Development and validation of a fetal genotyping assay with potential for noninvasive prenatal diagnosis of hereditary hearing loss

Chen, Ying; Wang, Benjing; Mao, Jun; Wang, Ting; Ye, Kan; Ye, Yanlin; Cram, David S.; Li, Hong

doi:10.1002/pd.4962

Cited by 17 publications

(16 citation statements)

References 33 publications

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“…Recombination of fetal alleles has often made NIPT more complicated. Recently, it has been shown that the reconstruction of only the paired end allelic reads suffice for NIPT 4 , 5 . However, it is not possible to make the whole process of MPS technology for NIPT any simpler or shorter, regardless of the frequency of target mutation.…”

Section: Discussionmentioning

confidence: 99%

“…Conventional methods for prenatal diagnosis have been amniocentesis and chorionic villus sampling, which carry a 1% risk of miscarriage 1 – 3 . Recently, noninvasive prenatal testing (NIPT) has been gaining popularity, as it only requires maternal peripheral blood 4 , 5 . NIPT is recommended as a primary trisomy screening test to all pregnant women 6 , 7 .…”

Section: Introductionmentioning

confidence: 99%

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One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR

Chang

Ahn

Kim

et al. 2018

Sci Rep

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Previously, we introduced a noninvasive prenatal testing (NIPT) protocol for diagnosing compound heterozygous autosomal recessive point mutations via maternal plasma DNA and simulated control genomic DNA sampling based on fetal DNA fraction. In our present study, we have improved our NIPT protocol to make it possible to diagnose homozygous autosomal recessive point mutations without the need to acquire fetal DNA fraction. Moreover, chi-squared test and empirical statistical range based on the proportion of mutant allele reads among the total reads served as the gatekeeping method. If this method yielded inconclusive results, then the Bayesian method was performed; final conclusion was drawn from the results of both methods. This protocol was applied to three families co-segregating congenital sensorineural hearing loss with monogenic homozygous mutations in prevalent deafness genes. This protocol successfully predicted the fetal genotypes from all families without the information about fetal DNA fraction using one-step dPCR reactions at least for these three families. Furthermore, we suspect that confirmatory diagnosis under this protocol is possible, not only by using picodroplet dPCR, but also by using the more readily available chip-based dPCR, making our NIPT protocol more useful in the diagnosis of autosomal recessive point mutations in the future.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR

Chang

Ahn

Kim

et al. 2018

Sci Rep

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“…Plasma was thawed, and cell-free DNA (cfDNA) was purified using the QIAamp Circulating Nucleic Acid Kit (Qiagen). The NIPT cSMART assay was performed as previously described 18. In brief, cfDNA libraries were prepared by end modification, adaptor ligation and amplified by 15 rounds of PCR.…”

Section: Methodsmentioning

confidence: 99%

Non-invasive prenatal testing of pregnancies at risk for phenylketonuria

Duan

Ning

Zhao

et al. 2018

Arch Dis Child Fetal Neonatal Ed

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“…Another potential approach to prevent the birth of children with monogenic disorders is non‐invasive prenatal testing (NIPT) of placental cell‐free DNA (cfDNA). In previous studies, we developed and validated circulating single‐molecule amplification and resequencing technology (cSMART) as a novel approach to quantitate the mutation load in pregnancy plasma, enabling fetal genotypes to be accurately deduced . More recently it was shown that cSMART could accurately genotype the fetus in pregnancies at risk for PKU; however, several limitations were noted, including using only primers to target the known parental mutations and the sole reliance of the plasma DNA mutation ratio to call fetal genotypes …”

Section: Introductionmentioning

confidence: 99%

Noninvasive fetal genotyping in pregnancies at risk for PKU using a comprehensive quantitative cSMART assay for PAH gene mutations: a clinical feasibility study

Wei

et al. 2019

BJOG

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Objective To assess the diagnostic performance of a novel circulating single molecule amplification and re‐sequencing technology (cSMART) method for noninvasive prenatal testing (NIPT) of Phenylketonuria (PKU). Design Blinded NIPT analysis of pregnancies at high risk for PKU. Setting Shanghai Xinhua Hospital and Hunan Jiahui Genetics Hospital, China. Population Couples (n = 33) with a child diagnosed with PKU. Methods Trio testing for pathogenic PAH mutations was performed by Sanger sequencing. In second pregnancies, invasive prenatal diagnosis (IPD) was used to determine fetal genotypes. NIPT was performed using a PAH gene‐specific cSMART assay. Based on the plasma DNA mutation ratio relative to the fetal DNA fraction, fetal genotypes were assigned using a maximum‐likelihood algorithm. Main outcome measures Concordance of fetal genotyping results between IPD and NIPT, and the sensitivity and specificity of the NIPT assay. Results Compared with gold standard IPD results, 32 of 33 fetuses (96.97%) were accurately genotyped by NIPT. The sensitivity and specificity of the NIPT assay was 100.00% (95% CI 59.04–100.00%) and 96.15% (95% CI 80.36–99.90%), respectively. Conclusions The novel cSMART assay demonstrated high accuracy for correctly calling fetal genotypes. We propose that this test has useful clinical utility for the rapid screening of high‐risk and low‐risk pregnancies with a known history of PKU on one or both sides of the family. Tweetable abstract NIPT of couples at high risk for PKU using a full‐coverage cSMART PAH gene test.

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Development and validation of a fetal genotyping assay with potential for noninvasive prenatal diagnosis of hereditary hearing loss

Abstract: The cSMART assay applied to cell-free DNA isolated from maternal plasma of pregnant women is highly accurate for calling correct fetal NSHL genotypes. © 2016 John Wiley & Sons, Ltd.

Cited by 17 publications

References 33 publications

One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR

One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR

Non-invasive prenatal testing of pregnancies at risk for phenylketonuria

Noninvasive fetal genotyping in pregnancies at risk for PKU using a comprehensive quantitative cSMART assay for PAH gene mutations: a clinical feasibility study

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