Massively Parallel Sequencing of 68 Insertion/Deletion Markers Identifies Novel Microhaplotypes for Utility in Human Identity Testing

• NCJ Number: 252447
• Date Published: November 2016
• Length: 12 pages
• Author(s): Frank R. Wendt; David H. Warshauer; Xiangpei Zeng; Jennifer D. Churchill; Nicole M. Novroski; Bing Song; Jonathan L. King; Bobby L. LaRue; Bruce Budowle
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical), Report (Study/Research), Report (Grant Sponsored), Program/Project Description
• Grant Number(s): 2013-DN-BX-K036
• Award: Development of improved insertion-deletion assays for human and ancestral identifications from degraded samples

Annotation

In this research project, the Nextera Rapid Capture Custom Enrichment Kit (Illumina, Inc., San Diego, CA) and massively parallel sequencing (MPS) on the Illumina MiSeq were used to sequence 68 well-characterized insertions/deletions (INDELs) in four major U.S. population groups, and the STR Allele Identification Tool: Razor (STRait Razor) was used in a novel way to analyze INDEL sequences and detect adjacent single nucleotide polymorphisms (SNPs) and other polymorphisms.

Abstract

Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed; however, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis. The INDEL marker allelic states range in size from two to six base pairs, enabling small amplicon size. In addition, heterozygote balance may be increased by minimizing preferential amplification of the smaller allele, as is more common with STR markers. Multiplexing a large number of INDELs allows for generating panels with high discrimination power. The current study's application enabled the discovery of unique allelic variants, which increased the discrimination power and decreased the single-locus random match probabilities (RMPs) of 22 of these well-characterized INDELs, which can be considered as microhaplotypes. These findings suggest that additional microhaplotypes containing human identification (HID) INDELs may exist elsewhere in the genome. (Publisher abstract modified)