Dennis McNevin, Jessica Watson, Kelly Grisedale, Ayusha Dahal, Corey Goodwin, Jodie Ward
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Two TAS platforms were compared in this study: Ion AmpliSeq™ panels coupled with Ion Torrent sequencing on an Ion GeneStudio™ S5 Plus System, manufactured by Thermo Fisher Scientific, and the ForenSeq® Kintelligence Kit coupled with Illumina sequencing on the MiSeq FGx® Sequencing System, manufactured by QIAGEN. Four Ion AmpliSeq™ panels (Precision ID Identity, Precision ID Ancestry, DNA Phenotyping and HID Y-SNP) share 177 SNPs with the ForenSeq® Kintelligence Kit and all five were used to profile the DNA extracted from the petrous part of the temporal bone from six skeletonised cadavers. Of the 6 × 177 = 1,062 SNP genotype comparisons, 1,055 (99%) were concordant between the Ion AmpliSeq™ panels and Kintelligence Kit. Of the seven (< 1%) non-concordant SNPs, only three of them (0.3%) would have resulted in erroneous genotypes being reported as a result of allele dropout by either assay, using our optimised relative variant frequency windows for allele calling. We conclude that both the Ion AmpliSeq™ panels and the ForenSeq® Kintelligence Kit were suitable for TAS applied to the human remains in this study.</p>","PeriodicalId":14071,"journal":{"name":"International Journal of Legal Medicine","volume":" ","pages":""},"PeriodicalIF":2.2000,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Comparison of commercial targeted amplicon sequencing assays for human remains identification casework.\",\"authors\":\"Dennis McNevin, Jessica Watson, Kelly Grisedale, Ayusha Dahal, Corey Goodwin, Jodie Ward\",\"doi\":\"10.1007/s00414-024-03335-8\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Targeted amplicon sequencing (TAS) facilitates the genotyping of forensically informative single nucleotide polymorphisms (SNPs) using massively parallel sequencing (MPS). 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引用次数: 0
摘要
靶向扩增片段测序(TAS)有助于利用大规模并行测序(MPS)对具有法医参考价值的单核苷酸多态性(SNPs)进行基因分型。在人类遗骸鉴定中,提取的任何 DNA 都有可能降解,因此当使用毛细管电泳进行短串联重复序列 (STR) 分析失败时,TAS 可能会取得成功。此外,SNP 除了能提供身份信息外,还能提供有关祖先、表型、亲缘关系和父系血统(Y 染色体单倍型)的信息。本研究比较了两种 TAS 平台:Ion AmpliSeq™ 面板与赛默飞世尔科技公司生产的 Ion GeneStudio™ S5 Plus 系统上的 Ion Torrent 测序相结合,以及 ForenSeq® Kintelligence 套件与 QIAGEN 公司生产的 MiSeq FGx® 测序系统上的 Illumina 测序相结合。四个 Ion AmpliSeq™ 面板(Precision ID Identity、Precision ID Ancestry、DNA Phenotyping 和 HID Y-SNP)与 ForenSeq® Kintelligence 套件共享 177 个 SNPs,所有五个面板都用于对从六具骸骨尸体的颞骨岩石部分提取的 DNA 进行特征分析。在 6 × 177 = 1,062 个 SNP 基因型比较中,有 1,055 个(99%)在 Ion AmpliSeq™ 面板和 Kintelligence Kit 之间是一致的。在 7 个(
Comparison of commercial targeted amplicon sequencing assays for human remains identification casework.
Targeted amplicon sequencing (TAS) facilitates the genotyping of forensically informative single nucleotide polymorphisms (SNPs) using massively parallel sequencing (MPS). For human remains identification, where any extracted DNA is likely to be degraded, TAS may succeed when short tandem repeat (STR) profiling using capillary electrophoresis fails. Further, as well as yielding identity information, SNPs can provide information about ancestry, phenotype, kinship and paternal lineage (Y chromosome haplotypes). Two TAS platforms were compared in this study: Ion AmpliSeq™ panels coupled with Ion Torrent sequencing on an Ion GeneStudio™ S5 Plus System, manufactured by Thermo Fisher Scientific, and the ForenSeq® Kintelligence Kit coupled with Illumina sequencing on the MiSeq FGx® Sequencing System, manufactured by QIAGEN. Four Ion AmpliSeq™ panels (Precision ID Identity, Precision ID Ancestry, DNA Phenotyping and HID Y-SNP) share 177 SNPs with the ForenSeq® Kintelligence Kit and all five were used to profile the DNA extracted from the petrous part of the temporal bone from six skeletonised cadavers. Of the 6 × 177 = 1,062 SNP genotype comparisons, 1,055 (99%) were concordant between the Ion AmpliSeq™ panels and Kintelligence Kit. Of the seven (< 1%) non-concordant SNPs, only three of them (0.3%) would have resulted in erroneous genotypes being reported as a result of allele dropout by either assay, using our optimised relative variant frequency windows for allele calling. We conclude that both the Ion AmpliSeq™ panels and the ForenSeq® Kintelligence Kit were suitable for TAS applied to the human remains in this study.
期刊介绍:
The International Journal of Legal Medicine aims to improve the scientific resources used in the elucidation of crime and related forensic applications at a high level of evidential proof. The journal offers review articles tracing development in specific areas, with up-to-date analysis; original articles discussing significant recent research results; case reports describing interesting and exceptional examples; population data; letters to the editors; and technical notes, which appear in a section originally created for rapid publication of data in the dynamic field of DNA analysis.