Noninvasive Detection of Fetal Genetic Variations through Polymorphic Sites Sequencing of Maternal Plasma DNA

10.1101/2021.01.26.21250573 ◽

2021 ◽

Author(s):

Song Gao

Keyword(s):

Goodness Of Fit ◽

Genetic Model ◽

Prenatal Testing ◽

Amplicon Sequencing ◽

Maternal Plasma ◽

Genetic Variations ◽

Plasma Dna ◽

Goodness Of Fit Test ◽

Risk Pregnancy ◽

Fetal Aneuploidies

AbstractNon-invasive prenatal testing (NIPT) for common fetal aneuploidies using circulating cell free DNA in maternal plasma has been widely adopted in clinical practice for its sensitivity and accuracy. However, the detection of subchromosomal abnormalities or monogenetic variations using such a method showed no cost-effectiveness or satisfactory accuracy. Here we show that with the aid of polymorphic sites sequencing, fetal fraction of the sample and genotype of the target site were determined with high accuracy. Then genetic variations at the chromosomal, subchromosomal and nucleotide levels were detected using the overall allelic goodness-of-fit test of all target polymorphic sites to each possible genetic model. Finally, relative allelic distributions for each amplicon were visualized and genetic variations at the chromosomal, subchromosomal and nucleotide levels were determined by distinct characteristic clusters on allelic distribution plot of each possible genetic model. As no parental genetic information was required and all allelic information retained for amplicon sequencing, the reported approach has the potential to simultaneously detect genetic variations at different levels, facilitating the extension of NIPT to all common genetic conditions for general low-risk pregnancies and target variations for certain high-risk pregnancy groups.

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Faculty Opinions recommendation of Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718240750.793490357 ◽

2014 ◽

Author(s):

Nicola Normanno ◽

Antonella De Luca

Keyword(s):

Lung Cancer ◽

Noninvasive Detection ◽

Next Generation ◽

Plasma Dna ◽

Egfr Mutant ◽

Free Plasma

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Faculty Opinions recommendation of COFFEE: control-free noninvasive fetal chromosomal examination using maternal plasma DNA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727280732.793559908 ◽

2019 ◽

Author(s):

Tomas Szemes

Keyword(s):

Maternal Plasma ◽

Plasma Dna

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Noninvasive Prenatal Diagnosis of Monogenic Diseases by Targeted Massively Parallel Sequencing of Maternal Plasma: Application to β-Thalassemia

Clinical Chemistry ◽

10.1373/clinchem.2012.189589 ◽

2012 ◽

Vol 58 (10) ◽

pp. 1467-1475 ◽

Cited By ~ 112

Author(s):

Kwan-Wood G Lam ◽

Peiyong Jiang ◽

Gary J W Liao ◽

K C Allen Chan ◽

Tak Y Leung ◽

...

Keyword(s):

Prenatal Diagnosis ◽

Massively Parallel Sequencing ◽

Globin Gene ◽

Maternal Plasma ◽

Massively Parallel ◽

Sequencing Data ◽

Plasma Dna ◽

Parallel Sequencing ◽

Noninvasive Prenatal Diagnosis ◽

Monogenic Diseases

Abstract BACKGROUND A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. Relative haplotype dosage (RHDO) analysis, a core step of this procedure, would allow one to elucidate the maternally inherited half of the fetal genome. For clinical applications, the cost and complexity of data analysis might be reduced via targeted application of this approach to selected genomic regions containing disease-causing genes. There is thus a need to explore the feasibility of performing RHDO analysis in a targeted manner. METHODS We performed target enrichment by using solution-phase hybridization followed by massively parallel sequencing of the β-globin gene region in 2 families undergoing prenatal diagnosis for β-thalassemia. We used digital PCR strategies to physically deduce parental haplotypes. Finally, we performed RHDO analysis with target-enriched sequencing data and parental haplotypes to reveal the β-thalassemic status for the fetuses. RESULTS A mean sequencing depth of 206-fold was achieved in the β-globin gene region by targeted sequencing of maternal plasma DNA. RHDO analysis was successful for the sequencing data obtained from the target-enriched samples, including a region in one of the families in which the parents had similar haplotype structures. Data analysis revealed that both fetuses were heterozygous carriers of β-thalassemia. CONCLUSIONS Targeted sequencing of maternal plasma DNA for NIPD of monogenic diseases is feasible.

