Automated Genotyping of a Highly Informative Panel of 40 Short Insertion-Deletion Polymorphisms Resolved in Polyacrylamide Gels for Forensic Identification and Kinship Analysis

Abstract

Objective: Short insertion-deletion polymorphisms (indels) are the second most abundant form of genetic variations in humans after SNPs. Since indel alleles differ in size, they can be typed using the same methodological approaches and equipment currently utilized for microsatellite genotyping, which is already operational in forensic laboratories. We have previously shown that a panel of 40 carefully chosen indels has excellent potential for forensic identification, with combined probability of identity (match probability) of 7.09 × 10^–17 for Europeans. Methods: We describe the successful development of a multiplex system for genotyping the 40-indel panel in long thin denaturing polyacrylamide gels with silver staining. We also demonstrate that the system can be easily fully automated with a simple large scanner and commercial software. Results and Conclusion: The great advantage of the new system of typing is its very low cost. The total price for laboratory equipment is less than EUR 10,000.–, and genotyping of an individual patient will cost less than EUR 10.– in supplies. Thus, the 40indel panel described here and the newly developed ‘low-tech’ analysis platform represent useful new tools for forensic identification and kinship analysis in laboratories with limited budgets, especially in developing countries.

A multiplex panel of short-amplicon insertion-deletion DNA polymorphisms for forensic analysis

“…Extremely low match probabilities were similarly observed for populations from other geographical regions, including Brazil (Pimenta and Pena, 2010;Pena and Pena, 2012).…”

“…This, of course, matched our expectations, since the reduction of amplicon size occurred only in the region surrounding the INDEL and did not interfere with its sequence. Thus, we could apply the same allele frequency properties and match probabilities obtained for the regular-sized amplicons to the short-amplicon INDELs, which had been extensively validated and analyzed in several studies (Bastos-Rodrigues et al, 2006;Pimenta and Pena, 2010;Pena et al, 2009Pena et al, , 2011Pena and Pena, 2012).…”

MULTINDELS-BOV: Zebu traceback method based on DNA insertion-deletion polymorphisms

“…To make indel analysis less expensive and independent of sophisticated equipment, we successfully adapted our primers and multiplex systems for genotyping in long thin denaturing polyacrylamide gels with silver staining, exactly as described previously (Pena and Pena, 2012). These gels can be easily run and fully automated with a simple large scanner and commercial software as described by Pena and Pena (2012).…”

“…These gels can be easily run and fully automated with a simple large scanner and commercial software as described by Pena and Pena (2012).…”

100 Years after von Dungern & Hirschfeld: Kinship Investigation from Blood Groups to SNPs

“…Furthermore, Phillips et al [8] report about the application of both the SNPforID panel and high-density SNP arrays including about 1.8 million SNP and indel markers. The current progress of introducing diallelic markers to forensic genetics is amended by the work of Pena and Pena [9] who describe a powerful and low-cost method for typing of 40 indels with a widespread chromosomal location.…”