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三种高通量测序平台用于法医遗传学中单核苷酸多态性(SNP)基因分型的比较。

Comparison of three massively parallel sequencing platforms for single nucleotide polymorphism (SNP) genotyping in forensic genetics.

机构信息

Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.

School of Medicine, Jiaying University, Meizhou, 514015, People's Republic of China.

出版信息

Int J Legal Med. 2023 Sep;137(5):1361-1372. doi: 10.1007/s00414-023-03035-9. Epub 2023 Jun 19.

Abstract

Three MPS platforms are being used in forensic genetic analysis, i.e., MiSeq FGx, Ion S5 XL, and MGISEQ-2000. However, few studies compared their performance. In this study, we sequenced 83 common SNPs of 71 samples using the ForenSeq™ DNA Signature Prep Kit on MiSeq FGx, the Precision ID Identity Panel on Ion S5 XL, and the MGIEasy Signature Identification Library Prep Kit on MGISEQ-2000 and then the performance was compared. Results showed that the MiSeq FGx had the highest sequence quality but the lowest sequencing depth and allele balance. Discordant genotypes were observed at six SNPs, which may be caused by variants at primer binding regions, indel errors, or misalignments. Besides, two kinds of background noises, allele-specific miscalled reads (ASMR) and allele-nonspecific miscalled reads (ANMR), were characterized. MGISEQ-2000 showed the highest level of ASMR while Ion S5 XL had the highest level of ANMR. Site- and genotype-dependent miscalled patterns were observed at several SNPs on Ion S5 XL and MGISEQ-2000, but few on MiSeq FGx. In conclusion, the three MPS platforms perform differently with respect to sequencing quality, sequencing depth, allele balance, concordance, and background noise. These findings may be useful for data comparison, mixture deconvolution, and heteroplasmy analysis in forensic genetics.

摘要

三种 MPS 平台(MiSeq FGx、Ion S5 XL 和 MGISEQ-2000)被用于法医遗传学分析。然而,很少有研究对它们的性能进行比较。在本研究中,我们使用 MiSeq FGx 上的 ForenSeq™ DNA Signature Prep Kit、Ion S5 XL 上的 Precision ID Identity Panel 和 MGISEQ-2000 上的 MGIEasy Signature Identification Library Prep Kit 对 71 个样本的 83 个常见 SNP 进行测序,并比较了它们的性能。结果表明,MiSeq FGx 具有最高的序列质量,但测序深度和等位基因平衡最低。在 6 个 SNP 上观察到不一致的基因型,这可能是由引物结合区域的变异、插入缺失错误或错配引起的。此外,还对两种背景噪声(等位基因特异性错误读取(ASMR)和等位基因非特异性错误读取(ANMR))进行了特征描述。MGISEQ-2000 表现出最高的 ASMR,而 Ion S5 XL 则表现出最高的 ANMR。在 Ion S5 XL 和 MGISEQ-2000 上的几个 SNP 上观察到与位点和基因型相关的错误读取模式,但在 MiSeq FGx 上很少观察到。总之,这三种 MPS 平台在测序质量、测序深度、等位基因平衡、一致性和背景噪声方面表现不同。这些发现可能有助于法医遗传学中的数据比较、混合物解卷积和异质性分析。

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