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Freud LR, Galloway S, Crowley TB, Moldenhauer J, Swillen A, Breckpot J, Borrell A, Vora NL, Cuneo B, Hoffman H, Gilbert L, Nowakowska B, Geremek M, Kutkowska-Kaźmierczak A, Vermeesch JR, Devriendt K, Busa T, Sigaudy S, Vigneswaran T, Simpson JM, Dungan J, Gotteiner N, Gloning KP, Digilio MC, Unolt M, Putotto C, Marino B, Repetto G, Fadic M, Garcia-Minaur S, Achón Buil A, Thomas MA, Fruitman D, Beecroft T, Hui PW, Oskarsdottir S, Bradshaw R, Criebaum A, Norton ME, Lee T, Geiger M, Dunnington L, Isaac J, Wilkins-Haug L, Hunter L, Izzi C, Toscano M, Ghi T, McGlynn J, Romana Grati F, Emanuel BS, Gaiser K, Gaynor JW, Goldmuntz E, McGinn DE, Schindewolf E, Tran O, Zackai EH, Yan Q, Bassett AS, Wapner R, McDonald-McGinn DM. Prenatal vs postnatal diagnosis of 22q11.2 deletion syndrome: cardiac and noncardiac outcomes through 1 year of age. Am J Obstet Gynecol 2024; 230:368.e1-368.e12. [PMID: 37717890 DOI: 10.1016/j.ajog.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND The 22q11.2 deletion syndrome is the most common microdeletion syndrome and is frequently associated with congenital heart disease. Prenatal diagnosis of 22q11.2 deletion syndrome is increasingly offered. It is unknown whether there is a clinical benefit to prenatal detection as compared with postnatal diagnosis. OBJECTIVE This study aimed to determine differences in perinatal and infant outcomes between patients with prenatal and postnatal diagnosis of 22q11.2 deletion syndrome. STUDY DESIGN This was a retrospective cohort study across multiple international centers (30 sites, 4 continents) from 2006 to 2019. Participants were fetuses, neonates, or infants with a genetic diagnosis of 22q11.2 deletion syndrome by 1 year of age with or without congenital heart disease; those with prenatal diagnosis or suspicion (suggestive ultrasound findings and/or high-risk cell-free fetal DNA screen for 22q11.2 deletion syndrome with postnatal confirmation) were compared with those with postnatal diagnosis. Perinatal management, cardiac and noncardiac morbidity, and mortality by 1 year were assessed. Outcomes were adjusted for presence of critical congenital heart disease, gestational age at birth, and site. RESULTS A total of 625 fetuses, neonates, or infants with 22q11.2 deletion syndrome (53.4% male) were included: 259 fetuses were prenatally diagnosed (156 [60.2%] were live-born) and 122 neonates were prenatally suspected with postnatal confirmation, whereas 244 infants were postnatally diagnosed. In the live-born cohort (n=522), 1-year mortality was 5.9%, which did not differ between groups but differed by the presence of critical congenital heart disease (hazard ratio, 4.18; 95% confidence interval, 1.56-11.18; P<.001) and gestational age at birth (hazard ratio, 0.78 per week; 95% confidence interval, 0.69-0.89; P<.001). Adjusting for critical congenital heart disease and gestational age at birth, the prenatal cohort was less likely to deliver at a local community hospital (5.1% vs 38.2%; odds ratio, 0.11; 95% confidence interval, 0.06-0.23; P<.001), experience neonatal cardiac decompensation (1.3% vs 5.0%; odds ratio, 0.11; 95% confidence interval, 0.03-0.49; P=.004), or have failure to thrive by 1 year (43.4% vs 50.3%; odds ratio, 0.58; 95% confidence interval, 0.36-0.91; P=.019). CONCLUSION Prenatal detection of 22q11.2 deletion syndrome was associated with improved delivery management and less cardiac and noncardiac morbidity, but not mortality, compared with postnatal detection.
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Affiliation(s)
- Lindsay R Freud
- Hospital for Sick Children, University of Toronto, Toronto, Canada.
| | - Stephanie Galloway
- NewYork-Presbyterian Hospital, Columbia University Irving Medical Center, New York City, NY
| | | | - Julie Moldenhauer
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ann Swillen
- University Hospitals Leuven, Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- University Hospitals Leuven, Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
| | - Antoni Borrell
- Hospital Clinic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Neeta L Vora
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bettina Cuneo
- Children's Hospital Colorado, University of Colorado, Denver, CO
| | - Hilary Hoffman
- Children's Hospital Colorado, University of Colorado, Denver, CO
| | - Lisa Gilbert
- Children's Hospital Colorado, University of Colorado, Denver, CO
| | | | | | | | - Joris R Vermeesch
- University Hospitals Leuven, Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
| | - Koen Devriendt
- University Hospitals Leuven, Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
| | - Tiffany Busa
- Hôpital de la Timone, Marseille University, Marseille, France
| | - Sabine Sigaudy
- Hôpital de la Timone, Marseille University, Marseille, France
| | - Trisha Vigneswaran
- Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust and Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom
| | - John M Simpson
- Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust and Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom
| | - Jeffrey Dungan
- Prentice Women's Hospital, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Nina Gotteiner
- Prentice Women's Hospital, Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | | | - Marta Unolt
- Children's Hospital of Philadelphia, Philadelphia, PA; Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | | | | | - Gabriela Repetto
- Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Magdalena Fadic
- Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | | | | | - Mary Ann Thomas
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Deborah Fruitman
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Taylor Beecroft
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX
| | - Pui Wah Hui
- Queen Mary Hospital, Tsan Yuk Hospital, University of Hong Kong, Hong Kong, China
| | | | - Rachael Bradshaw
- SSM Health Cardinal Glennon St. Louis Fetal Care Institute, Saint Louis University, St. Louis, MO
| | - Amanda Criebaum
- SSM Health Cardinal Glennon St. Louis Fetal Care Institute, Saint Louis University, St. Louis, MO
| | - Mary E Norton
- University of California, San Francisco, San Francisco, CA
| | - Tiffany Lee
- University of California, San Francisco, San Francisco, CA
| | - Miwa Geiger
- Kravis Children's Hospital, Mount Sinai Medical Center, New York City, NY
| | - Leslie Dunnington
- Memorial Hermann-Texas Medical Center, University of Texas Health Science Center at Houston, Houston, TX
| | | | | | - Lindsey Hunter
- Royal Hospital for Children, University of Glasgow, Glasgow, United Kingdom
| | - Claudia Izzi
- Children's Hospital of Philadelphia, Philadelphia, PA; Azienda Socio Sanitaria Territoriale (ASST) degli Spedali Civili di Brescia, Brescia, Italy
| | | | - Tullio Ghi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | - Beverly S Emanuel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kimberly Gaiser
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - J William Gaynor
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth Goldmuntz
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel E McGinn
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Erica Schindewolf
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Oanh Tran
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elaine H Zackai
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Qi Yan
- NewYork-Presbyterian Hospital, Columbia University Irving Medical Center, New York City, NY
| | - Anne S Bassett
- Centre for Addiction and Mental Health and Toronto General Hospital, University of Toronto, Toronto, Canada
| | - Ronald Wapner
- NewYork-Presbyterian Hospital, Columbia University Irving Medical Center, New York City, NY
| | - Donna M McDonald-McGinn
- Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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2
