The Universal Set of 99 InDel Markers for Human Identification

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.