарова³

et al. 2016

Science Evolution

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Dispersal of the human population out of the place of origin in East Africa over the globe proceeded rapidly (on the evolutionary scale) and was associated with change of climatic zones and associated changes in habitat parameters - temperature, humidity, insolation, and infectious load. The aim of the study is to develop a method for genotyping of genetic markers associated with adaptation to climate according to the literature data and functional analysis of genes; and identification of signals of adaptation to cold climate in two indigenous Siberian populations. In the course of study, genes and genetic markers were selected, which show reliable signals of natural selection in populations living in cold arctic and subarctic climates in previously published papers and which are involved in biological processes having a cold adaptation potential. A panel of 28 single nucleotide markers (SNP) was selected, and a method of their multiplex genotyping was developed based on multiplex PCR and separating DNA fragments by MALDI-TOF mass spectrometry. Allele frequencies of 28 SNPs in two indigenous Siberian populations (Yakuts and Kets) were determined. A low level of intrapopulation diversity in these populations and significant genetic differences between them were found. Loci under natural selection conditions were detected by analyzing the distribution of the observed Fst values in comparison with the expected distribution, obtained in the simulation calculations based on the hierarchical island model of population structure. The possible role of selection (p<0.1) in differentiation of populations between allele frequencies was determined for 2 markers - rs133036 in MKL1 gene and rs2305508 in CPT1A gene, which are candidate in terms of climate change adaptation.

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Forensic and population genetic characteristics of 62 X chromosome SNPs revealed by multiplex PCR and MALDI-TOF mass spectrometry genotyping in 4 North Eurasian populations

Cited by 11 publications

References 18 publications

Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

Testing the Applicability of MALDI-TOF MS as an Alternative Stock Identification Method in a Cryptic Species Complex

Simultaneous multiple single nucleotide polymorphism detection based on click chemistry combined with DNA-encoded probes

Development of Multiplex Genotyping Methodof Polymorphic Markers for Genes Involved in Human Adaptation to Cold Climate

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