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Martin K, Norton ME, MacPherson C, Demko Z, Egbert M, Haeri S, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Strong N, Silver R, Vohra N, Hyett J, Kao C, Hakonarson H, Jacobson B, Dar P. Impact of high-risk prenatal screening results for 22q11.2 deletion syndrome on obstetric and neonatal management: Secondary analysis from the SMART study. Prenat Diagn 2023; 43:1574-1580. [PMID: 38066724 DOI: 10.1002/pd.6483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
OBJECTIVE One goal of prenatal genetic screening is to optimize perinatal care and improve infant outcomes. We sought to determine whether high-risk cfDNA screening for 22q11.2 deletion syndrome (22q11.2DS) affected prenatal or neonatal management. METHODS This was a secondary analysis from the SMART study. Patients with high-risk cfDNA results for 22q11.2DS were compared with the low-risk cohort for pregnancy characteristics and obstetrical management. To assess differences in neonatal care, we compared high-risk neonates without prenatal genetic confirmation with a 1:1 matched low-risk cohort. RESULTS Of 18,020 eligible participants enrolled between 2015 and 2019, 38 (0.21%) were high-risk and 17,982 (99.79%) were low-risk for 22q11.2DS by cfDNA screening. High-risk participants had more prenatal diagnostic testing (55.3%; 21/38 vs. 2.0%; 352/17,982, p < 0.001) and fetal echocardiography (76.9%; 10/13 vs. 19.6%; 10/51, p < 0.001). High-risk newborns without prenatal diagnostic testing had higher rates of neonatal genetic testing (46.2%; 6/13 vs. 0%; 0/51, P < 0.001), echocardiography (30.8%; 4/13 vs. 4.0%; 2/50, p = 0.013), evaluation of calcium levels (46.2%; 6/13 vs. 4.1%; 2/49, P < 0.001) and lymphocyte count (53.8%; 7/13 vs. 15.7%; 8/51, p = 0.008). CONCLUSIONS High-risk screening results for 22q11.2DS were associated with higher rates of prenatal and neonatal diagnostic genetic testing and other 22q11.2DS-specific evaluations. However, these interventions were not universally performed, and >50% of high-risk infants were discharged without genetic testing, representing possible missed opportunities to improve outcomes for affected individuals.
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Affiliation(s)
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Washington, District of Columbia, USA
| | | | | | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia Presbyterian Medical Center, New York, New York, USA
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone, New York, New York, USA
| | - Asma Khalil
- Department of Obstetrics and Gynecology, St. George's Hospital, University of London, London, UK
| | - Revital Faro
- Department of Obstetrics and Gynecology, St. Peter's University Hospital, New Brunswick, New Jersy, USA
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, USA
| | - Noel Strong
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, Utah, USA
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, New South Wales, Australia
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Bo Jacobson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynaecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
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3
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Biggs SE, Gilchrist B, May KR. Chromosome 22q11.2 Deletion (DiGeorge Syndrome): Immunologic Features, Diagnosis, and Management. Curr Allergy Asthma Rep 2023; 23:213-222. [PMID: 36897497 PMCID: PMC9999075 DOI: 10.1007/s11882-023-01071-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/11/2023]
Abstract
PURPOSE OF REVIEW This review focuses on immunologic findings, relationships among immunologic findings and associated conditions of autoimmunity and atopy, and management of immunologic disease in chromosome 22q11.2 deletion syndrome (22q11.2DS, historically known as DiGeorge syndrome). RECENT FINDINGS The implementation of assessment of T cell receptor excision circles (TRECs) in newborn screening has led to increased detection of 22q11.2 deletion syndrome. While not yet applied in clinical practice, cell-free DNA screening for 22q11.2DS also has the potential to improve early detection, which may benefit prompt evaluation and management. Multiple studies have further elucidated phenotypic features and potential biomarkers associated with immunologic outcomes, including the development of autoimmune disease and atopy. The clinical presentation of 22q11.2DS is highly variable particularly with respect to immunologic manifestations. Time to recovery of immune system abnormalities is not well-defined in current literature. An understanding of the underlying causes of immunologic changes found in 22q11.2DS, and the progression and evolution of immunologic changes over the lifespan have expanded over time and with improved survival. An included case highlights the variability of presentation and potential severity of T cell lymphopenia in partial DiGeorge syndrome and demonstrates successful spontaneous immune reconstitution in partial DiGeorge syndrome despite initial severe T cell lymphopenia.
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Affiliation(s)
- Sarah E Biggs
- Division of Allergy-Immunology & Pediatric Rheumatology, Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Bailee Gilchrist
- Division of Allergy-Immunology & Pediatric Rheumatology, Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Kathleen R May
- Division of Allergy-Immunology & Pediatric Rheumatology, Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, GA, USA.
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4
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Goldring G, Trotter C, Meltzer JT, Souter V, Pais L, DiNonno W, Xu W, Weitzel JN, Vora NL. Maternal Malignancy After Atypical Findings on Single-Nucleotide Polymorphism-Based Prenatal Cell-Free DNA Screening. Obstet Gynecol 2023; 141:791-800. [PMID: 36897127 PMCID: PMC10026947 DOI: 10.1097/aog.0000000000005107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/15/2022] [Indexed: 03/11/2023]
Abstract
OBJECTIVE To evaluate the incidence and clinical outcomes of cell-free DNA results suspicious for maternal malignancy on prenatal cell-free DNA screening with single-nucleotide polymorphism (SNP)-based technology. METHODS This retrospective cohort study included data from SNP-based, noninvasive prenatal screening samples from a commercial laboratory from January 2015 to October 2021. Maternal plasma was screened for trisomy 21, 18, and 13; monosomy X; and triploidy. Cases were considered suspicious for maternal malignancy if retrospective bioinformatics and visual inspection of the SNP plot were suggestive of multiple maternal copy number variants across at least two of the tested chromosomes. Clinical follow-up on patients was obtained by contacting individual referring clinician offices by telephone, facsimile, or email. RESULTS A total of 2,004,428 noninvasive prenatal screening samples during the study period met criteria for inclusion in the analysis. Of these, 38 samples (0.002% or 1 in 52,748, 95% CI 1:74,539-1:38,430) had SNP-plot results that were suspicious for maternal malignancy. Maternal health outcomes were obtained in 30 of these patients (78.9%); eight were lost to follow-up. Maternal malignancy or suspected malignancy was identified in 66.7% (20/30) of the 30 patients with clinical follow-up provided by the clinic. The most common maternal malignancies were lymphoma (n=10), breast cancer (n=5), and colon cancer (n=3). CONCLUSION Results suspicious for maternal malignancy are rare with SNP-based noninvasive prenatal screening (1:53,000), but two thirds of patients who had a noninvasive prenatal screening result concerning for malignancy in this study had a cancer diagnosis. Investigation for malignancy should be recommended for all pregnant patients with this type of result. FUNDING SOURCE This study was funded by Natera, Inc.
