Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing

Frank R Wendt; David H Warshauer; Xiangpei Zeng; Jennifer D Churchill; Nicole M M Novroski; Bing Song; Jonathan L King; Bobby L LaRue; Bruce Budowle

doi:10.1016/j.fsigen.2016.09.005

Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing

Forensic Sci Int Genet. 2016 Nov:25:198-209. doi: 10.1016/j.fsigen.2016.09.005. Epub 2016 Sep 20.

Authors

Frank R Wendt¹, David H Warshauer², Xiangpei Zeng³, Jennifer D Churchill³, Nicole M M Novroski³, Bing Song³, Jonathan L King³, Bobby L LaRue⁴, Bruce Budowle⁵

Affiliations

¹ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. Electronic address: Frank.Wendt@my.unthsc.edu.
² Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA.
³ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA.
⁴ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA; Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77341, USA.
⁵ Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA; Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.

PMID: 27685342
DOI: 10.1016/j.fsigen.2016.09.005

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 2 to 6 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 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 INDELs in four major US population groups. In addition, 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. This 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.

Keywords: INDELs; Massively parallel sequencing; MiSeq™; Microhaplotypes; Population genetics; SNPs; STRait Razor.

MeSH terms

DNA Fingerprinting / methods*
Genetic Markers*
Genetics, Population
Haplotypes*
Heterozygote
High-Throughput Nucleotide Sequencing*
Humans
INDEL Mutation*
Polymorphism, Single Nucleotide
Racial Groups / genetics

Substances

Genetic Markers