Evaluation of a Microhaplotype-Based Noninvasive Prenatal Test in Twin Gestations: Determination of Paternity, Zygosity, and Fetal Fraction

Bai, Zhaochen; Zhao, Hu; Lin, Shaobin; Huang, Liwu; He, Zhiming; Wang, Huan

doi:10.3390/genes12010026

Cited by 19 publications

(10 citation statements)

References 38 publications

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“…Research on FF in cases of multiple pregnancies remains limited (74). A large prospective, multicenter study demonstrated a FF range of 3-36% in twin pregnancies, with a mean FF of 12.2% (75).…”

Section: Fetal-placental Characteristicsmentioning

confidence: 99%

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

Deng

Liu

2022

Front. Pediatr.

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A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.

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Section: Fetal-placental Characteristicsmentioning

confidence: 99%

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

Deng

Liu

2022

Front. Pediatr.

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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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“…Another useful application of the MH methods is for detection of CNV anomalies in fetal DNA in Non-invasive prenatal testing (NIPT). MH methods are already in use for paternity testing (35)(36)(37)(38). For NIPT, panels can be designed to focus on genomic regions with the most likely copy number variation (e. g. chr 5, 13, 18, or 21) and the frequency of 3 rd MHs in targeted regions compared to the rest of the genome.…”

Section: Discussionmentioning

confidence: 99%

Sensitive detection of DNA contamination in tumor samples via microhaplotypes

Whitty¹,

Thompson²

2020

Preprint

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BackgroundLow levels of sample contamination can have disastrous effects on the accurate identification of somatic variation in tumor samples. Detection of sample contamination in DNA is generally based on observation of low frequency variants that suggest more than a single source of DNA is present. This strategy works with standard DNA samples but is especially problematic in solid tumor FFPE samples because there can be huge variations in allele frequency (AF) due to massive copy number changes arising from large gains and losses across the genome. The tremendously variable allele frequencies make detection of contamination challenging. A method not based on individual AF is needed for accurate determination of whether a sample is contaminated and to what degree.MethodsWe used microhaplotypes to determine whether sample contamination is present. Microhaplotypes are sets of variants on the same sequencing read that can be unambiguously phased. Instead of measuring AF, the number and frequency of microhaplotypes is determined. Contamination detection becomes based on fundamental genomic properties, linkage disequilibrium (LD) and the diploid nature of human DNA, rather than variant frequencies. We optimized microhaplotype content based on 164 single nucleotide variant sets located in genes already sequenced within a cancer panel. Thus, contamination detection uses existing sequence data and does not require sequencing of any extraneous regions. The content is chosen based on LD data from the 1000 Genomes Project to be ancestry agnostic, providing the same sensitivity for contamination detection with samples from individuals of African, East Asian, and European ancestry.ResultsDetection of contamination at 1% and below is possible using this design. The methods described here can also be extended to other DNA mixtures such as forensic and non-invasive prenatal testing samples where DNA mixes of 1% or less can be similarly detected.ConclusionsThe microhaplotype method allows sensitive detection of DNA contamination in FFPE tumor samples. These methods provide a foundation for examining DNA mixtures in a variety of contexts. With the appropriate panels and high sequencing depth, low levels of secondary DNA can be detected and this can be valuable in a variety of applications.

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Evaluation of a Microhaplotype-Based Noninvasive Prenatal Test in Twin Gestations: Determination of Paternity, Zygosity, and Fetal Fraction

Cited by 19 publications

References 38 publications

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

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

Sensitive detection of DNA contamination in tumor samples via microhaplotypes

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