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Affiliation(s)
- Georgina Goldring
- Natera, Inc., Austin, Texas; and the Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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5
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Lüthgens K, Sinzel M, Kolar M, Kagan KO. Screen-positive rate in cell-free DNA screening for microdeletion 22q11.2. Prenat Diagn 2023; 43:288-293. [PMID: 36738442 DOI: 10.1002/pd.6328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To examine the impact of the fetal fraction (FF) on the screen-positive rate in screening for microdeletion 22q11.2. METHODS This study is based on samples that were analyzed using the Harmony® Prenatal Test (Roche Inc). The study cohort comprised samples from women with singleton pregnancies who were at least 16 years old and at least at 11 weeks' gestation. Logistic regression analysis was used to determine significant covariates that carry an impact on the screen-positive rate. RESULTS The study population consisted of 52,019 pregnancies, including 309 pregnancies with a high-risk result for microdeletion 22q11.2. Thus, the overall screen-positive rate was 0.59%. In the low-risk group, the FF was 10.1%, and in the high-risk group, it was 7.3%. Regression analysis indicated a strong correlation between the FF and the screen-positive rate. In the cases with an FF of <11.0%, the screen-positive rate was 0.92%, while it was 0.13% in the group with a higher FF. CONCLUSION The screen-positive rate depends on the FF. In order to keep the rate low, we recommend restricting the analysis to samples with a FF of 11% and more.
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Affiliation(s)
| | | | | | - Karl Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
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6
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Raymond YC, Acreman ML, Bussolaro S, Mol BW, Fernando S, Menezes M, Da Silva Costa F, Fantasia I, Rolnik DL. The accuracy of cell-free DNA screening for fetal segmental copy number variants: A systematic review and meta-analysis. BJOG 2023; 130:549-559. [PMID: 36655363 DOI: 10.1111/1471-0528.17386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND The performance of cell-free DNA (cfDNA) screening for microscopic copy number variants (CNVs) is unclear. OBJECTIVES This was a systematic review and meta-analysis to investigate the sensitivity, specificity and positive predictive value (PPV) of cfDNA screening for CNVs. SEARCH STRATEGY Articles published in EMBASE, PubMed or Web of Science before November 2022 were screened for inclusion. This protocol was registered with PROSPERO (23 March 2021, CRD42021250849) prior to initiation. SELECTION CRITERIA Articles published in English, detailing diagnostic outcomes for at least 10 high-risk CNV results with cfDNA were considered for inclusion. DATA COLLECTION AND ANALYSIS The PPV was calculated and pooled with random-effects models for double-arcsine transformed proportions, using cases with diagnostic confirmation. Overall sensitivity, specificity and a summary receiver-operating characteristics (ROC) curve were calculated using bivariate models. The risk of bias was assessed using QUADAS-2. MAIN RESULTS In all, 63 articles were included in the final analysis, detailing 1 591 459 cfDNA results. The pooled PPV was 37.5% (95% confidence interval [CI] 30.6-44.8), with substantial statistical heterogeneity (I2 = 93.9%). Bivariate meta-analysis estimated sensitivity and specificity to be 77.4% (95% CI 65.7-86.0) and 99.4% (95% CI 98.0-99.8), respectively, with an area under the summary ROC curve of 0.947 (95% CI 0.776-0.984). CONCLUSIONS Approximately one-third of women who screen high-risk for CNVs with cfDNA will have an affected fetus. This value is of importance for screening counselling.
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Affiliation(s)
- Yvette C Raymond
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia
| | - Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Ipswich, Queensland, Australia
| | - Sofia Bussolaro
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Ben W Mol
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Aberdeen Centre for Women's Health Research, University of Aberdeen, Aberdeen, UK
| | - Shavi Fernando
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fabricio Da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Ilaria Fantasia
- Obstetrics & Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Daniel Lorber Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
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7
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Hu T, Wang J, Zhu Q, Zhang Z, Hu R, Xiao L, Yang Y, Liao N, Liu S, Wang H, Niu X, Liu S. Clinical experience of noninvasive prenatal testing for rare chromosome abnormalities in singleton pregnancies. Front Genet 2022; 13:955694. [PMID: 36226167 PMCID: PMC9549601 DOI: 10.3389/fgene.2022.955694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives: The study aimed to investigate the clinical use of noninvasive prenatal testing (NIPT) for common fetal aneuploidies as a prenatal screening tool for the detection of rare chromosomal abnormalities (RCAs). Methods: Gravidas with positive NIPT results for RCAs who subsequently underwent amniocentesis for a single nucleotide polymorphism array (SNP array) were recruited. The degrees of concordance between the NIPT and SNP array were classified into full concordance, partial concordance, and discordance. The positive predictive value (PPV) was used to evaluate the performance of NIPT. Results: The screen-positivity rate of NIPT for RCAs was 0.5% (842/158,824). Of the 528 gravidas who underwent amniocentesis, 29.2% (154/528) were confirmed to have positive prenatal SNP array results. PPVs for rare autosomal trisomies (RATs) and segmental imbalances were 6.1% (7/115) and 21.1% (87/413), respectively. Regions of homozygosity/uniparental disomy (ROH/UPD) were identified in 9.5% (50/528) of gravidas. The PPV for clinically significant findings was 8.0% (42/528), including 7 cases with mosaic RATs, 30 with pathogenic/likely pathogenic copy number variants, and 5 with imprinting disorders. Conclusion: NIPT for common fetal aneuploidies yielded low PPVs for RATs, moderate PPVs for segmental imbalances, and incidental findings for ROH/UPD. Due to the low PPV for clinically significant findings, NIPT for common fetal aneuploidies need to be noticed for RCAs.
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Affiliation(s)
- Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qian Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yunyuan Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Sha Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaoyu Niu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- *Correspondence: Ting Hu, ; Xiaoyu Niu, ; Shanling Liu,
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8
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Wojas A, Martin KA, Koyen Malashevich A, Hashimoto K, Parmar S, White R, Demko Z, Billings P, Jelsema R, Rebarber A. Clinician-reported Chorionicity and Zygosity Assignment using single-nucleotide polymorphism-based cell-free DNA Lessons learned from 55,344 Twin Pregnancies. Prenat Diagn 2022; 42:1235-1241. [PMID: 35997139 PMCID: PMC9541063 DOI: 10.1002/pd.6218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022]
Abstract
Objective Prenatal chorionicity assessment relies on ultrasound, which can be confounded by many factors. Noninvasive assessment of zygosity is possible using single nucleotide polymorphism (SNP)‐based cell‐free DNA testing. Our objective was to determine the relationship between provider‐reported chorionicity and SNP‐cfDNA assignment of twin zygosity. Methods All twin pregnancy blood samples received by a reference laboratory between September 27, 2017 and September 8, 2021 were included. Chorionicity assignment was requested on the requisition, recorded as; monochorionic (MC), dichorionic, or “don't know”. SNP‐cfDNA zygosity results, monozygotic (MZ) or dizygotic (DZ), were correlated with chorionicity assignment. Results 59,471 twin samples (median gestational age = 12.0 weeks at draw) were received and analyzed; 55,344 (93.1%) received zygosity assignment. SNP‐cfDNA reported 16,673 (30.1%) MZ and 38,671 (69.9%) as DZ. Provider‐reported chorionicity was compared to the zygosity assignment for each case. Of 6283 provider‐reported MC twins, 318 (5.1%) were reported as DZ using SNP‐cfDNA. Conclusion(s) One in 20 suspected MC twin pregnancies were reported as DZ using SNP‐cfDNA. Approximately 30% of 55,344 twin pregnancies were found to be MZ, including cases where chorionicity was unknown. SNP‐cfDNA zygosity assessment is a useful adjunct assessment for twin pregnancies, particularly those reported as MC or without determined chorionicity. What's already known about the topic? The assignment of chorionicity early in pregnancy can improve perinatal outcomes of twin pregnancies. Prenatal assessment of chorionicity relies on ultrasound (US), and the accuracy of US can be confounded by many factors, including gestational age (GA) and operator experience. Noninvasive assessment of zygosity is now possible using single nucleotide polymorphism (SNP)‐based cell‐free DNA (cfDNA).
