At a meeting of the Siberian Branch of the Russian Academy of Sciences on January 29, Academician Vadim Stepanov, Director of Tomsk NRMC, presented a technology developed at the Research Institute of Medical Genetics, Tomsk NRMC, for determining an individual's origin from DNA. This technology enables far more effective identification of an individual's population group compared to current methods.
Population genomics has revealed several important patterns. First is genome variability, where individual differences — constituting only 0.1% of the entire genome — shape all human diversity on the planet. Second is the understanding that each person's genome consists of components inherited from ancestral populations, encoding their genetic history. The structure of genetic diversity reflects geography, shaped by human migration patterns.
A key element in population genetics research is the Y chromosome, present only in males and transmitted through the paternal line. Since surnames are also typically passed down through the male line, Y-chromosome variants become linked to surnames and, in societies preserving clan structures, to specific lineages. This makes it a highly useful tool for geneticists and forensic experts. Given that most traditional societies practice patrilocality, Y-chromosome variants become tied to the specific residence locations of their male carriers — sometimes pinpointing individual villages. This feature can serve various purposes, including identifying criminals from their DNA.
How Genetics Aids Crime Investigation
Characterizing the crime situation, Academician Stepanov cited 2024 Ministry of Internal Affairs statistics: of nearly two million committed crimes, just over half (51.4%) are solved. The clearance rate is even lower for serious and especially grave crimes. The primary reason is the inability to identify perpetrators. The backlog of such unsolved crimes accumulates year after year.
Genetic analysis has long been used in forensic science, employing genetic markers — DNA regions consisting of short tandem repeats (STRs). Many countries use the CODIS (Combined DNA Index System), which includes 20 such markers. Their combination in the genome is unique to each individual (except identical twins) and far exceeds the human population. Using CODIS, criminals can be unmistakably identified from DNA traces at crime scenes if their genetic profile exists in a database. Russia has the Federal Database of Genomic Information (FBDGI), established in 2008. Since 2023, it has been mandatory to include genomic data from individuals sentenced to imprisonment, as well as suspects and accused persons. Currently, it contains about 2 million genetic profiles (less than 1.5% of the country's population).
Can genetics help identify a criminal whose profile is not in the database? It turns out, yes. This was demonstrated in identifying the terrorist behind the 2011 Domodedovo airport attack. The Investigative Committee had the terrorist's DNA but no database match. The DNA was sent for research to the Vavilov Institute of General Genetics, Russian Academy of Sciences, where population geneticists from Dr. Oleg Balanovsky's group worked on it.
The terrorist carried a relatively rare Y-chromosome variant, which was clearly traced to his region of origin. After this information was provided to the Investigative Committee, the perpetrator was identified relatively quickly. A second case involved the Tomsk Research Institute of Medical Genetics. In 2013, DNA analysis established the ethno-territorial origin of the "Novosibirsk maniac" who committed a series of rapes. Scientists determined the perpetrator belonged to an ethnic group extremely rare in the city where the crimes occurred. This information was given to investigators, and within two weeks, the individual was found.
Method for Determining Population Affiliation Using SNP Markers
These two cases prompted the Union State program "DNA Identification," aimed at developing innovative genomic technologies for personal identification based on studying the gene pools of Russian and Belarusian regions. The program ran from 2017 to 2022, led by a team headed by the Vavilov Institute of General Genetics, RAS, and the National Academy of Sciences of Belarus (led by Academician N.K. Yankovsky and Academician A.V. Kilchevsky). Specialists from the Tomsk Research Institute of Medical Genetics also participated.
During the program, a technology was developed to determine an individual's population affiliation from genomic data. This utilized SNP markers — variable genome regions differing by a single nucleotide, or "letter." Through population genetics research, a reference database was created for over six thousand SNP markers, documenting their frequencies across 84 populations. An algorithm for bioinformatic data processing comparing unknown DNA samples with this reference database was developed, along with a user software interface. This method provided accurate diagnosis of individual origin, including mixed ancestry. However, it proved poorly suited for practical application by investigative bodies due to technological complexity. The method requires genomic sequencing, which remains difficult and expensive for routine practice.
StepOr: A DNA Identification Method
The Tomsk NRMC team, led by Academician V.A. Stepanov, succeeded in creating another method that is significantly simpler to use. It was developed in collaboration with Gordiz, a leading Russian manufacturer of DNA identification kits. The method, named StepOr, is based on Y-chromosome analysis using the aforementioned STR markers (regions with varying repeat counts, whose combinations are unique).
The StepOr kit consists of 37 Y-STR markers. An unknown individual's Y chromosome is compared against these markers using a reference database containing over 10,000 samples from more than 100 populations across Russian territory. Comparison employs a proprietary algorithm and software interface. The result determines, with a certain probability, the individual's ethno-territorial origin.
StepOr has two limitations: first, it is designed only for analyzing male samples (though statistics show 80% of crimes are committed by men). Second, the accuracy of determining ethno-territorial affiliation is somewhat lower than the SNP-marker method described above. A significant advantage is that StepOr is far less technologically demanding, can be performed on equipment available to law enforcement agencies, and importantly, is designed for domestically produced equipment.
Academician Stepanov presented data comparing StepOr's effectiveness with the standard CODIS system. For comparison, samples from 50 individuals representing five different ethnic groups from Russia and neighboring countries (Avars, Kazakhs, Komi, Russians, Yakuts) were analyzed. On the CODIS-generated plot, representatives of different groups were widely scattered, with all group areas overlapping. Thus, CODIS cannot determine an individual's specific ethnic affiliation. In contrast, on the StepOr-generated plot, individuals from each ethnic group formed compact, clearly distinguishable clusters. StepOr successfully answers the question of ethno-territorial origin.
StepOr vs. CODIS for Determining Population Affiliation
Compared to foreign analogues also using Y-chromosome markers, StepOr surpasses them both in marker count and accuracy.
"We have tested our method on several database samples, samples provided by the Russian Investigative Committee, and samples from the Belarusian Forensic Examination Committee. The kit demonstrated approximately 90-95% effectiveness. That is, in 90-95% of cases, we can establish an individual's ethno-territorial origin with some degree of accuracy," explained Vadim Stepanov. He noted that researchers have received over 150 requests for StepOr-based examinations from regional investigative committees and Interior Ministry bodies — spanning from Crimea to Sakhalin — and have conducted these analyses.
The StepOr technology is patented by Tomsk NRMC. The kit itself is already available in the Gordiz company catalog. The authors estimate that implementing this technology could increase the clearance rate for serious and especially grave crimes by 20% and save approximately 46 billion rubles over five years. Beyond crime fighting, StepOr technology can be applied to other tasks: monitoring migration processes; tracking cross-border traffic of any objects carrying DNA traces; and identifying disaster victims and participants in past and current military conflicts.
"To implement this technology in practice, the database must first be expanded. This requires further research into the genomic characteristics of indigenous peoples of Russia, neighboring countries, and possibly beyond. Legislative initiatives are needed to authorize the use of ethno-territorial origin diagnostic technologies — such as mandatory genomic registration of migrants using not only the CODIS system but also StepOr," summarized Vadim Stepanov.
More information about the "DNA Identification" program can be found in a Russian Academy of Sciences "Scientific and Methodological" project video filmed at the Vavilov Institute of General Genetics, RAS.
Source: Vavilov Institute of General Genetics, RAS, press service