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Li K, Guo Z, Li F, Lu S, Zhang M, Gong Y, Tan J, Sheng C, Hao W, Yang X. Non-invasive determination of gene expression in placental tissue using maternal plasma cell-free DNA fragmentation characters. Gene 2024; 928:148789. [PMID: 39047956 DOI: 10.1016/j.gene.2024.148789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND The expression profiles of placental genes are crucial for understanding the pathogenesis of fetal development and placental-origin pregnancy syndromes. However, owing to ethical limitations and the risks of puncture sampling, it is difficult to obtain placental tissue samples repeatedly, continuously, multiple times, or in real time. Establishing a non-invasive method for predicting placental gene expression profiles through maternal plasma cell-free DNA (cfDNA) sequencing, which carries information about the source tissue and gene expression, can potentially solve this problem. METHODS Peripheral blood and placental samples were collected simultaneously from pregnant women who underwent cesarean section. Deep sequencing was performed on the separated plasma cfDNA and single-cell sequencing was performed on peripheral blood mononuclear cells (PBMC), chorioamniotic membranes (CAM), placental villi (PV), and decidua basalis (DB). The aggregation of corresponding information for each gene was combined with the transcriptome of PBMCs and a differential resolution transcriptome of the placenta. This combined information was then utilized for the construction of gene expression prediction models. After training, all models evaluated the correlation between the predicted and actual gene expression levels using external test set data. RESULTS From five women, more than 20 million reads were obtained using deep sequencing for plasma cfDNA; PBMCs obtained 32,401 single-cell expression profiles; and placental tissue obtained 156,546 single-cell expression profiles (59,069, 44,921, and 52,556 for CAM, PV, and DB, respectively). The cells in the PBMC and placenta were clustered and annotated into five and eight cell types, respectively. A "DEPICT" gene expression prediction model was successfully constructed using deep neural networks. The predicted correlation coefficients were 0.75 in PBMCs, 0.84 in the placenta, and 0.78, 0.80, and 0.77 in CAM, BP, and PV respectively, and greater than 0.68 in different cell lines in the placenta. CONCLUSION The DEPICT model, which can noninvasively predict placental gene expression profiles based on maternal plasma cfDNA fragmentation characteristics, was constructed to overcome the limitation of the inability to obtain real-time placental gene expression profiles and to improve research on noninvasive prediction of placental origin pregnancy syndrome.
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Affiliation(s)
- Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Zhiwei Guo
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Fenxia Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Shijing Lu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Min Zhang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yuyan Gong
- Beijing SeekGene BioSciences Co., Ltd, Beijing, China
| | - Jiayu Tan
- ICU of Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan 528403, China
| | - Chao Sheng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Wenbo Hao
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China.
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Faieta M, Falcone R, Duca S, Corsetti E, Giannico R, Gigante L, Diano L, Calugi G, Spinella F, Pizzuti F. Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center. Prenat Diagn 2024; 44:936-945. [PMID: 38686956 DOI: 10.1002/pd.6580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation. METHOD In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes. RESULTS Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected. CONCLUSIONS Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.
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Affiliation(s)
- Monica Faieta
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | - Rossella Falcone
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Sara Duca
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | | | | | - Laura Gigante
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Laura Diano
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Graziella Calugi
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
| | - Francesca Spinella
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
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Lund ICB, Becher N, Lildballe D, Andreasen L, Horsholt Thomsen S, Vestergaard EM, Vogel I. Use of cell-free non-invasive prenatal testing in pregnancies affected by placental mosaicism. Prenat Diagn 2024; 44:562-571. [PMID: 38520498 DOI: 10.1002/pd.6558] [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: 09/05/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
OBJECTIVE To evaluate cell-free non-invasive prenatal testing (cfNIPT) in pregnancies affected by mosaicism. METHOD We assessed paired cfNIPT and chorionic villus sample (CVS) results from the same pregnancies in a case series of mosaicism detected in Central and North Denmark Regions from April 2014 to September 2018. Indications for the clinically obtained CVS, pregnancy markers and outcome were retrieved from The Danish Fetal Medicine Database. RESULTS Mosaicisms in CVS involved common aneuploidy, n = 14; sex chromosomal aneuploidies, n = 14; rare autosomal trisomies (RATs), n = 16 and copy number variants (CNVs) >5Mb, n = 9. Overall, 24/53 (45.3%; CI 95%: 31.8%-59.4%) of cases with mosaicism were detected by cfNIPT; highest for RATs (56%) and lowest for CNVs (22%). CfNIPT more commonly detected high-level than low-level mosaic cases (p = 0.000). CfNIPT detected 7/16 (43.8%; CI 95%: 21%-69%) clinically significant mosaic cases, either true fetal mosaicism or confined placental mosaicisms with adverse pregnancy outcome. There was a trend toward a higher risk for adverse outcome in pregnancies where mosaicism was detected by cfNIPT compared to pregnancies where mosaicism was not detected by cfNIPT (p = 0.31). CONCLUSION CfNIPT has a low detection rate of mosaicism, including pregnancies with clinically significant mosaicism. However, abnormal cfNIPT results may be a predictor of adverse pregnancy outcomes.