What does this study add? This is the first population‐based study describing the correlation between cfDNA assessment of zygosity and chorionicity. In 55,344 twin pregnancies, approximately 30% were found to be monozygotic (MZ), including cases where chorionicity was unknown. We found that one in 20 suspected monochorionic (MC) twin pregnancies were reported as dizygotic (DZ) twins (DZ) by SNP‐cfDNA testing. SNP‐cfDNA zygosity assessment is a useful adjunct assessment for twin pregnancies, particularly those reported as MC or without determined chorionicity.
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Affiliation(s)
- Anna Wojas
- Department of Obstetrics, Gynecology, and Reproductive Science, Mt. Sinai, New York, NY, USA
| | | | | | | | | | | | | | | | | | - Andrei Rebarber
- Department of Obstetrics, Gynecology, and Reproductive Science, Mt. Sinai, New York, NY, USA
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9
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Genovese G, Mello CJ, Loh PR, Handsaker RE, Kashin S, Whelan CW, Bayer-Zwirello LA, McCarroll SA. Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions. Sci Rep 2022; 12:12025. [PMID: 35835769 PMCID: PMC9283487 DOI: 10.1038/s41598-022-14049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes—also known as chromosomal phase—to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient’s same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Curtis J Mello
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lucy A Bayer-Zwirello
- Steward St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, 02135, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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10
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Zaninović L, Bašković M, Ježek D, Katušić Bojanac A. Validity and Utility of Non-Invasive Prenatal Testing for Copy Number Variations and Microdeletions: A Systematic Review. J Clin Med 2022; 11:jcm11123350. [PMID: 35743413 PMCID: PMC9224664 DOI: 10.3390/jcm11123350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.
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Affiliation(s)
- Luca Zaninović
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
| | - Marko Bašković
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-3636-379
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
- Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Kišpatićeva 12, 10 000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
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11
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Dar P, Jacobsson B, Clifton R, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Edwards L, Strong N, Haeri S, Silver R, Vohra N, Hyett J, Demko Z, Martin K, Rabinowitz M, Flood K, Carlsson Y, Doulaveris G, Daly S, Hallingström M, MacPherson C, Kao C, Hakonarson H, Norton ME. Cell-free DNA screening for prenatal detection of 22q11.2 deletion syndrome. Am J Obstet Gynecol 2022; 227:79.e1-79.e11. [PMID: 35033576 DOI: 10.1016/j.ajog.2022.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Historically, prenatal screening has focused primarily on the detection of fetal aneuploidies. Cell-free DNA now enables noninvasive screening for subchromosomal copy number variants, including 22q11.2 deletion syndrome (or DiGeorge syndrome), which is the most common microdeletion and a leading cause of congenital heart defects and neurodevelopmental delay. Although smaller studies have demonstrated the feasibility of screening for 22q11.2 deletion syndrome, large cohort studies with confirmatory postnatal testing to assess test performance have not been reported. OBJECTIVE This study aimed to assess the performance of single-nucleotide polymorphism-based, prenatal cell-free DNA screening for detection of 22q11.2 deletion syndrome. STUDY DESIGN Patients who underwent single-nucleotide polymorphism-based prenatal cell-free DNA screening for 22q11.2 deletion syndrome were prospectively enrolled at 21 centers in 6 countries. Prenatal or newborn DNA samples were requested in all cases for genetic confirmation using chromosomal microarrays. The primary outcome was sensitivity, specificity, positive predictive value, and negative predictive value of cell-free DNA screening for the detection of all deletions, including the classical deletion and nested deletions that are ≥500 kb, in the 22q11.2 low-copy repeat A-D region. Secondary outcomes included the prevalence of 22q11.2 deletion syndrome and performance of an updated cell-free DNA algorithm that was evaluated with blinding to the pregnancy outcome. RESULTS Of the 20,887 women enrolled, a genetic outcome was available for 18,289 (87.6%). A total of 12 22q11.2 deletion syndrome cases were confirmed in the cohort, including 5 (41.7%) nested deletions, yielding a prevalence of 1 in 1524. In the total cohort, cell-free DNA screening identified 17,976 (98.3%) cases as low risk for 22q11.2 deletion syndrome and 38 (0.2%) cases as high risk; 275 (1.5%) cases were nonreportable. Overall, 9 of 12 cases of 22q11.2 were detected, yielding a sensitivity of 75.0% (95% confidence interval, 42.8-94.5); specificity of 99.84% (95% confidence interval, 99.77-99.89); positive predictive value of 23.7% (95% confidence interval, 11.44-40.24), and negative predictive value of 99.98% (95% confidence interval, 99.95-100). None of the cases with a nonreportable result was diagnosed with 22q11.2 deletion syndrome. The updated algorithm detected 10 of 12 cases (83.3%; 95% confidence interval, 51.6-97.9) with a lower false positive rate (0.05% vs 0.16%; P<.001) and a positive predictive value of 52.6% (10/19; 95% confidence interval, 28.9-75.6). CONCLUSION Noninvasive cell-free DNA prenatal screening for 22q11.2 deletion syndrome can detect most affected cases, including smaller nested deletions, with a low false positive rate.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY.
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca Clifton
- The Biostatistics Center, George Washington University, Rockville, MD
| | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynaecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY
| | | | - Noel Strong
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, New South Wales, Australia
| | | | | | | | - Karen Flood
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ylva Carlsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Georgios Doulaveris
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY
| | - Sean Daly
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maria Hallingström
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Rockville, MD
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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12
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Leonard SJ. Reproductive genetic screening for information: evolving paradigms? J Perinat Med 2021; 49:998-1002. [PMID: 34448384 DOI: 10.1515/jpm-2021-0353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/26/2022]
Abstract
Reproductive genetic screening has introduced the possibility for pregnant women to learn, during the pregnancy or sometimes earlier, about the likelihood of their baby being affected with certain genetic conditions. As medicine progresses, the options afforded by this early information have expanded. This has led to a shifting paradigm in prenatal screening, wherein the early knowledge is seen as useful not solely for its inherent value to the pregnant woman, but also as enabling an expansion of conditions whose identification may allow early intervention and clinical impact. This article discusses this paradigm against the backdrop of prenatal genetic screening that is available today.
