Evaluation of an MPS-Based Microhaplotype Assay for Non-Invasive Prenatal Paternity Testing.

IF 2.5 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

ELECTROPHORESIS Pub Date : 2025-09-17 DOI:10.1002/elps.70021

Ranran Zhang, Jiaming Xue, Mengyu Tan, Fan Yang, Guihong Liu, Yazi Zheng, Qiushuo Wu, Miao Liao, Meili Lv, Chengtao Li, Suhua Zhang, Shengqiu Qu, Weibo Liang

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引用次数: 0

Abstract

Non-invasive prenatal paternity testing (NIPPT) enables the genotyping of cell-free DNA (cfDNA) from maternal plasma through deep sequencing. Microhaplotypes (MHs) combine the advantages of short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs) and have attracted much attention in NIPPT. In this study, we optimized 45 MHs from our previous study and confirmed the effectiveness of the 45plex MH panel through different kinship inferences using real samples, including duos, trios, full siblings, and second-to-fifth-degree relatives, and excluding unrelated individuals. Furthermore, we tested 11 cfDNA and reference mother-child pairs in the first trimester (7 + 4-12 + 6 weeks) and 11 cfDNA and reference trios in the second trimester (18+ weeks). The R packages Familias and RelMix and the software EuroForMix were used for data interpretation. The results showed that MHs of cfDNA could be effectively detected using our sequencing and genotyping pipelines. We correctly determined paternity in 11 NIPPT cases, with Log₁₀LR > 10, which were significantly separated from real unrelated males. Our study indicates that this massively parallel sequencing (MPS)-based 45plex MH panel provides more robust relationship inference capabilities than standard STR systems, complements NIPPT, and may help solve relevant issues for relative DNA mixtures.

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评价基于mps的微单倍型测定法用于无创产前亲子鉴定。

无创产前亲子鉴定（NIPPT）可以通过深度测序对母体血浆中的游离DNA （cfDNA）进行基因分型。微单倍型（Microhaplotypes, mh）结合了短串联重复序列（STRs）和单核苷酸多态性（SNPs）的优点，在NIPPT中受到了广泛的关注。在本研究中，我们从之前的研究中优化了45个MH，并通过不同的亲属关系推断，使用真实样本，包括二人、三人、全兄弟姐妹和二至五度亲属，并排除无血缘关系的个体，证实了45plex MH面板的有效性。此外，我们在妊娠早期（7 + 4-12 + 6周）检测了11对cfDNA和参考母子对，在妊娠中期（18+周）检测了11对cfDNA和参考母子对。使用R软件包Familias和RelMix以及EuroForMix软件进行数据解释。结果表明，利用我们的测序和基因分型管道可以有效地检测cfDNA的mhh。我们正确地确定了11例NIPPT病例的父系关系，Log10LR bbb1010，这些病例与真正的无亲缘关系的男性显著分离。我们的研究表明，这种基于大规模平行测序（MPS）的45plex MH面板比标准STR系统提供了更强大的关系推断能力，补充了NIPPT，并可能有助于解决相对DNA混合物的相关问题。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

ELECTROPHORESIS 生物-分析化学

CiteScore

6.30

自引率

13.80%

发文量

244

审稿时长

1.9 months

期刊介绍： ELECTROPHORESIS is an international journal that publishes original manuscripts on all aspects of electrophoresis, and liquid phase separations (e.g., HPLC, micro- and nano-LC, UHPLC, micro- and nano-fluidics, liquid-phase micro-extractions, etc.). Topics include new or improved analytical and preparative methods, sample preparation, development of theory, and innovative applications of electrophoretic and liquid phase separations methods in the study of nucleic acids, proteins, carbohydrates natural products, pharmaceuticals, food analysis, environmental species and other compounds of importance to the life sciences. Papers in the areas of microfluidics and proteomics, which are not limited to electrophoresis-based methods, will also be accepted for publication. Contributions focused on hyphenated and omics techniques are also of interest. Proteomics is within the scope, if related to its fundamentals and new technical approaches. Proteomics applications are only considered in particular cases. Papers describing the application of standard electrophoretic methods will not be considered. Papers on nanoanalysis intended for publication in ELECTROPHORESIS should focus on one or more of the following topics: • Nanoscale electrokinetics and phenomena related to electric double layer and/or confinement in nano-sized geometry • Single cell and subcellular analysis • Nanosensors and ultrasensitive detection aspects (e.g., involving quantum dots, "nanoelectrodes" or nanospray MS) • Nanoscale/nanopore DNA sequencing (next generation sequencing) • Micro- and nanoscale sample preparation • Nanoparticles and cells analyses by dielectrophoresis • Separation-based analysis using nanoparticles, nanotubes and nanowires.