TY - JOUR
T1 - Analysis of short tandem repeat and single nucleotide polymorphism loci from single-source samples using a custom haloplex target enrichment system panel
AU - Wendt, Frank R.
AU - Zeng, Xiangpei
AU - Churchill, Jennifer D.
AU - King, Jonathan L.
AU - Budowle, Bruce
N1 - Publisher Copyright:
© Copyright 2016 Wolters Kluwer Health, Inc.
PY - 2016
Y1 - 2016
N2 - Short tandem repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short tandem repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE.With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing customselected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 short tandem repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment.
AB - Short tandem repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short tandem repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE.With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing customselected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 short tandem repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment.
KW - Agilent Haloplex
KW - Capture
KW - Short Tandem Repeat
KW - Single Nucleotide Polymorphism
UR - http://www.scopus.com/inward/record.url?scp=84960455671&partnerID=8YFLogxK
U2 - 10.1097/PAF.0000000000000228
DO - 10.1097/PAF.0000000000000228
M3 - Article
C2 - 27075592
AN - SCOPUS:84960455671
SN - 0195-7910
VL - 37
SP - 99
EP - 107
JO - American Journal of Forensic Medicine and Pathology
JF - American Journal of Forensic Medicine and Pathology
IS - 2
ER -