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Affiliation(s)
- Ida Charlotte Bay Lund
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Naja Becher
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Dorte Lildballe
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lotte Andreasen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Horsholt Thomsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Else Marie Vestergaard
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Clinical Biochemistry, Horsens Regional Hospital, Horsens, Denmark
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
- Center for Fetal Diagnostics, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus, Denmark
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Chen CP. Genetic counseling of non-invasive prenatal testing (NIPT) trisomy 7-positive pregnancies. Taiwan J Obstet Gynecol 2024; 63:293-296. [PMID: 38802190 DOI: 10.1016/j.tjog.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/29/2024] Open
Abstract
Trisomy 7 is the most common observed type of rare autosomal trisomies (RATs) detected at expanded genome-wide non-invasive prenatal testing (NIPT). Genetic counseling of NIPT trisomy 7-positive pregnancies remains to be not easy because the parents may worry about the likelihood of adverse pregnancy outcomes, fetal abnormality and the necessity of invasive procedures for confirmation of fetal mosaic trisomy 7 and uniparental disomy (UPD) 7. This review provides a comprehensive information on the update issues concerning genetic counseling of NIPT trisomy 7-positive pregnancies.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
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Pedrola Vidal L, Roselló Piera M, Martín-Grau C, Rubio Moll JS, Gómez Portero R, Marcos Puig B, Cervera Zamora JV, Quiroga R, Orellana Alonso C. Prenatal Genome-Wide Cell-Free DNA Screening: Three Years of Clinical Experience in a Hospital Prenatal Diagnostic Unit in Spain. Genes (Basel) 2024; 15:568. [PMID: 38790198 PMCID: PMC11121632 DOI: 10.3390/genes15050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Genome-wide prenatal cell-free DNA (cfDNA) screening can be used to screen for a wide range of fetal chromosomal anomalies in pregnant patients. In this study, we describe our clinical experience with a genome-wide cfDNA assay in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RAAs), and copy-number variations (CNVs) in about 6000 patients over a three-year period at our hospital's Prenatal Diagnostic Unit in Spain. Overall, 204 (3.3%) patients had a high-risk call, which included 76 trisomy 21, 21 trisomy 18, 7 trisomy 13, 29 SCAs, 31 RAAs, 31 CNVs, and 9 cases with multiple anomalies. The diagnostic outcomes were obtained for the high-risk cases when available, allowing for the calculation of positive predictive values (PPVs). Calculated PPVs were 95.9% for trisomy 21, 77.8% for trisomy 18, 66.7% for trisomy 13, 10.7% for RAAs, and 10.7% for CNVs. Pregnancy and birth outcomes were also collected for the majority of RAA and CNV cases. Adverse perinatal outcomes for some of these cases included preeclampsia, fetal growth restriction, preterm birth, reduced birth weight, and major congenital structural abnormalities. In conclusion, our study showed strong performance for genome-wide cfDNA screening in a large cohort of pregnancy patients in Spain.
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Affiliation(s)
- Laia Pedrola Vidal
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (L.P.V.); (J.V.C.Z.); (C.O.A.)
| | - Mónica Roselló Piera
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (L.P.V.); (J.V.C.Z.); (C.O.A.)
| | - Carla Martín-Grau
- Translational Genetics Research Group, Instituto de Investigación Sanitaria La Fe (IISLAFE), 46026 Valencia, Spain;
| | - Juan S. Rubio Moll
- Obstetrics and Gynecology Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (J.S.R.M.); (R.G.P.); (B.M.P.); (R.Q.)
| | - Rosa Gómez Portero
- Obstetrics and Gynecology Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (J.S.R.M.); (R.G.P.); (B.M.P.); (R.Q.)
| | - Beatriz Marcos Puig
- Obstetrics and Gynecology Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (J.S.R.M.); (R.G.P.); (B.M.P.); (R.Q.)
| | - Jose V. Cervera Zamora
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (L.P.V.); (J.V.C.Z.); (C.O.A.)
| | - Ramiro Quiroga
- Obstetrics and Gynecology Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (J.S.R.M.); (R.G.P.); (B.M.P.); (R.Q.)
| | - Carmen Orellana Alonso
- Genetics Unit, Hospital Universitari i Politècnic La Fe, 46026 Valencia, Spain; (L.P.V.); (J.V.C.Z.); (C.O.A.)
