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

Lv, Weigang; Li, Zhuo; Wei, Xiaojun; Zhu, Huimin; Teng, Yuanwen; Zhou, Miaojin; Gong, Yuyan; Cram, David S.; Han, Lianshu

doi:10.1111/1471-0528.15869

Cited by 13 publications

(19 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The optimised NIPD test for b-thalassaemia was based on a modification of the previously described phenylketonuria assay. 30 Here, we simply replaced the PAH gene targeting primers with nine HBB targeting primers closely positioned to cover the 46 different types of Southern Chinese HBB pathogenic variants (Figure 2A), and retained the 76 single nucleotide polymorphism (SNP) primers for estimating fetal DNA fraction. 33 For performing the NIPD assay, 10ml EDTA blood samples were collected and cfDNA was purified using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany).…”

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

“…Bioinformatic analysis was performed as previously described. 30 Briefly, after removal of poor-quality reads, paired fragments were joined using their overlapping sequences to reconstruct the original cfDNA sequence. Following SNP calling, the reads with the same barcode and genome location were grouped, and counted as consensus unique allelic reads.…”

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

“…33 Based on mutation ratios and the corresponding FF, fetal genotypes were assigned (Figure 2C). A maximum likelihood algorithm using variables such as read template number, mutation ratios and FF 30,34 was also used to determine a probability score that the manually assigned fetal genotypes were correct. For quality control (QC), the cut-off to call a valid result was a >500 sequencing templates (reads) analysed and a P value of >70%.…”

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

“…However, because of the difficulty in confidently calling the maternally inherited allele, it has not been possible to assign complete fetal genotypes in all cases. As an alternative approach for fetal HBB genotyping, we elected to develop a new NIPD test based on circulating Single Molecule Amplification and Re‐sequencing Technology (cSMART), which has been previously shown to accurately genotype the fetus for several autosomal recessive conditions 28–30 . In this study, we report on the performance of our NIPD assay for correctly genotyping the fetus in 102 pregnancies at high‐risk for β‐thalassaemia.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Noninvasive prenatal diagnosis for pregnancies at risk for β‐thalassaemia: a retrospective study

Linpeng

et al. 2020

BJOG

Self Cite

View full text Add to dashboard Cite

Objective To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for b-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART). Design zThrough carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping. Setting Chinese prenatal diagnostic centres specialising in thalassaemia testing. Population Chinese carrier couples at high genetic risk for bthalassaemia. Methods Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA. Main outcome measures Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD. Results Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively. Conclusions This study demonstrates that our cSMART-based NIPD assay for b-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples.

show abstract

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

Section: Nipd Csmart Assay For Assignment Of Hbb Fetal Genotypesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Noninvasive prenatal diagnosis for pregnancies at risk for β‐thalassaemia: a retrospective study

Linpeng

et al. 2020

BJOG

Self Cite

View full text Add to dashboard Cite

show abstract

“…It has been validated in multiple clinical cohorts that NIPS is highly sensitive and specific for patients at increased risk of T13, T18 and T21 aneuploidies [1][2][3]. It also has potential application value in the prenatal screening of copy number variables (CNV) and single nucleotide variables (SNV) by target sequencing and extending the sequencing depth [4,5]. Recently, NIPS is a widespread first-tier prenatal screening method used for high risk pregnancies of aneuploidy [6].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive predictive method for low fetal fraction in noninvasive prenatal screening

Hu¹,

Pei²,

Luo³

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundThe study was a retrospective cohort analysis based on the results of noninvasive prenatal screening (NIPS), complete blood count, thyroxin test and Down's syndrome screening in first or second trimester from 14043 pregnant women. Random forests algorithm was applied to predict the low fetal fraction of cell free DNA (with FF lower than 10th percentile) through individual and laboratory information. Performance of the model was evaluated and compared to prediction using maternal weight.To investigate factors associated with lower FF in the NIPS and to develop a new predictive method for low FF before NIPS. ResultsOf 14043 cases, maternal weight, RBC, HGB and free T3 were significantly negative correlated with FF while gestation age, free T4, PAPP-A, AFP, uE3 and β-hCG were significantly positive correlated with FF. Compared to prediction using maternal weight as isolated parameter, the model has a higher area under curve(AUC) of Receiver Operating Characteristic (ROC) and overall accuracy. ConclusionsThe comprehensive predictive method based on combined multiple factors was more effective than single-factor model in low FF status prediction. This method can provide more information for clinical choice and pre-test quality control of NIPS.

show abstract

Simultaneous detection of fetal aneuploidy, de novoFGFR3 mutations and paternally derived β‐thalassemia by a novel method of noninvasive prenatal testing

Yang

et al. 2021

Prenatal Diagnosis

View full text Add to dashboard Cite

Objective: The aim is to develop a novel noninvasive prenatal testing (NIPT) method that simultaneously performs fetal aneuploidy screening and the detection of de novo and paternally derived mutations. Methods: A total of 68 pregnancies, including 26 normal pregnancies, 7 cases with fetal aneuploidies, 7 cases with fetal achondroplasia or thanatophoric dysplasia, 18 cases with fetal skeletal abnormalities, and 10 cases with β-thalassemia high risk were recruited. Plasma cell-free DNA was amplified by Targeted And Genome-wide simultaneous sequencing (TAGs-seq) to generate around 99% of total reads covering the whole-genome region and around 1% covering the target genes. The reads on the whole-genome region were analyzed for fetal aneuploidy using a binary hypothesis T-score and the reads on target genes were analyzed for point mutations by calculating the minor allelic frequency of loci on FGFR3 and HBB. TAGs-seq results were compared with conventional NIPT and diagnostic results. Results: In each sample, TAGs-seq generated 44.7-54 million sequencing reads covering the whole-genome region of 0.1-3� and the target genes of >1000�depth. All cases of fetal aneuploidy and de novo mutations of achondroplasia/thanatophoric dysplasia were identified with high sensitivities and specificities except for one false-negative paternal mutation of β-thalassemia. Conclusions: TAGs-seq is a novel NIPT method that combines the fetal aneuploidy screening and the detection of de novo FGFR3 mutations and paternal HBB mutations. Lin Yang and Yujing Wu joint first authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

show abstract

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

Cited by 13 publications

References 29 publications

Noninvasive prenatal diagnosis for pregnancies at risk for β‐thalassaemia: a retrospective study

Noninvasive prenatal diagnosis for pregnancies at risk for β‐thalassaemia: a retrospective study

A comprehensive predictive method for low fetal fraction in noninvasive prenatal screening

Simultaneous detection of fetal aneuploidy, de novoFGFR3 mutations and paternally derived β‐thalassemia by a novel method of noninvasive prenatal testing

Contact Info

Product

Resources

About