{"title":"评价基于mps的微单倍型测定法用于无创产前亲子鉴定。","authors":"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","doi":"10.1002/elps.70021","DOIUrl":null,"url":null,"abstract":"<p><p>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 Log<sub>10</sub>LR > 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.</p>","PeriodicalId":11596,"journal":{"name":"ELECTROPHORESIS","volume":" ","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Evaluation of an MPS-Based Microhaplotype Assay for Non-Invasive Prenatal Paternity Testing.\",\"authors\":\"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\",\"doi\":\"10.1002/elps.70021\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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 Log<sub>10</sub>LR > 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.</p>\",\"PeriodicalId\":11596,\"journal\":{\"name\":\"ELECTROPHORESIS\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2025-09-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ELECTROPHORESIS\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1002/elps.70021\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ELECTROPHORESIS","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/elps.70021","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
Evaluation of an MPS-Based Microhaplotype Assay for Non-Invasive Prenatal Paternity Testing.
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.
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.
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