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Soster E, Mossfield T, Menezes M, Agenbag G, Dubois ML, Gekas J, Hardy T, Loggenberg K. Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium. Mol Cytogenet 2024; 17:9. [PMID: 38627791 PMCID: PMC11021009 DOI: 10.1186/s13039-024-00677-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Trisomy 20 has been shown to be one of the most frequent rare autosomal trisomies in patients that undergo genome-wide noninvasive prenatal testing. Here, we describe the clinical outcomes of cases that screened positive for trisomy 20 following prenatal genome-wide cell-free (cf.) DNA screening. These cases are part of a larger cohort of previously published cases. Members of the Global Expanded NIPT Consortium were invited to submit details on their cases with a single rare autosomal aneuploidy following genome-wide cfDNA screening for retrospective analysis. Clinical details including patient demographics, test indications, diagnostic testing, and obstetric pregnancy outcomes were collected. Genome-wide cfDNA screening was conducted following site-specific laboratory procedures. Cases which screened positive for trisomy 20 (n = 10) were reviewed. Clinical outcome information was available for 90% (9/10) of our screen-positive trisomy 20 cases; the case without diagnostic testing ended in a fetal demise. Of the nine cases with outcome information, one was found to have a mosaic partial duplication (duplication at 20p13), rather than a full trisomy 20. Only one case in the study cohort had placental testing; therefore, confined placental mosaicism could not be ruled out in most cases. Adverse pregnancy outcomes were seen in half of the cases, which could suggest the presence of underlying confined placental mosaicism or mosaic/full fetal trisomy 20. Based on our limited series, the likelihood of true fetal aneuploidy is low but pregnancies may be at increased risk for adverse obstetric outcomes and may benefit from additional surveillance.
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Affiliation(s)
- Erica Soster
- Labcorp, 3400 Computer Drive, Westborough, MA, 01581, USA.
| | | | - Melody Menezes
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | - Jean Gekas
- Department of Medical Genetics, CHU de Quebec Research and Mother and Child Center, University Hospital of Quebec, Laval University, Quebec City, QC, Canada
| | - Tristan Hardy
- SA Pathology, Adelaide, SA, 5000, Australia
- Monash IVF Group, Melbourne, Victoria, Australia
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Donze SH, Srebniak MI, Diderich KEM, van den Born M, Galjaard RJ, Govaerts LCP, van der Schoot V, Knapen MFCM, Joosten M, Van Opstal D. Limited additional value of karyotyping cultured amniotic fluid cell colonies in addition to microarray on uncultured cells for confirmation of abnormal non-invasive prenatal testing results. Prenat Diagn 2024; 44:401-408. [PMID: 38141050 DOI: 10.1002/pd.6499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
OBJECTIVES Non-invasive prenatal testing (NIPT) allows the detection of placental chromosome aberrations. To verify whether the fetus also has the chromosome aberration, diagnostic follow-up testing is required. The aim of this retrospective study was to assess the added value of analyzing amniotic fluid (AF) cell cultures in addition to uncultured AF cells for the detection of fetal mosaicism. METHOD NIPT was performed as part of the Dutch TRIDENT study. Cytogenetic studies in uncultured AF were performed using single nucleotide polymorphism (SNP)-array. Cultured AF cell colonies (in situ method) were investigated with fluorescent in situ hybridization and/or karyotyping. Clinical outcome data were collected in cases with discordant results. RESULTS Between April 2014 and December 2021, 368 amniocenteses were performed after a chromosomal aberration was detected with NIPT. Excluding 134 cases of common aneuploidies (confirmed by quantitative fluorescence polymerase chain reaction), 29 cases with investigation of uncultured cells only and 1 case without informed consent, 204 cases were eligible for this study. In 196 (96%) cases, the results in uncultured and cultured cells were concordant normal, abnormal or mosaic. Five cases (2%) showed mosaicism in cultured AF cells, whereas uncultured AF cells were normal. Two (1%) of these, one mosaic trisomy 13 and one mosaic trisomy 16, were considered true fetal mosaics. CONCLUSION The added value of investigating AF cell cultures in addition to uncultured cells is limited to two of 204 (1%) cases in which true fetal mosaicsm would otherwise be missed. The clinical relevance of one (trisomy 13) remained unknown and the other case also showed ultrasound anomalies, which determined pregnancy management. This seems to justify limiting prenatal cytogenetic confirmatory testing to SNP arrays on uncultured AF cells, considerably shortening the reporting time.