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13
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Bevilacqua E, Jani JC, Chaoui R, Suk EA, Palma‐Dias R, Ko T, Warsof S, Stokowski R, Jones KJ, Grati FR, Schmid M. Performance of a targeted cell-free DNA prenatal test for 22q11.2 deletion in a large clinical cohort. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:597-602. [PMID: 34090308 PMCID: PMC8518527 DOI: 10.1002/uog.23699] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
OBJECTIVE 22q11.2 deletion is more common than trisomies 18 and 13 combined, yet no routine approach to prenatal screening for this microdeletion has been established. This study evaluated the clinical sensitivity and specificity of a targeted cell-free DNA (cfDNA) test to screen for fetal 22q11.2 deletion in a large cohort, using blinded analysis of prospectively enrolled pregnancies and stored clinical samples. METHODS In order to ensure that the analysis included a meaningful number of cases with fetal 22q11.2 deletion, maternal plasma samples were obtained by prospective, multicenter enrolment of pregnancies with a fetal cardiac abnormality and from stored clinical samples from a research sample bank. Fetal genetic status, as evaluated by microarray analysis, karyotyping with fluorescence in-situ hybridization or a comparable test, was available for all cases. Samples were processed as described previously for the Harmony prenatal test, with the addition of DANSR (Digital Analysis of Selected Regions) assays targeting the 3.0-Mb region of 22q11.2 associated with 22q11.2 deletion syndrome. Operators were blinded to fetal genetic status. Sensitivity and specificity of the cfDNA test for 22q11.2 deletion were calculated based on concordance between the cfDNA result and fetal genotype. RESULTS The final study group consisted of 735 clinical samples, including 358 from prospectively enrolled pregnancies and 377 stored clinical samples. Of 46 maternal plasma samples from pregnancies with a 22q11.2 deletion, ranging in size from 1.25 to 3.25 Mb, 32 had a cfDNA result indicating a high probability of 22q11.2 deletion (sensitivity, 69.6% (95% CI, 55.2-80.9%)). All 689 maternal plasma samples without a 22q11.2 deletion were classified correctly by the cfDNA test as having no evidence of a 22q11.2 deletion (specificity, 100% (95% CI, 99.5-100%)). CONCLUSIONS The results of this large-scale prospective clinical evaluation of the sensitivity and specificity of a targeted cfDNA test for fetal 22q11.2 deletion demonstrate that this test can detect the common and smaller, nested 22q11.2 deletions with a low (0-0.5%) false-positive rate. Although the positive predictive value (PPV) observed in this study population was 100%, the expected PPV in the general pregnant population is estimated to be 12.2% at 99.5% specificity and 41.1% at 99.9% specificity. The use of this cfDNA test to screen for 22q11.2 deletion could enhance identification of pregnancies at risk for 22q11.2 deletion syndrome without significantly increasing the likelihood of maternal anxiety and unnecessary invasive procedures related to a false-positive result. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E. Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - J. C. Jani
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - R. Chaoui
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - E.‐K. A. Suk
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - R. Palma‐Dias
- The Royal Women's HospitalUniversity of MelbourneParkvilleVICAustralia
| | - T.‐M. Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics & Gynecology ClinicTaipei CityTaiwan
| | - S. Warsof
- Eastern Virginia Medical SchoolNorfolkVAUSA
| | | | - K. J. Jones
- Roche Sequencing Solutions, Inc.San JoseCAUSA
| | - F. R. Grati
- TOMA Advanced Biomedical Assays S.p.A, Impact Lab.Busto ArsizioItaly
| | - M. Schmid
- Roche Sequencing Solutions, Inc.San JoseCAUSA
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14
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Bajka A, Bajka M, Chablais F, Burkhardt T. Audit of the first > 7500 noninvasive prenatal aneuploidy tests in a Swiss genetics center. Arch Gynecol Obstet 2021; 305:1185-1192. [PMID: 34533609 PMCID: PMC9013335 DOI: 10.1007/s00404-021-06203-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 08/20/2021] [Indexed: 11/29/2022]
Abstract
Objectives Noninvasive prenatal testing (NIPT) is actually the most accurate method of screening for fetal chromosomal aberration (FCA). We used pregnancy outcome record to evaluate a complete data set of single nucleotide polymorphism-based test results performed by a Swiss genetics center. Materials and methods The Panorama® test assesses the risk of fetal trisomies (21, 18 and 13), gonosomal aneuploidy (GAN), triploidy or vanishing twins (VTT) and five different microdeletions (MD). We evaluated all 7549 test results meeting legal and quality requirements taken in women with nondonor singleton pregnancies between April 2013 and September 2016 classifying them as high or low risk. Follow-up ended after 9 months, data collection 7 months later. Results The Panorama® test provided conclusive results in 96.1% of cases, detecting 153 FCA: T21 n = 76, T18 n = 19, T13 n = 15, GAN n = 19, VTT n = 13 and MD n = 11 (overall prevalence 2.0%). Pregnancy outcome record was available for 68.6% of conclusive laboratory results, including 2.0% high-risk cases. In this cohort the Panorama® test exhibited 99.90% sensitivity for each trisomy; specificity was 99.90% for T21, 99.98% for T18 and 99.94% for T13. False positive rate was 0.10% for T21, 0.02% for T18 and 0.06% for T13. Conclusion SNP-based testing by a Swiss genetics center confirms the expected accuracy of NIPT in FCA detection.
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Affiliation(s)
- Anahita Bajka
- Department of Obstetrics, University Hospital Zurich, Frauenklinikstr. 10, 8091, Zurich, Switzerland
| | - Michael Bajka
- Department of Gynecology, University Hospital of Zurich, Zurich, Switzerland
| | - Fabian Chablais
- Genetica, Human Genetics and Genetic Counselling Unit, 8001, Zurich, Switzerland
| | - Tilo Burkhardt
- Department of Obstetrics, University Hospital Zurich, Frauenklinikstr. 10, 8091, Zurich, Switzerland.
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15
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Lin TY, Hsieh TT, Cheng PJ, Hung TH, Chan KS, Tsai C, Shaw SW. Taiwanese Clinical Experience with Noninvasive Prenatal Testing for DiGeorge Syndrome. Fetal Diagn Ther 2021; 48:672-677. [PMID: 34569534 DOI: 10.1159/000519057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVE DiGeorge syndrome (DGS) is associated with microdeletions of chromosome 22q11. It is the second most common cause of congenital heart disease and is an important consideration whenever a conotruncal cardiac anomaly is identified. The availability of noninvasive prenatal testing (NIPT) is altering the practice of prenatal genetics and maternal-fetal medicine, resulting in a decline in invasive testing. Antenatal ultrasound and other biomarkers have their own limitation. NIPT was proposed to screen DGS with cell-free DNA in Taiwan. Here, we present our experience of prenatal diagnosis of DGS in our center. METHODS This was a retrospective study between November 1, 2019, and August 31, 2020, in Taiwan. Data were collected from 7,826 pregnant women self-referred for DGS screening with massive parallel shotgun sequencing-based NIPT. High-risk cases subsequently received amniocentesis for array comparative genomic hybridization (aCGH) to confirm the diagnosis. Characteristics of pregnancies were documented when participants received the test. Report of NIPT was completed 2 weeks after the test. Follow-up on high-risk cases was completed by telephone interview on January 30, 2021. RESULTS Thirteen cases showed high risk by NIPT, and 7 cases were confirmed by aCGH. The sensitivity and specificity were 100% (95% confidence interval [CI] 64.57-100.00%) and 99.92% (95% CI 99.83-99.96%). The prevalence of DGS was 1 in 1,118 pregnancies. The positive predictive rate was 53.85% (95% CI 29.14-76.79%). One true positive (TP) showed US anomaly, and 5 TPs selected termination. DISCUSSION/CONCLUSION NIPT demonstrated good performance in DGS screening. Detection of 22q11.2 deletion could be combined with routine screening to facilitate proper intervention.
