Detection of Fetal Subchromosomal Abnormalities by Sequencing Circulating Cell-Free DNA from Maternal Plasma

Zhao, Chen; Tynan, John A.; Ehrich, Mathias; Hannum, Gregory; McCullough, Ron; Saldivar, Juan‐Sebastian; Oeth, Paul; Boom, Dirk van den; Deciu, Cosmin

doi:10.1373/clinchem.2014.233312

Cited by 136 publications

(175 citation statements)

References 32 publications

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“…Expanding NIPS to include detection of specific conditions caused by a CNV (e.g., 22q11.2 deletion, 1p36 deletion, 15q11.2-13 deletion) is technically possible (analytical validity). [60][61][62][63] The phenotypes associated with these conditions can be severe; therefore, they may be appropriate conditions for prenatal screening. However, providers and patients must be aware that expanding the use of NIPS to include the detection of CNVs requires in-depth knowledge of the limitations of the technology, return of results, and follow-up.…”

Section: Acmg Statement Should Nips Be Offered For Detection Of Copy mentioning

confidence: 99%

“…Validation studies make the point that DR and SPEC depend on many variables (e.g., depth of read), 10,[60][61][62][63] which can change the false-positive and false-negative rate when NIPS is used for prenatal detection of CNVs. Pretest and posttest counseling is further confounded by variable expressivity and penetrance of the conditions being screened, size of the deletion being screened, specific genes within the critical region of the locus interrogated, and the number of genes within the critical region being screened.…”

Section: Acmg Statement Should Nips Be Offered For Detection Of Copy mentioning

confidence: 99%

See 1 more Smart Citation

Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics

Gregg

Skotko

Benkendorf

et al. 2016

Genetics in Medicine

600

560

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guidelines and statements have assisted patients seeking prenatal screening information and health-care providers responsible for providing accurate and up-to-date information to their patients. [1][2][3] Until recently, noninvasive prenatal screening for aneuploidy relied on measurements of maternal serum analytes and/or ultrasonography. These have a false-positive rate of approximately 5% and detection rates of 50-95%, depending on the specific screening strategy used. Advances in genomic technologies led to noninvasive prenatal screening that relies on the presence of cell-free DNA derived from the placenta but circulating in maternal blood, which is referred to here as noninvasive prenatal screening (NIPS). Massive parallel sequencing of maternal and placental (also called fetal when speaking of the fraction of this DNA in maternal blood) fragments of DNA occurs simultaneously. Sequencing with quantification can be random, targeted, and followed by quantification or exploitation of single-nucleotide polymorphisms. [4][5][6][7][8] Alternatively, sequencing can take place by measuring the release of hydrogen ions as nucleotides are added to a DNA template (i.e., semiconductor sequencing). 9 Microarray technology can also be used to quantify DNA. 10 Bioinformatics that enable these methodologies is complex and proprietary. Since the introduction of NIPS in 2011, health-care providers and patients have experienced marketing pressures, rapidly evolving professional practice guidelines, and confusion regarding the appropriate role of Noninvasive prenatal screening using cell-free DNA (NIPS) has been rapidly integrated into prenatal care since the initial American College of Medical Genetics and Genomics (ACMG) statement in 2013. New evidence strongly suggests that NIPS can replace conventional screening for Patau, Edwards, and Down syndromes across the maternal age spectrum, for a continuum of gestational age beginning at 9-10 weeks, and for patients who are not significantly obese. This statement sets forth a new framework for NIPS that is supported by information from validation and clinical utility studies. Pretest counseling for NIPS remains crucial; however, it needs to go beyond discussions of Patau, Edwards, and Down syndromes. The use of NIPS to include sex chromosome aneuploidy screening and screening for selected copy-number variants (CNVs) is becoming commonplace because there are no other screening options to identify these conditions. Providers should have a more thorough understanding of patient preferences and be able to educate about the current drawbacks of NIPS across the prenatal screening spectrum. Laboratories are encouraged to meet the needs of providers and their patients by delivering meaningful screening reports and to engage in education. With health-care-provider guidance, the patient should be able to make an educated decision about the current use of NIPS and the ramifications of a positive, negative, or no-call result. Genet Med advance online publication 28 July 2016Key Words: cell-f...