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Affiliation(s)
- Stephany H Donze
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Myrthe van den Born
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Robert-Jan Galjaard
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Lutgarde C P Govaerts
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Maarten F C M Knapen
- Department of Obstetrics and Prenatal Medicine, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, ErasmusMC, University Medical Center, Rotterdam, The Netherlands
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Riggan KA, Barwise A, Yap JQ, Condon N, Allyse MA. Patient experiences with prenatal cell-free DNA screening in a safety net setting. Prenat Diagn 2024; 44:409-417. [PMID: 38423995 PMCID: PMC11027152 DOI: 10.1002/pd.6541] [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: 09/30/2023] [Revised: 01/12/2024] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVES Thirty-five states, including Florida, now cover cell-free DNA (cfDNA) screening of fetuses for all pregnant patients enrolled in state public insurance programs. We interviewed Black and Hispanic obstetric patients at a safety net clinic in Florida shortly after the state rolled out cfDNA as a first-tier screening method for publicly insured patients. METHODS Black and Hispanic patients receiving prenatal care from a prenatal or maternal fetal medicine clinic at a federally qualified health center in Jacksonville, FL were invited to participate in a qualitative interview in English or Spanish to explore experiences and perceptions of prenatal cfDNA screening. Participants were recruited following their first prenatal visit when cfDNA is typically introduced. Interview transcripts were qualitatively analyzed for iterative themes based on principles of grounded theory. RESULTS One hundred Black and Hispanic patients (n = 51 non-Hispanic Black, n = 43 Hispanic, n = 3 Hispanic Black, n = 3 Not Reported/Other) completed an interview. Participants described minimal opportunity for pre-screening counseling and limited health literacy about cfDNA or its uses. Some believed that cfDNA could positively impact pregnancy health. Many were unsure if they had received cfDNA even though they were aware of the information provided by it. Most participants expressed an interest in cfDNA as a means for early detection of fetal sex and as an additional indication of general fetal health. CONCLUSIONS Patient experiences indicate limited informed consent and decision-making for cfDNA, discordant with professional guidelines on pre-screen counseling. Our findings suggest that there should be additional investment in implementing cfDNA in safety net settings to ensure that patients and providers receive the support necessary for effective patient counseling and follow-on care for the ethical implementation of cfDNA.
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Affiliation(s)
| | - Amelia Barwise
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
| | - Jane Q. Yap
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL
| | - Niamh Condon
- Department of Maternal-Fetal Medicine, University of Florida Health, Jacksonville, FL
| | - Megan A. Allyse
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN
- Department of Obstetrics & Gynecology, Mayo Clinic, Rochester, MN
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Raymond Y, Fernando S, Menezes M, Mol BW, McLennan A, da Silva Costa F, Hardy T, Rolnik DL. Placental, maternal, fetal, and technical origins of false-positive cell-free DNA screening results. Am J Obstet Gynecol 2024; 230:381-389. [PMID: 38008147 DOI: 10.1016/j.ajog.2023.11.1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The introduction of noninvasive prenatal testing has resulted in substantial reductions to previously accepted false-positive rates of prenatal screening. Despite this, the possibility of false-positive results remains a challenging consideration in clinical practice, particularly considering the increasing uptake of genome-wide noninvasive prenatal testing, and the subsequent increased proportion of high-risk results attributable to various biological events besides fetal aneuploidy. Confined placental mosaicism, whereby chromosome anomalies exclusively affect the placenta, is perhaps the most widely accepted cause of false-positive noninvasive prenatal testing. There remains, however, a substantial degree of ambiguity in the literature pertaining to the clinical ramifications of confined placental mosaicism and its potential association with placental insufficiency, and consequentially adverse pregnancy outcomes including fetal growth restriction. Other causes of false-positive noninvasive prenatal testing include vanishing twin syndrome, in which the cell-free DNA from a demised aneuploidy-affected twin triggers a high-risk result, technical failures, and maternal origins of abnormal cell-free DNA such as uterine fibroids or unrecognized mosaicisms. Most concerningly, maternal malignancies are also a documented cause of false-positive screening results. In this review, we compile what is currently known about the various causes of false-positive noninvasive prenatal testing.