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Affiliation(s)
- Tzu-Yi Lin
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - T'sang-T'ang Hsieh
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Po-Jen Cheng
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tai-Ho Hung
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Kok-Seong Chan
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | | | - Steven W Shaw
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan.,Prenatal Cell and Gene Therapy Group, Institute for Women's Health University College London, London, United Kingdom
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Bianco K, Sherwin EB, Konigshofer Y, Girsen AI, Sylvester KG, Garlick RK. Novel Approaches to Develop Critical Reference Materials for Noninvasive Prenatal Testing: A Pilot Study. J Appl Lab Med 2021; 6:1492-1504. [PMID: 34080621 DOI: 10.1093/jalm/jfab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Highly characterized reference materials are required to expand noninvasive prenatal testing (NIPT) for low incidence aneuploidies and microdeletions. The goal of this study was to develop reference materials for the development of next generation circulating cell-free DNA (ccfDNA) assays. METHODS This was a prospective study of pregnancies complicated by positive prenatal genetic screening. ccfDNA was isolated from maternal plasma and amplified. Lymphoblastoid cell lines were prepared from maternal peripheral blood mononuclear cells and fetal cord blood cells. Cells were Epstein-Barr virus immortalized and expanded. Amplified DNA and to a limited extent formulated lymphoblastoid-derived ccfDNA was tested in SNP-based and chromosome counting (CC) based massively parallel sequencing assays. RESULTS Enrolled cases included fetuses with: T21 (2), T18 (1), T18-XXX (1), XYY (1), microdeletions (1), and euploid (2). Three lymphoblastoid cells lines were prepared. Genomic DNA was extracted from cell lines and fragmented to simulate ccfDNA. ccfDNA isolation yielded about 2000 usable genome equivalents of DNA for each case for amplification. Although the sonicated genomic DNA derived from lymphoblastoid cell lines did not yield results compatible with NIPT assays, when blinded, NIPT platforms correctly identified the amplified ccfDNA isolated from blood in the majority of cases. CONCLUSIONS This study showed that maternal blood samples from pregnancies complicated by common chromosomal abnormalities can be used to generate materials for the development and evaluation of NIPT assays.
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Affiliation(s)
- Katherine Bianco
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth B Sherwin
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anna I Girsen
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Karl G Sylvester
- Division of Pediatric Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
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17
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Bedei I, Wolter A, Weber A, Signore F, Axt-Fliedner R. Chances and Challenges of New Genetic Screening Technologies (NIPT) in Prenatal Medicine from a Clinical Perspective: A Narrative Review. Genes (Basel) 2021; 12:501. [PMID: 33805390 PMCID: PMC8065512 DOI: 10.3390/genes12040501] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has been applied since the 1960s by using maternal age as the risk parameter. Since then, several advances have been made. First trimester screening, combining maternal age, maternal serum parameters and ultrasound findings, emerged in the 1990s with a detection rate (DR) of around 90-95% and a false positive rate (FPR) of around 5%, also looking for trisomy 13 and 18. With the development of high-resolution ultrasound, around 50% of fetal anomalies are now detected in the first trimester. Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012, in some countries without a systematic screening program. Concomitant with the rise in technology, the possibility of screening for other genetic conditions by analysis of cfDNA, such as sex chromosome anomalies (SCAs), rare autosomal anomalies (RATs) and microdeletions and duplications, is offered by different providers to an often not preselected population of pregnant women. Most of the research in the field is done by commercial providers, and some of the tests are on the market without validated data on test performance. This raises difficulties in the counseling process and makes it nearly impossible to obtain informed consent. In parallel with the advent of new screening technologies, an expansion of diagnostic methods has begun to be applied after invasive procedures. The karyotype has been the gold standard for decades. Chromosomal microarrays (CMAs) able to detect deletions and duplications on a submicroscopic level have replaced the conventional karyotyping in many countries. Sequencing methods such as whole exome sequencing (WES) and whole genome sequencing (WGS) tremendously amplify the diagnostic yield in fetuses with ultrasound anomalies.
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Affiliation(s)
- Ivonne Bedei
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Aline Wolter
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Axel Weber
- Institute of Human Genetics, Justus Liebig University Giessen, 35392 Giessen, Germany;
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Opedale S. Eugenio, 00144 Rome, Italy;
| | - Roland Axt-Fliedner
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
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18
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Zhu X, Chen M, Wang H, Guo Y, Chau MHK, Yan H, Cao Y, Kwok YKY, Chen J, Hui ASY, Zhang R, Meng Z, Zhu Y, Leung TY, Xiong L, Kong X, Choy KW. Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:459-465. [PMID: 32198896 DOI: 10.1002/uog.22021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies. METHODS This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results. RESULTS Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result. CONCLUSION CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- X Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - H Wang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Guo
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M H K Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - H Yan
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Y Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Y K Y Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - J Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - A S Y Hui
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - R Zhang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Z Meng
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Zhu
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - T Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - L Xiong
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
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Welker NC, Lee AK, Kjolby RAS, Wan HY, Theilmann MR, Jeon D, Goldberg JD, Haas KR, Muzzey D, Chu CS. High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening. Genet Med 2020; 23:443-450. [PMID: 33190143 PMCID: PMC7935715 DOI: 10.1038/s41436-020-01009-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Purpose The percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%). Methods A scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)–based NIPS. All samples were tested with and without FFA. Results Zero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity. Conclusion FFA transforms low-FF samples into high-FF samples. By combining FFA with WGS–based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.
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Affiliation(s)
| | - Albert K Lee
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Helen Y Wan
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Diana Jeon
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Kevin R Haas
- Myriad Women's Health, South San Francisco, CA, USA
| | - Dale Muzzey
- Myriad Women's Health, South San Francisco, CA, USA.
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20
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Kagan KO, Hoopmann M, Pfaff T, Prodan N, Wagner P, Schmid M, Dufke A, Mau-Holzmann U, Brucker S, Marcato L, Malvestiti B, Grati FR. First Trimester Screening for Common Trisomies and Microdeletion 22q11.2 Syndrome Using Cell-Free DNA: A Prospective Clinical Study. Fetal Diagn Ther 2020; 47:841-852. [PMID: 32877902 DOI: 10.1159/000510069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/08/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aims of the study were to assess the false-positive and uninformative test rate with first trimester cell-free DNA (cfDNA) screening for common trisomies and microdeletion 22q11.2 (22q11.2DS) and to examine women's attitudes toward such an approach. METHODS This is a prospective study at the Prenatal Medicine Department of the University of Tübingen, Germany, at 11-13 weeks. In all pregnancies, a detailed ultrasound examination was carried out, followed by a cfDNA analysis for common trisomies and 22q11.2DS. In cases where the cfDNA analysis indicated 22q11.2DS, invasive prenatal diagnostic testing and parental testing were performed. After delivery, a detailed neonatal clinical examination was carried out including further genetic testing. Prior to counselling about the study, we asked the pregnant women who were potentially eligible for the study to anonymously report on their knowledge about 22q11.2DS. RESULTS A total of 1,127 pregnancies were included in the final analysis of the study. The first cfDNA test was uninformative in 15 (1.33%) pregnancies. In 10 (0.89%) cases, the test remained uninformative, even after the second blood sample. There were 3 (0.27%) cases with a positive cfDNA test for 22q11.2DS. In all, 983 women returned the anonymous questionnaire prior to study participation. Only 80 (8.1%) women responded that they felt familiar or very familiar with 22q11.2DS. CONCLUSION The addition of 22q11.2DS in first trimester cfDNA screening for common trisomies is feasible. The uninformative test rate for common trisomies and 22q11.2DS is 0.9%, and the false-positive rate for 22q11.2DS is 0.3%. Awareness and education around 22q11.2DS should be improved.
