TY - JOUR
T1 - Massively parallel sequencing of 68 insertion/deletion markers identifies novel microhaplotypes for utility in human identity testing
AU - Wendt, Frank R.
AU - Warshauer, David H.
AU - Zeng, Xiangpei
AU - Churchill, Jennifer D.
AU - Novroski, Nicole M.M.
AU - Song, Bing
AU - King, Jonathan L.
AU - LaRue, Bobby L.
AU - Budowle, Bruce
N1 - Funding Information:
Portions of this project were supported by National Institute of Justice grant award 2013-DN-BX-K036 .
Publisher Copyright:
© 2016 Elsevier Ireland Ltd
PY - 2016/11/1
Y1 - 2016/11/1
N2 - 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.
AB - 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.
KW - INDELs
KW - Massively parallel sequencing
KW - MiSeq™
KW - Microhaplotypes
KW - Population genetics
KW - SNPs
KW - STRait Razor
UR - http://www.scopus.com/inward/record.url?scp=84988715286&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2016.09.005
DO - 10.1016/j.fsigen.2016.09.005
M3 - Article
C2 - 27685342
AN - SCOPUS:84988715286
VL - 25
SP - 198
EP - 209
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
SN - 1872-4973
ER -