Methods and research
The major method is a gene geographic study of the space-time structure of gene pools of different hierarchical levels. The research bases on three pillars: Northern Eurasia Biobank, gene pools databases of the peoples of Russia and the world, and cartographic technologies for bioinformatic analysis.
Стоим на трёх китах - Based on Three Pillars
Биобанк - Biobank
База данных о генофонде народов мира - World's Populations Gene Pool Database
Картографическая технология (анализ данных) - Cartographic technology (data analysis)
To extract DNA, we use the most reliable phenol-chloroform method, though the most time-consuming, and we evaluate the DNA quality with particular care using a wide range of methods - from classical agarose gel electrophoresis and Nanodrop use to the DNA concentration measurements using Qubit and PCR in real time.
The analysis of individual markers is carried out by real-time PCR (SNP markers), fragment analysis (STR markers), and as well as Sanger sequencing. Genomic analysis uses both Illumina chips genotyping and NGS (whole-exome sequencing, in some cases whole-genome sequencing) in cooperation with other Russian institutions. At the beginning of 2019, our Laboratory will become a base for a mass population screening of marker panels using OpenArray method (simultaneous genotyping of up to 256 markers on one sample).
The listed experimental methods are used to analyze autosomal, Y-chromosomal and mitochondrial DNA-markers.
The development of population databases: full and partial sequences database is for mtDNA and Y-chromosome, STR polymorphisms; genome-wide panels, whole-genome and whole-exome data for autosomal markers. NGS analysis (whole-genome or whole-exome sequences) and genome-wide panels (Illumina, Affimetrix) of the current and ancient human DNA. The major modern methods of population analysis (population structure, drift, migration, selection): PC (principal component method), IBD (Identity-By-Descent), ADMIXTURE (analysis of ancestral components), F2, F3 and D statistics, qpAdm, TreeMix, Population Branch Statistic, FineMAV, Extended Haplotype Homozygosity (and its variations), Finestructure, Chromopainter, Fay&Wu's H and Tajima's D statistics, EMMAX and other algorithms based on the use of a full range of machine learning methods. Analysis of whole-genome data, phylogenetic analysis, software development for handling the NGS data, clustering and phylogeography, including analysis of ancient and damaged DNA sequences are used for haploid systems (Y chromosome and mitochondrial DNA).
GeneGeo software is updated annually and allows using the most bioinformatics methods for their cartographic analysis. An extensive range of computer gene geographic methods (from building the interpolation maps of the individual features distribution to a variety of generalized maps) allows you to reconstruct and see for yourself the main migration flows and historical stages in the formation of the gene pool. Cartographic analysis is made for any types of polymorphisms data.