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Affiliation(s)
- Yvette Raymond
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia.
| | - Shavi Fernando
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Monash Obstetrics, Melbourne, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia; Monash IVF Group, Melbourne, Australia
| | - Ben W Mol
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Centre for Women's Health Research, The University of Aberdeen, Aberdeen, UK
| | - Andrew McLennan
- Sydney Ultrasound for Women, Sydney, Australia; Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney, Sydney, Australia
| | - Fabricio da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Queensland, Australia; School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia
| | - Tristan Hardy
- Monash IVF Group, Melbourne, Australia; Repromed Adelaide, Dulwich, Australia
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Monash Ultrasound for Women, Melbourne, Australia
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Arumugam S, Kalluri SS, Sharmila V, Mocherla A, Subbiah NK, Kulkarni JP, Ghoshal JA. Understanding the Awareness of Prenatal Genetic Screening Tests Among Pregnant Women in India: A Cross-Sectional Study. Cureus 2024; 16:e56932. [PMID: 38665723 PMCID: PMC11043792 DOI: 10.7759/cureus.56932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction Genetic disorders pose a significant health challenge in India, with chromosomal abnormalities ranking second only to congenital anomalies in terms of disease burden. Prenatal testing offers a crucial strategy for identifying and managing these disorders. However, the awareness and understanding of prenatal screening tests among pregnant women in India remain understudied. This study aims to fill this gap by investigating the awareness quotient of prenatal screening tests for genetic disorders among pregnant women in India. Methods A hospital-based cross-sectional study was conducted at the Genetics Unit, Department of Anatomy, and Department of Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri. Ethical clearance was obtained, and data were collected using a self-administered questionnaire covering demographic characteristics and awareness assessment. Descriptive statistics, chi-square tests, and logistic regression analysis were employed for data analysis. Results Among the 200 pregnant women surveyed, the majority demonstrated inadequate awareness of prenatal screening tests for genetic disorders, with only 36.5% possessing adequate knowledge. Significant associations were found between awareness levels and factors such as age, trimester of pregnancy, and education level. Notably, awareness about non-invasive prenatal testing (NIPT) was notably low at 7%, indicating a need for targeted educational interventions. Comparison with international studies revealed varying levels of awareness across different populations, highlighting the influence of socio-cultural factors and healthcare systems. Conclusion This study underscores the need for improved awareness of prenatal screening tests among pregnant women in India. Addressing disparities in awareness, particularly among younger age groups and those with lower education levels, is crucial for informed decision-making in prenatal care. Targeted educational interventions can empower pregnant women to make informed choices, ultimately contributing to better maternal and child health outcomes. Further research should explore the effectiveness of such interventions in diverse settings to enhance prenatal care delivery.
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Affiliation(s)
- Sangeetha Arumugam
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Sri Sowmya Kalluri
- Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri, IND
- Obstetrics and Gynecology, Siddhartha Medical College, Government General Hospital, Vijayawada, IND
| | - Vijayan Sharmila
- Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Akarsh Mocherla
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Nandha Kumar Subbiah
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Jyoti P Kulkarni
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Joy A Ghoshal
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
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Eggenhuizen GM, Go ATJI, Sauter Z, Hoffer MJV, Haak MC, Geeven G, Diderich KEM, Joosten M, van den Born M, Srebniak MI, Van Opstal D. The role of confined placental mosaicism in fetal growth restriction: A retrospective cohort study. Prenat Diagn 2024; 44:289-296. [PMID: 38342960 DOI: 10.1002/pd.6533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVE To evaluate which cytogenetic characteristics of confined placental mosaicism (CPM) detected in the first trimester chorionic villi and/or placentas in terms of chromosome aberration, cell lineage involved and trisomy origin will lead to fetal growth restriction and low birthweight. METHODS Cohort study using routinely collected perinatal data and cytogenetic data of non-invasive prenatal testing, the first trimester chorionic villi sampling and postnatal placentas. RESULTS 215 CPM cases were found. Fetal growth restriction (FGR) and low birthweight below the 10th percentile (BW < p10) were seen in 34.0% and 23.1%, respectively. Excluding cases of trisomy 16, 29.1% showed FGR and 17.9% had a BW < p10. The highest rate of FGR and BW < p10 was found in CPM type 3, but differences with type 1 and 2 were not significant. FGR and BW < p10 were significantly more often observed in cases with meiotic trisomies. CONCLUSION There is an association between CPM and FGR and BW < p10. This association is not restricted to trisomy 16, neither to CPM type 3, nor to CPM involving a meiotic trisomy. Pregnancies with all CPM types and origins should be considered to be at increased risk of FGR and low BW < p10. A close prenatal fetal monitoring is indicated in all cases of CPM.
