Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms

Abstract

ABSTRACT. We developed a panel of 40 multiplexed short insertiondeletion (indel) polymorphic loci with widespread chromosomal locations and allele frequencies close to 0.50 in the European population. We genotyped these markers in 360 unrelated self-classified White Brazilians and 50 mother-child-probable father trios with proven paternity. The average heterozygosity (gene diversity) per locus was 0.48, and the combined probability of identity (matching probability) for the 40-locus set was 3.48 x 10 -17. The combined power of exclusion of the indel panel was 0.9997. The efficiency of the 40 indel set in the exclusion of falsely accused individuals in paternity casework was equivalent to the CODIS set of 13 microsatellites. The geometric mean of the paternity indices of the 50 mother-child-probable father trios was 17,607. This panel of 40 short indels was found to have excellent performance. Thus, especially because of its simplicity and low cost, and the fact that it is composed of genomic markers that have very low mutation rates, it represents a useful new tool for human paternity testing.

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).…”

“…Both of these polymorphism types are biallelic, which allows them to be amplified by polymerase chain reaction (PCR) with relatively small amplicon sizes. However, their biallelic property also means that these markers are individually less informative than microsatellites, which can be compensated for by using a larger number of markers (Pimenta and Pena, 2010). The typing of SNPs, which depends on qualitative base identification, is best accomplished with microarray hybridization; however, this requires complex equipment that is not generally available in identification laboratories.…”

Genetic analysis of 30 InDel markers for forensic use in five different Chinese populations

“…Several different InDel marker panels have been published in the last two years (Edelmann et al, 2009;Pereira et al, 2009;Li et al, 2010;Pimenta and Pena, 2010), including the 29plex panel with the SNPlex genotyping system in our previous study (Li et al, 2010). This report of allele frequencies of 30 new InDel markers would serve as a valuable reference database for individual identification in the 5 Chinese populations studied in the future.…”

Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms

“…Highly polymorphic and biallelic deletions and insertions have been described to be attractive alternatives to microsatellite and short tandem repeat analyses for forensic human identification and paternity testing (8,9 ).…”