Simple Summary: For many decades, human identification by DNA has used the difference in the length of certain loci in the human genome—the so-called fragment analysis. Their main drawback is that they are too long, which interferes with the analysis if the DNA is damaged by environmental factors (rotting, sunlight, or chemical agents). Another drawback of using these regions for human identification is their high mutability, which leads to errors in determining kinship. The interest of forensic researchers in short polymorphisms like InDels has been a􀄴racted because of their potential advantages, such as low mutation rates and improved application in the analysis of degraded samples. We selected 99 InDels from the entire human genome in such a way as to create a universal set of markers that have the same identification potential regardless of the population in which it is used. In order to experimentally verify the correctness of our calculations, we examined two populations located on different continents: Russian and Ecuadorian. The results confirmed the correctness of our choice of markers. In this paper, we propose a set of markers and a biochip method for their genotyping which can be used for human identification in any population.

Abstract: The aim of this work was to select InDel markers sufficient for human identification and to create a routine method for their genotyping. We analyzed the allele distribution of all known InDels in European, East Asian, South Asian, African, and American populations and selected markers whose minor allele frequency, MAF, was ≥ 0.30. Thus, a set of 99 polymorphisms was formed with an average MAF for all five populations of 0.397 and a distance between markers of ≥3 million bp. The expected values of combined random match probability differ very little between the five superpopulations and are in the range of 1.44 × 10−41–3.68 × 10−41. For the genotyping of this set of markers, we have developed a method that includes single-step multiplex PCR followed by hybridization on a biochip. The average amplicon length was 72 bp. Aiming to verify the usefulness of 99
biallelic InDels in genetic identification and kinship testing, two phylogenetically distant populations were studied: Russian and Ecuadorian. For the Russian population, the combined random match probability was 2.09 × 10−40, and the combined power of exclusion, CPE, was 0.999999989. For the Ecuadorian population, the combined random match probability was 1.02 × 10−40, and the combined power of exclusion was 0.999999978. The proposed method is intended to become an alternative to human identification based on differences in the length of STR loci.

Keywords: human identification; InDel; microarray; biochip; forensic genetics; Ecuadorian population; Russian population