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Affiliation(s)
- Geerke M Eggenhuizen
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Attie T J I Go
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Zoë Sauter
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique C Haak
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Leiden, The Netherlands
| | - Geert Geeven
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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12
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Bakkeren IM, Henneman L, van Vliet-Lachotzki EH, Martin L, Gitsels-van der Wal JT, Polak MG, Bekker MN, Galjaard RJH. Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study. Eur J Hum Genet 2024; 32:302-308. [PMID: 38057584 PMCID: PMC10923886 DOI: 10.1038/s41431-023-01504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/01/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023] Open
Abstract
In the Netherlands, genome-wide non-invasive prenatal testing (NIPT) is offered to all pregnant women as part of the nationwide TRIDENT-2 study. Findings other than trisomy 21, 18, or 13, which are called "additional findings", are reported only on request of the pregnant woman. This study examined: (1) women's pre-test perceptions and reasons to opt for additional findings and (2) women's experiences with- and the psychological impact of being informed about an additional finding. A questionnaire, consisting of the anxiety measure State-Trait Anxiety Inventory (STAI), distress measure Impact of Event Scale (IES) and questions developed specifically for this study, was retrospectively administered to 402 women who received an additional finding. A total of 227 (56.5%) women completed the questionnaire. Most (60.2%) chose to know additional findings because they wanted as much information as possible about the health of their fetus. Almost all (92%) stated that receiving the additional finding was unexpected, a shock, and/or they were in disbelief, for 85% it caused a lot of worry. Post-test, high anxiety (STAI) levels were reported in 15.5% of women, and 7.5% reported severe distress (IES). Women who gave birth to an affected child (n = 10) experienced most psychological impact (STAI and IES). Eighty-six percent of women with a fetal aberration would opt for additional findings again, compared to 49.2% of women whose result was confined to the placenta. Pre-test counseling should focus on explaining the different results NIPT can generate. Post-test counseling should focus on guiding pregnant women through this uncertain and anxious time.
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Affiliation(s)
- Iris M Bakkeren
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | | | - Linda Martin
- Department of Midwifery Science, AVAG, Amsterdam Public Health research institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Janneke T Gitsels-van der Wal
- Department of Midwifery Science, AVAG, Amsterdam Public Health research institute, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Marike G Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Mireille N Bekker
- Department of Obstetrics and Gynecology, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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13
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Tang X, Wang Z, Chen M, Zhang Y, Du Y, Zhang F, Tan J, Yin T, Wang L. Combined Z-scores to assess the impact of rare autosomal trisomies that results in non-invasive prenatal screening on pregnancy outcomes. Clin Chim Acta 2024; 554:117758. [PMID: 38184139 DOI: 10.1016/j.cca.2023.117758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/19/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
OBJECTIVE This study aimed to combine Z-scores to evaluate the effects of rare autosomal trisomies (RATs) in non-invasive prenatal screening (NIPS) on pregnancy outcomes at a single center. METHODS We retrospectively collected the clinical data of women with high-risk RATs results using NIPS at a single center between January 2017 and December 2021. NIPS-positive results were separated into three groups based on the Z-value of RATs (Group1: 6 ≤ Z < 10; Group2: 10 ≤ Z < 15; Group 3: Z ≥ 15). Pregnancy outcomes of women with RATs were compared with the low-risk NIPS group. RESULTS Overall, 83 RATs were identified in 23,321 NIPS results at our center. Prenatal diagnosis was conducted for 55 patients, and no case was confirmed, with a positive predictive value (PPV) of zero. Fifteen of these patients had adverse pregnancy outcomes, including delivered preterm and/or birth weight (9/15, 60.0 %), structural abnormalities (4/15, 26.7 %), miscarriage (1/15, 6.7 %), and intrauterine death (1/15, 6.7 %). There were 8 (8/22, 36.4 %) adverse pregnancy outcomes in Group 3, which was significantly higher than that in the low-risk NIPS group (p < 0.01). No significant difference was observed between the control group and Group 1 and Group 2 (p > 0.01). CONCLUSIONS Clinicians should pay more attention to the RATs results when the Z-score is ≥ 15. The data are available for clinicians to guide the prenatal diagnosis of RATs and pregnancy management.
