Evaluation of a custom GeneRead™ massively parallel sequencing assay with 210 ancestry informative SNPs using the Ion S5™ and MiSeq platforms.
Custom GeneRead panel
Forensic genetics
Ion S5
Massively parallel sequencing
MiSeq
Single nucleotide polymorphisms
Journal
Forensic science international. Genetics
ISSN: 1878-0326
Titre abrégé: Forensic Sci Int Genet
Pays: Netherlands
ID NLM: 101317016
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
03
03
2020
revised:
14
10
2020
accepted:
19
10
2020
pubmed:
12
11
2020
medline:
6
7
2021
entrez:
11
11
2020
Statut:
ppublish
Résumé
A custom GeneRead DNAseq SNP panel with 210 markers was evaluated using the Ion S5 and MiSeq sequencing platforms. Sensitivity, PCR cycle number, and the use of half volume of reagents for target enrichment and library preparation were tested. Furthermore, genotype concordance between results obtained with the different sequencing platforms and with known profiles generated using other sequencing assays was analysed. The GeneRead DNASeq SNP assay gave reproducible results with an input of 200 pg DNA on both platforms. A total of 204 loci were successfully sequenced. Three loci failed completely in the PCR amplification, and three additional loci displayed frequent locus drop-outs due to low read depth or high heterozygote imbalance. Overall, the read depth across the loci was more well-balanced with the MiSeq, while the heterozygote balance was less variable with the Ion S5. Noise levels were low on both platforms (median< 0.2 %). Two simple criteria for genotyping were applied: A minimum threshold of 45 reads and an acceptable heterozygote balance range of 0.3-3.0. Complete concordance between platforms was observed except for three genotypes in one of the poorly performing loci, rs1470637. This locus had relatively low read depths on both platforms, skewed heterozygote balance, and frequent locus drop-outs. There was also full genotype concordance between the results from the GeneRead assay and known profiles generated with the QIAseq and Ion AmpliSeq assays. The few discordant results were either due to locus drop-outs in the poorly performing loci or allele drop-outs in the QIAseq assay. Profiles with a minimum of 179 SNPs were obtained from four challenging case work samples (blood swabs, bone, or blood from a corpse). Overall, the GeneRead DNASeq assay showed considerable potential and could provide a reliable method for SNP genotyping in cases involving identification of individuals, prediction of phenotypic traits, and ancestry inference.
Identifiants
pubmed: 33176271
pii: S1872-4973(20)30183-6
doi: 10.1016/j.fsigen.2020.102411
pii:
doi:
Types de publication
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
102411Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.