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Section: Acmg Statement Should Nips Be Offered For Detection Of Copy mentioning

confidence: 99%

Section: Acmg Statement Should Nips Be Offered For Detection Of Copy mentioning

confidence: 99%

Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics

Gregg

Skotko

Benkendorf

et al. 2016

Genetics in Medicine

600

560

View full text Add to dashboard Cite

show abstract

“…Reports from reference laboratories have been broadly consistent with the estimates of detection rates (DRs) and false-positive rates (FPRs) established in these trials [2][3][4][5][6]. Additionally, both proof of principle [7][8][9] and data from reference laboratories [10,11] have indicated that screening is possible for select sets of microdeletion syndromes.…”

Section: Introductionmentioning

confidence: 53%

A National Referral Laboratory’s Experience with the Implementation of SNP-Based Non-invasive Prenatal Screening for Fetal Aneuploidy and Select Microdeletion Syndromes

Santamaría¹,

Bermejo²,

Cigarrán³

et al. 2018

Journal of Fetal Medicine

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To retrospectively evaluate the successful test rate and performance of non-invasive prenatal screening (NIPS) for aneuploidies and microdeletions with international transportation of samples. Blood samples from Iberian women with singleton pregnancies were sent to a US laboratory for NIPS for aneuploidy and microdeletion syndromes (22q11.2, 1p36, Cri-du-chat, Prader Willi and Angelman). The NIPS methodology involved the analysis of single nucleotide polymorphisms in cell-free DNA in maternal plasma. Women with high-risk results were offered karyotyping and/or microarray confirmatory studies. Based on 14,175 women with successful testing (98.76% of all referrals), the overall test positive rate was 2.37% (1.9% for aneuploidy and 0.47% for microdeletion syndromes). Based on cases with known outcome, the positive predictive values (PPVs) were: for trisomy 21, 98.6%; trisomy 18, 85.7%; trisomy 13, 71.4%; monosomy-X, 87.5%; other sex chromosome aneuploidies, 100%; 22q11.2 deletion, 15.4%; and other microdeletions combined, 20%. With a protocol change that involved selective use of resequencing at a higher depth of read, the PPV for 22q11.2 deletion increased to 33.3 and 75% for the other microdeletions. Effective NIPS for both aneuploidies and select microdeletion syndromes can be provided even when this involves international transportation of blood specimens.

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“…Schématique-ment, une lecture correspond à un fragment séquencé), ce qui est très onéreux [14]. Depuis, diverses équipes ont publié des cas de microdélétions/microduplications détectées par MPS de l'ADNfc avec une diminution du nombre de lectures nécessaires et donc du coût, et ce, grâce à des améliora-tions techniques (séquençage ciblé) [21,22] ou bioinformatiques [23] (Tableau 3). Les données publiées à ce jour concernent diverses régions chromosomiques et restent insuffisantes pour évaluer les performances des différentes approches proposées pour chaque anomalie.…”

Section: Anomalies Subchromosomiquesunclassified

Test non invasif et anomalies chromosomiques : jusqu’où faut-il aller ?

Khattabi

Dupont

2016

Rev. med. perinat.

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La découverte de l'ADN foetal circulant (ADNfc) dans le sang maternel, associée aux avancées techniques du séquençage, ont permis une amélioration notable du dépis-tage des trisomies 21, 18 et 13. On observe cependant une tendance à élargir le champ de ce dépistage, y compris pour les microdélétions. Cet article reprend les données publiées pour analyser les performances réelles de ces tests, rappelle les contraintes biologiques incontournables associées à l'analyse de l'ADNfc, pour expliquer et comprendre les recommandations actuelles visant à limiter le champ du dépistage. Mots clés Dépistage prénatal non invasif · ADN foetal circulant · Séquençage massif en parallèle · Aneuploïdies · DysgonosomiesAbstract The recent discovery of circulating free fetal DNA in maternal blood followed by major technological advances in genome sequencing led to a significant increase in screening efficiency for trisomies 13, 18, and 21. However, we are witnessing a general trend to screen for more abnormalities including microdeletions. This article relies on published data to analyze true analytical performance of these tests, and emphasizes on technical and biological issues to help understand actual recommendations for a focused use of noninvasive screening.

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Detection of Fetal Subchromosomal Abnormalities by Sequencing Circulating Cell-Free DNA from Maternal Plasma

Cited by 136 publications

References 32 publications

Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics

Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics

A National Referral Laboratory’s Experience with the Implementation of SNP-Based Non-invasive Prenatal Screening for Fetal Aneuploidy and Select Microdeletion Syndromes

Test non invasif et anomalies chromosomiques : jusqu’où faut-il aller ?

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