Highlights
- •Evaluation experiments demonstrate that the HID-Ion AmpliSeq™ Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay.
- •Some underperformed loci were identified including strand bias, low locus coverage, heterozygote imbalance and high background signals.
- •Full profile could be obtained from as low as 100 pg input DNA. Compared with STR assays, this panel gives prominence to advantage on detection to degraded sample.
- •FST across all 90 autosomal SNP loci showed no significant difference between Southern and Northern Chinese Han or between male and female samples.
- •Forensic parameters for A-SNPs were calculated as >99.999% (CDP), 0.999999724 (CPE), 1.390 × 1011 (CLR of trios) and 2.361 × 106 (CLR of duos). HD for Y-SNPs was equal to 0.684.
Abstract
The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect
124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS)
technology on the Ion Torrent PGM™ platform, including 90 individual identification
SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on
Y chromosome. In this study, we evaluated performance for the HID Identity Panel to
provide a reference for NGS-SNP application, focusing on locus strand balance, locus
coverage balance, heterozygote balance, and background signals. Besides, several experiments
were carried out to find out improvements and limitations of this panel, including
studies of species specificity, repeatability and concordance, sensitivity, mixtures,
case-type samples and degraded samples, population genetics and pedigrees following
the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition,
Southern and Northern Chinese Han were investigated to assess applicability of this
panel. Results showed this panel led to cross-reactivity with primates to some extent
but rarely with non-primate animals. Repeatable and concordant genotypes could be
obtained in triplicate with one exception at rs7520386. Full profiles could be obtained
from 100 pg input DNA, but the optimal input DNA would be 1 ng–200 pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered
as a mixture by the number of homozygotes, and full profiles belonging to minor contributors
could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also,
this assay could be used for case-type samples and degraded samples. For autosomal
SNPs (A-SNPs), FST across all 90 loci was not significantly different between Southern and Northern Chinese Han or
between male and female samples. All A-SNP loci were independent in Chinese Han population.
Except for 18 loci with He <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms.
Forensic parameters were calculated as >99.999% for combined discrimination power
(CDP), 0.999999724 for combined power of exclusion (CPE), 1.390 × 1011 for combined likelihood ratio (CLR) of trios, and 2.361 × 106 for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with
the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is
a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully
meet requirements for individual identification and paternity testing in forensic
science.
Keyword
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Article info
Publication history
Published online: July 29, 2016
Accepted:
July 28,
2016
Received in revised form:
July 10,
2016
Received:
January 20,
2016
Identification
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