Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population

Satoshi Hirata,Kaname Kojima,Kazuharu Misawa,Olivier Gervais,Yosuke Kawai,Masao Nagasaki

doi:10.1016/j.heliyon.2018.e00625

Abstract

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Highlights

Forensic DNA typing is widely used to confirm the identification of missing persons in large-scale disasters and plays a central role in legal profiling [1]
Using the evaluated results and polymorphic scores, e.g. heterozygosity (HZ), polymorphic information content (PIC) [28], and Power of discrimination (PD) [29], we identify short tandem repeat (STR) loci that could be applied to STR typing
Results at many of the STR loci were consistent between data sets, except for six STR loci with highly complex patterns or with many STR repeats

Summary

Introduction

Forensic DNA typing is widely used to confirm the identification of missing persons in large-scale disasters and plays a central role in legal profiling [1]. DNA typing kits with a larger number of loci, such as GlobalFilerÒ PCR Amplification Kit (Thermo Fisher Scientific) [11] and PowerPlexÒ Fusion System (Promega, Madison, WI) [12], have become available, leading to more accurate sibship tests [13]. The reason for this is that accuracy generally improves as the number of examined STR loci increases [14, 15]

Methods

Results

Conclusion