Universal Panel of Insertion–Deletion Polymorphism for Human Genetic Identification and a Biochip-Based Kit <i>ChipID106</i> for This Purpose

Abstract

The paper proposes a panel of 106 insertion–deletion (InDel) polymorphisms and practical testing of the method of their genotyping on biochips. Such fundamental properties of InDel markers as short length and low mutation rate provide them with significant advantages in expert practice over widely used tandem repeats (STRs). In this work, we analyzed the allele distribution of InDel polymorphisms in the five largest world populations (European, East Asian, South Asian, African and American), and selected markers that meet the following criteria: minor allele frequency of more than 0.30, physical distance between markers more than 3 million bp, the absence of polymorphisms, tandem repeats and palindromes in the flanking sequences, the proximity of the AT/GC ratio to 1. As a result, a panel of 106 polymorphisms was formed with an average frequency of the minor allele for all five populations of 0.396. For panel genotyping, a method was developed that included one-step multiplex PCR followed by hybridization on a biological microarray. The average amplicon length was 72 bp. On a sample of 201 residents of Moscow and St. Petersburg, the main characteristics of the formed panel were determined: the probability of a random match (MP) 1.89 × 10–43, the paternity exclusion potential (CPE) 0.99999999063. The proposed method is an alternative to molecular genetic identification of a person based on variations in the lengths of STR loci.