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Affiliation(s)
- Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Min Chen
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yue Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Yunqiu Du
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Juan Tan
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Ting Yin
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, People's Republic of China.
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14
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Parijs I, Brison N, Vancoillie L, Baetens M, Blaumeiser B, Boulanger S, Désir J, Dimitrov B, Fieremans N, Janssens K, Janssens S, Marichal A, Menten B, Meunier C, Van Berkel K, Van Den Bogaert A, Devriendt K, Van Den Bogaert K, Vermeesch JR. Population screening for 15q11-q13 duplications: corroboration of the difference in impact between maternally and paternally inherited alleles. Eur J Hum Genet 2024; 32:31-36. [PMID: 37029316 PMCID: PMC10772068 DOI: 10.1038/s41431-023-01336-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 04/09/2023] Open
Abstract
Maternally inherited 15q11-q13 duplications are generally found to cause more severe neurodevelopmental anomalies compared to paternally inherited duplications. However, this assessment is mainly inferred from the study of patient populations, causing an ascertainment bias towards patients at the more severe end of the phenotypic spectrum. Here, we analyze the low coverage genome-wide cell-free DNA sequencing data obtained from pregnant women during non-invasive prenatal screening (NIPS). We detect 23 15q11-q13 duplications in 333,187 pregnant women (0.0069%), with an approximately equal distribution between maternal and paternal duplications. Maternally inherited duplications are always associated with a clinical phenotype (ranging from learning difficulties to intellectual impairment, epilepsy and psychiatric disorders), while paternal duplications are normal or associated with milder phenotypes (mild learning difficulties and dyslexia). This data corroborates the difference in impact between paternally and maternally inherited 15q11-q13 duplications, contributing to the improvement of genetic counselling. We recommend reporting 15q11-q13 duplications identified during genome-wide NIPS with appropriate genetic counselling for these pregnant women in the interest of both mothers and future children.
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Affiliation(s)
- Ilse Parijs
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Machteld Baetens
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Bettina Blaumeiser
- Center of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Sébastien Boulanger
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Julie Désir
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Boyan Dimitrov
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Nathalie Fieremans
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Katrien Janssens
- Center of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Axel Marichal
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Björn Menten
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Colombine Meunier
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Kim Van Berkel
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Ann Van Den Bogaert
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
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15
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Lannoo L, Van Camp J, Brison N, Parijs I, Vancoillie L, Van Den Bogaert K, Vermeesch JR, Devriendt K, Van Calsteren K. What helps define outcomes in persistent uninterpretable non-invasive prenatal testing: Maternal factors, fetal fraction or quality scores? Prenat Diagn 2023; 43:1333-1343. [PMID: 37592442 DOI: 10.1002/pd.6423] [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: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
OBJECTIVES To assess maternal characteristics and comorbidities in patients with persistent uninterpretable non-invasive prenatal testing (NIPT) and to evaluate the association with adverse pregnancy outcome in a general risk population. METHODS A retrospective cohort study (July 2017-December 2020) was conducted of patients with persistent uninterpretable NIPT samples. Maternal characteristics and pregnancy outcomes were compared with the general Belgian obstetric population. RESULTS Of the 148 patients with persistent uninterpretable NIPT, 37 cases were due to a low fetal fraction (LFF) and 111 due to a low quality score (LQS). Both groups (LFF, LQS) showed more obesity (60.6%, 42.4%), multiple pregnancies (18.9%, 4.5%) and more obstetrical complications. In the LQS group, a high rate of maternal auto-immune disorders (30.6%) was seen and hypertensive complications (17.6%), preterm birth (17.6%) and neonatal intensive care unit (NICU) admission (22%) were significantly increased. In the LFF group hypertensive complications (21.6%), gestational diabetes (20.6%), preterm birth (27%), SGA (25.6%), major congenital malformations (11.4%), c-section rate (51.4%) and NICU admission (34.9%) were significantly increased. Chromosomal abnormalities were not increased in both groups. CONCLUSIONS Patients with persistent uninterpretable NIPT have significantly more maternal obesity, comorbidities and adverse pregnancy outcome than the general population and should receive high-risk pregnancy care. Distinguishing between LFF and LQS optimizes counseling because maternal characteristics and pregnancy outcome differ between these groups.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Joke Van Camp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
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Benn P, Cuckle H. Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing. Clin Obstet Gynecol 2023; 66:536-556. [PMID: 37650667 DOI: 10.1097/grf.0000000000000803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.