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Noninvasive prenatal diagnostics by maternal plasma DNA sequencing

Expert Review of Molecular Diagnostics ◽

10.1586/erm.12.35 ◽

2012 ◽

Vol 12 (5) ◽

pp. 445-447

Author(s):

Cees B Oudejans

Keyword(s):

Dna Sequencing ◽

Maternal Plasma ◽

Prenatal Diagnostics ◽

Plasma Dna

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Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment

Clinical Chemistry ◽

10.1373/clinchem.2015.245076 ◽

2015 ◽

Vol 61 (10) ◽

pp. 1305-1306 ◽

Cited By ~ 21

Author(s):

Suk Hang Cheng ◽

Peiyong Jiang ◽

Kun Sun ◽

Yvonne K Y Cheng ◽

K C Allen Chan ◽

...

Keyword(s):

Prenatal Testing ◽

Maternal Plasma ◽

Nanopore Sequencing ◽

Plasma Dna ◽

Noninvasive Prenatal Testing ◽

Feasibility Assessment

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Size Distributions of Maternal and Fetal DNA in Maternal Plasma

Clinical Chemistry ◽

10.1373/clinchem.2003.024893 ◽

2004 ◽

Vol 50 (1) ◽

pp. 88-92 ◽

Cited By ~ 364

Author(s):

K C Allen Chan ◽

Jun Zhang ◽

Angela B Y Hui ◽

Nathalie Wong ◽

Tze K Lau ◽

...

Keyword(s):

Pregnant Women ◽

Size Distribution ◽

Maternal Plasma ◽

Rapid Expansion ◽

Molecular Characteristics ◽

Dna Fragments ◽

Dna Molecules ◽

Plasma Dna ◽

Fetal Dna ◽

Noninvasive Prenatal Diagnosis

Abstract Background: The discovery of fetal DNA in maternal plasma has opened up an approach for noninvasive prenatal diagnosis. Despite the rapid expansion in clinical applications, the molecular characteristics of plasma DNA in pregnant women remain unclear. Methods: We investigated the size distribution of plasma DNA in 34 nonpregnant women and 31 pregnant women, using a panel of quantitative PCR assays with different amplicon sizes targeting the leptin gene. We also determined the size distribution of fetal DNA in maternal plasma by targeting the SRY gene. Results: The median percentages of plasma DNA with size >201 bp were 57% and 14% for pregnant and nonpregnant women, respectively (P <0.001, Mann–Whitney test). The median percentages of fetal-derived DNA with sizes >193 bp and >313 bp were 20% and 0%, respectively, in maternal plasma. Conclusion: Plasma DNA molecules are mainly short DNA fragments. The DNA fragments in the plasma of pregnant women are significantly longer than those in the plasma of nonpregnant women, and the maternal-derived DNA molecules are longer than the fetal-derived ones.

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Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases

Clinical Chemistry ◽

10.1373/clinchem.2016.268375 ◽

2017 ◽

Vol 63 (2) ◽

pp. 513-524 ◽

Cited By ~ 54

Author(s):

Winnie W I Hui ◽

Peiyong Jiang ◽

Yu K Tong ◽

Wing-Shan Lee ◽

Yvonne K Y Cheng ◽

...

Keyword(s):

Single Gene ◽

Family Members ◽

Prenatal Testing ◽

Maternal Plasma ◽

Nucleotide Polymorphisms ◽

Plasma Dna ◽

Sequencing Technology ◽

Noninvasive Prenatal Testing ◽

Haplotype Phasing ◽

Mutational Status

Abstract BACKGROUND Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members. Recently, microfluidics-based linked-read sequencing technology has become available and allows the direct haplotype phasing of the whole genome rapidly. We explored the feasibility of applying this direct haplotyping technology in noninvasive prenatal testing. METHODS We first resolved the haplotypes of parental genomes with the use of linked-read sequencing technology. Then, we identified SNPs within and flanking the genes of interest in maternal plasma DNA by targeted sequencing. Finally, we applied relative haplotype dosage analysis to deduce the mutation inheritance status of the fetus. RESULTS Haplotype phasing and relative haplotype dosage analysis of 12 out of 13 families were successfully achieved. The mutational status of these 12 fetuses was correctly classified. CONCLUSIONS High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.

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