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Affiliation(s)
- Karl Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany,
| | - Markus Hoopmann
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Theresa Pfaff
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Natalia Prodan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Philipp Wagner
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Maximilian Schmid
- Roche Sequencing Solutions Inc., Ariosa Diagnostics Inc., San Jose, California, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ulrike Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sara Brucker
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Livia Marcato
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Barbara Malvestiti
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Francesca Romana Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
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21
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Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions. PLoS One 2020; 15:e0238245. [PMID: 32845907 PMCID: PMC7449492 DOI: 10.1371/journal.pone.0238245] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
To study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes. We used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts. The in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples. Our results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors.
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22
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Current Status of Noninvasive Prenatal Testing and Counselling Considerations: An Indian Perspective. JOURNAL OF FETAL MEDICINE 2020. [DOI: 10.1007/s40556-019-00228-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Du Q, de la Morena MT, van Oers NSC. The Genetics and Epigenetics of 22q11.2 Deletion Syndrome. Front Genet 2020; 10:1365. [PMID: 32117416 PMCID: PMC7016268 DOI: 10.3389/fgene.2019.01365] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.
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Affiliation(s)
- Qiumei Du
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - M. Teresa de la Morena
- Department of Pediatrics, The University of Washington and Seattle Children’s Hospital, Seattle, WA, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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24
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Sullivan KE. Chromosome 22q11.2 deletion syndrome and DiGeorge syndrome. Immunol Rev 2019; 287:186-201. [PMID: 30565249 DOI: 10.1111/imr.12701] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
Abstract
Chromosome 22q11.2 deletion syndrome is the most common microdeletion syndrome in humans. The effects are protean and highly variable, making a unified approach difficult. Nevertheless, commonalities have been identified and white papers with recommended evaluations and anticipatory guidance have been published. This review will cover the immune system in detail and discuss both the primary features and the secondary features related to thymic hypoplasia. A brief discussion of the other organ system involvement will be provided for context. The immune system, percolating throughout the body can impact the function of other organs through allergy or autoimmune disease affecting organs in deleterious manners. Our work has shown that the primary effect of thymic hypoplasia is to restrict T cell production. Subsequent homeostatic proliferation and perhaps other factors drive a Th2 polarization, most obvious in adulthood. This contributes to atopic risk in this population. Thymic hypoplasia also contributes to low regulatory T cells and this may be part of the overall increased risk of autoimmunity. Collectively, the effects are complex and often age-dependent. Future goals of improving thymic function or augmenting thymic volume may offer a direct intervention to ameliorate infections, atopy, and autoimmunity.
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Affiliation(s)
- Kathleen E Sullivan
- The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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25
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Chau MHK, Cao Y, Kwok YKY, Chan S, Chan YM, Wang H, Yang Z, Wong HK, Leung TY, Choy KW. Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis. Am J Obstet Gynecol 2019; 221:493.e1-493.e11. [PMID: 31207233 DOI: 10.1016/j.ajog.2019.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution, and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications. OBJECTIVES The aim was to investigate the spectrum and characteristics of pathogenic copy number variants in prenatal genetic diagnosis and to provide recommendations for expanding the scope of noninvasive prenatal screening for microdeletions and microduplications. STUDY DESIGN This was a retrospective study of 1510 pregnant women who underwent invasive prenatal diagnostic testing by chromosomal microarray analysis. Prenatal samples were retrieved by amniocentesis or chorionic villus sampling and sent to our prenatal genetic diagnosis laboratory for chromosomal microarray analysis. The risk of carrying a fetus with pathogenic copy number variants is stratified by the patients' primary indication for invasive testing. We searched the literature for published prenatal chromosomal microarray data to generate a large cohort of 23,865 fetuses. The characteristics and spectrum of pathogenic copy number variants including the type of aberrations (gains or losses), genomic loci, sizes, and the mode of inheritance were studied. RESULTS Overall, 375 of 23,865 fetuses (1.6%) carried pathogenic copy number variants for any indication for invasive testing, and 44 of them (11.7%) involve 2 or more pathogenic copy number variants. A total of 428 pathogenic copy number variants were detected in these fetuses, of which 280 were deletions and 148 were duplications. Three hundred sixty (84.1%) were less than 5 Mb in size and 68 (15.9%) were between 5 and 10 Mb. The incidence of carrying a pathogenic copy number variant in the high-risk group is 1 in 36 and the low-risk group is 1 in 125. Parental inheritance study results were available for 311 pathogenic copy number variants, 71 (22.8%) were maternally inherited, 36 (11.6%) were paternally inherited, and 204 (65.6%) occurred de novo. CONCLUSION Collectively, pathogenic copy number variants are common in pregnancies. High-risk pregnancies should be offered invasive testing with chromosomal microarray analysis for the most comprehensive investigation. Detection limits on size, parental inheritance, and genomic distribution should be carefully considered before implementing copy number variant screening in expanded noninvasive prenatal screening.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne Ka Yin Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Samantha Chan
- Warwick Medical School at the University of Warwick, Coventry, United Kingdom
| | - Yiu Man Chan
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Huilin Wang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Department of Central Laboratory, Bao'an Maternity and Child Healthcare Hospital, Jinan University School of Medicine, Key Laboratory of Birth Defects Research, Birth Defects Prevention Research, and Transformation Team, Shenzhen, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Zhenjun Yang
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hoi Kin Wong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China; The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China.
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26
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DiNonno W, Demko Z, Martin K, Billings P, Egbert M, Zneimer S, Keen-Kim D, Benn P. Quality Assurance of Non-Invasive Prenatal Screening (NIPS) for Fetal Aneuploidy Using Positive Predictive Values as Outcome Measures. J Clin Med 2019; 8:jcm8091311. [PMID: 31454954 PMCID: PMC6780279 DOI: 10.3390/jcm8091311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/28/2022] Open
Abstract
Non-invasive prenatal screening (NIPS) based on the analysis of cell-free DNA in maternal plasma has been shown to have high sensitivity and specificity. We gathered follow-up information for pregnancies in women with test-positive NIPS results from 2014–2017 with quarterly assessments of positive predictive values (PPVs). A non-inferiority analysis with a minimum requirement of 70%/80% of expected performance for trisomy 21 and 18 was used to ensure testing met expectations. PPVs were evaluated in the context of changes in the population receiving testing. For all quarters, PPVs for trisomies 21 and 18 exceeded the requirement of > 70% of the reference PPV. Overall observed PPVs for trisomy 21, 18, 13 and monosomy X were similar for women aged <35 (90.9%, 95% Confidence Interval (CI) 88.6–92.7%) compared to women with advanced maternal age (94.5%, 95% CI 93.1–95.6%). Despite significant declines in test-positive rates from 1.18% to 0.62% for trisomy 21, and from 0.75% to 0.48% for trisomies 18, 13 and monosomy X combined, PPVs remained stable through the four-year interval. We conclude that quarterly evaluation of PPV provides an overview of past testing and helps demonstrate long-term consistency in test performance, even in the setting of increasing use by women with lower a priori risks.
