A case of heteropaternal superfecundation identified by microhap sequencing of maternal plasma cell-free DNA

Bai, Zhaochen

doi:10.1016/j.fsigen.2020.102458

Cited by 5 publications

(1 citation statement)

References 37 publications

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“…In addition, current research towards cffDNA detection is still in the exploratory stage. Preliminary shows that MPS combines microhaplotypes and mature SNPs and STR kit has certain application potential in NIPPT ( Bai et al, 2020 ; Ou and Qu 2020 ; Ou and Bai 2021 ; Shen et al, 2021 ). In this study, based on the CE platform, the 15 SNP-SNPs, provide a new and cost-effective strategy for NIPPT.…”

Section: Discussionmentioning

confidence: 99%

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing

Zhang

Wang

et al. 2022

Front. Genet.

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Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging. We developed a new set of SNP-SNP microhaplotypes with short amplicons, and we successfully genotyped them using the new method of amplification-refractory mutation system PCR (ARMS-PCR) combined with SNaPshot technology based on a capillary electrophoresis (CE) platform. This panel reflects a high polymorphism in the Southwest Chinese Han population and thus has excellent potential for mixture studies. We evaluated the feasibility of this panel for UDM detection and noninvasive prenatal paternity testing (NIPPT). Fifteen SNP-SNPs detected minor DNA of homemade DNA mixtures, with a sensitivity of 0.025–0.05 ng and a specificity of 1:1,000. In addition, the panel successfully genotyped degraded DNA from single and mixed samples. Finally, 15 SNP-SNPs were applied to 26 trios. All samples displayed positive results with at least one marker to detect cffDNA. Besides, all fetal alleles in maternal plasma were confirmed by genotyping fetal genomic DNA from amniocentesis and paternal genomic DNA from peripheral blood. The results indicated that the SNP-SNP strategy based on the CE platform was useful for UDM detection and NIPPT.

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Section: Discussionmentioning

confidence: 99%

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing

Zhang

Wang

et al. 2022

Front. Genet.

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Applications of Probabilistic Genotyping Method for Combining Evidence Across Microhaplotype DNA Mixture Profiles

Ling,

Han,

Lin

et al. 2024

Electrophoresis

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In cases of serious crimes that involve challenging DNA samples from the perpetrator (e.g., a minor contributor to a mixture), there is justification to combine different mixture profiles. In our previous study, we developed a massively parallel sequencing (MPS)–based assay targeting 140 microhaplotype markers. In this study, we extended the use of the microhaplotype panel to common scenarios, such as determining the presence of a common contributor or relatedness between different mixture profiles when no reference source is available. Data interpretation was performed using the R package KinMix. Our findings revealed that correct assignments of a common contributor and relatedness were made between relatively balanced mixtures. However, when profiles suffered from allele imbalance, inclusive assignments were significantly associated with the suspect's mixture proportion. Additionally, our analysis showed zero false‐positive rates in the studied scenarios. These results indicate that microhaplotype data can be reliably interpreted for identifying a common donor or related donors among different mixtures. Further research based on larger sample sizes may yield more reliable results, which could assist in solving issues related to complex scenarios where multiple mixed profiles were involved.

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An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project

Xue

Tan

et al. 2022

Int J Legal Med

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A case of heteropaternal superfecundation identified by microhap sequencing of maternal plasma cell-free DNA

Cited by 5 publications

References 37 publications

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing

Applications of Probabilistic Genotyping Method for Combining Evidence Across Microhaplotype DNA Mixture Profiles

An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project

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