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Affiliation(s)
| | | | | | | | | | | | | | - Peter Benn
- UConn Health, Farmington, CT 06030, USA.
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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Norwitz ER, McNeill G, Kalyan A, Rivers E, Ahmed E, Meng L, Vu P, Egbert M, Shapira M, Kobara K, Parmar S, Goel S, Prins SA, Aruh I, Persico N, Robins JC, Kirshon B, Demko ZP, Ryan A, Billings PR, Rabinowitz M, Benn P, Martin KA, Hedriana HL. Validation of a Single-Nucleotide Polymorphism-Based Non-Invasive Prenatal Test in Twin Gestations: Determination of Zygosity, Individual Fetal Sex, and Fetal Aneuploidy. J Clin Med 2019; 8:E937. [PMID: 31261782 PMCID: PMC6679081 DOI: 10.3390/jcm8070937] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 12/19/2022] Open
Abstract
We analyzed maternal plasma cell-free DNA samples from twin pregnancies in a prospective blinded study to validate a single-nucleotide polymorphism (SNP)-based non-invasive prenatal test (NIPT) for zygosity, fetal sex, and aneuploidy. Zygosity was evaluated by looking for either one or two fetal genome complements, fetal sex was evaluated by evaluating Y-chromosome loci, and aneuploidy was assessed through SNP ratios. Zygosity was correctly predicted in 100% of cases (93/93; 95% confidence interval (CI) 96.1%-100%). Individual fetal sex for both twins was also called with 100% accuracy (102/102; 95% weighted CI 95.2%-100%). All cases with copy number truth were also correctly identified. The dizygotic aneuploidy sensitivity was 100% (10/10; 95% CI 69.2%-100%), and overall specificity was 100% (96/96; 95% weighted CI, 94.8%-100%). The mean fetal fraction (FF) of monozygotic twins (n = 43) was 13.0% (standard deviation (SD), 4.5%); for dizygotic twins (n = 79), the mean lower FF was 6.5% (SD, 3.1%) and the mean higher FF was 8.1% (SD, 3.5%). We conclude SNP-based NIPT for zygosity is of value when chorionicity is uncertain or anomalies are identified. Zygosity, fetal sex, and aneuploidy are complementary evaluations that can be carried out on the same specimen as early as 9 weeks' gestation.
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Affiliation(s)
- Errol R Norwitz
- Tufts Medical Center and Tufts University School of Medicine, Boston, MA 02111, USA
| | | | | | | | | | - Ling Meng
- Natera, Inc., San Carlos, CA 94070, USA
| | | | | | | | | | | | | | | | - Israel Aruh
- Dr. Israel Aruh's IVF and Infertility Clinic, 35220 Izmir, Turkey
| | | | - Jared C Robins
- Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian Kirshon
- Houston Perinatal Associates, Houston, TX 77054, USA
| | | | | | | | | | | | | | - Herman L Hedriana
- Natera, Inc., San Carlos, CA 94070, USA.
- University of California Davis Health, Sacramento, CA 95819, USA.
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Noninvasive Prenatal Testing for Trisomies 21, 18, and 13, Sex Chromosome Aneuploidies, and Microdeletions: A Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2019; 19:1-166. [PMID: 30847010 PMCID: PMC6395059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND Pregnant people have a risk of carrying a fetus affected by a chromosomal anomaly. Prenatal screening is offered to pregnant people to assess their risk. Noninvasive prenatal testing (NIPT) has been introduced clinically, which uses the presence of circulating cell-free fetal DNA in the maternal blood to quantify the risk of a chromosomal anomaly. At the time of writing, NIPT is publicly funded in Ontario for pregnancies at high risk of a chromosomal anomaly. METHODS We completed a health technology assessment, which included an evaluation of clinical benefits and harms, value for money, budget impact, and patient preferences related to NIPT. We performed a systematic literature search for studies on NIPT for trisomies 21, 18, and 13, sex chromosome aneuploidies, and microdeletions in the average-risk or general population. We evaluated the cost-effectiveness of traditional prenatal screening, NIPT as a second-tier test (performed after traditional prenatal screening), and NIPT as a first-tier test (performed instead of traditional prenatal screening). We also conducted a budget impact analysis to estimate the additional costs of funding first-tier NIPT. We interviewed people who had lived experience with NIPT and people living with the conditions NIPT screens for, or their families. RESULTS The pooled clinical sensitivity of NIPT in the average-risk or general population was 99.5% (95% confidence interval [CI] 81.8%-99.9%) for trisomy 21, 93.1% (95% CI 75.9%-98.3%) for trisomy 18, and 92.7% (95% CI 81.6%-99.9%) for trisomy 13. The clinical specificity for any trisomy was 99.9% (95% CI 99.8%-99.9%). Compared with traditional prenatal screening, NIPT was more accurate in detecting trisomies 21, 18, and 13, and decreased the need for diagnostic testing. We found limited evidence on NIPT for sex chromosome aneuploidies or microdeletions in the average-risk or general population. Positive NIPT results should be confirmed by diagnostic testing.Compared with traditional prenatal screening, second-tier NIPT detected more affected fetuses, substantially reduced the number of diagnostic tests performed, and slightly reduced the total cost of prenatal screening. Compared with second-tier NIPT, first-tier NIPT detected more affected cases, but also led to more diagnostic tests and additional budget of $35 million per year for average-risk pregnant people in Ontario.People who had undergone NIPT were largely supportive of the test and the benefits of earlier, more accurate results. However, many discussed the need for improved pre- and post-test counselling and raised concerns about the quality of the information they received from health care providers about the conditions NIPT can screen for. CONCLUSIONS NIPT is an effective and safe prenatal screening method for trisomies 21, 18, and 13 in the average-risk or general population. Compared with traditional prenatal screening, second-tier NIPT improved the overall performance of prenatal screening and slightly decreased costs. Compared with second-tier NIPT, first-tier NIPT detected more chromosomal anomalies, but resulted in a considerable increase in the total budget. Interviewees were generally positive about NIPT, but they raised concerns about the lack of good informed-choice conversations with primary care providers and the quality of the information they received from health care providers about chromosomal anomalies.
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Grati FR, Gross SJ. Noninvasive screening by cell-free DNA for 22q11.2 deletion: Benefits, limitations, and challenges. Prenat Diagn 2019; 39:70-80. [PMID: 30625249 DOI: 10.1002/pd.5391] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022]
Abstract
Cell-free DNA (cfDNA) testing for fetal aneuploidy is one of the most important technical advances in prenatal care. Additional chromosome targets beyond common aneuploidies, including the 22q11.2 microdeletion, are now available because of this clinical testing technology. While there are numerous potential benefits, 22q11.2 microdeletion screening using cfDNA testing also presents significant limitations and pitfalls. Practitioners who are offering this test should provide comprehensive pretest and posttest prenatal counselling. The discussion should include the possibility of an absence of a result, as well as the risk of possible discordance between cfDNA screening results and the actual fetal genetic chromosomal constitution. The goal of this review is to provide an overview of the cfDNA testing technologies for 22q11.2 microdeletions screening, describe the current state of test validation and clinical experience, review "no results" and discordant findings based on differing technologies, and discuss management options.
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Affiliation(s)
- Francesca Romana Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Busto Arsizio (Varese), Italy
| | - Susan J Gross
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
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