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Affiliation(s)
- Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut
| | - Howard Cuckle
- Department of Obstetrics and Gynecology, Faculty of Medicine, Tel Aviv University, Israel
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Soster E, Tynan J, Gibbons C, Meschino W, Wardrop J, Almasri E, Schwartz S, McLennan G. Laboratory performance of genome-wide cfDNA for copy number variants as compared to prenatal microarray. Mol Cytogenet 2023; 16:10. [PMID: 37301962 DOI: 10.1186/s13039-023-00642-4] [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: 02/20/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) allows for screening of fetal aneuploidy and copy number variants (CNVs) from cell-free DNA (cfDNA) in maternal plasma. Professional societies have not yet embraced NIPT for fetal CNVs, citing a need for additional performance data. A clinically available genome-wide cfDNA test screens for fetal aneuploidy and CNVs larger than 7 megabases (Mb). RESULTS This study reviews 701 pregnancies with "high risk" indications for fetal aneuploidy which underwent both genome-wide cfDNA and prenatal microarray. For aneuploidies and CNVs considered 'in-scope' for the cfDNA test (CNVs ≥ 7 Mb and select microdeletions), sensitivity and specificity was 93.8% and 97.3% respectively, with positive and negative predictive values of 63.8% and 99.7% as compared to microarray. When including 'out-of-scope' CNVs on array as false negatives, the sensitivity of cfDNA falls to 48.3%. If only pathogenic out-of-scope CNVs are treated as false negatives, the sensitivity is 63.8%. Of the out-of-scope CNVs identified by array smaller than 7 Mb, 50% were classified as variants of uncertain significance (VUS), with an overall VUS rate in the study of 2.29%. CONCLUSIONS While microarray provides the most robust assessment of fetal CNVs, this study suggests that genome-wide cfDNA can reliably screen for large CNVs in a high-risk cohort. Informed consent and adequate pretest counseling are essential to ensuring patients understand the benefits and limitations of all prenatal testing and screening options.
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Affiliation(s)
| | - John Tynan
- Labcorp®, La Jolla, CA, USA
- PetDx, The Center for Novel Therapeutics, La Jolla, CA, USA
| | - Clare Gibbons
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - Wendy Meschino
- Genetics Program, North York General Hospital, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
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Soster E, Dyr B, Rafalko J, Almasri E, Cacheris P. Positive cfDNA screening results for 22q11.2 deletion syndrome—Clinical and laboratory considerations. Front Genet 2023; 14:1146669. [PMID: 36968594 PMCID: PMC10036386 DOI: 10.3389/fgene.2023.1146669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Introduction: Non-invasive prenatal screening (NIPS) via cell-free DNA (cfDNA) screens for fetal chromosome disorders using maternal plasma, including 22q11.2 deletion syndrome (22q11.2DS). While it is the commonest microdeletion syndrome and has potential implications for perinatal management, prenatal screening for 22q11.2DS carries some inherent technical, biological, and counseling challenges, including varying deletion sizes/locations, maternal 22q11.2 deletions, confirmatory test choice, and variable phenotype.Materials and methods: This study addresses these considerations utilizing a retrospective cohort of 307 samples with screen-positive 22q11.2 NIPS results on a massively parallel sequencing (MPS) platform.Results: Approximately half of the cases reported ultrasound findings at some point during pregnancy. In 63.2% of cases with diagnostic testing, observed positive predictive values were 90.7%–99.4%. cfDNA identified deletions ranging from <1 Mb to 3.55 Mb, with significant differences in confirmed fetal versus maternal deletion sizes; estimated cfDNA deletion size was highly concordant with microarray findings. Mosaicism ratio proved useful in predicting the origin of a deletion (fetal versus maternal). Prediction of deletion size, location, and origin may help guide confirmatory testing.Discussion: The data shows that MPS-based NIPS can screen for 22q11.2DS with a high PPV, and that collaboration between the laboratory and clinicians allows consideration of additional metrics that may guide diagnostic testing and subsequent management.
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Affiliation(s)
- Erica Soster
- Labcorp, La Jolla, CA, United States
- *Correspondence: Erica Soster,
| | | | - Jill Rafalko
- Labcorp, La Jolla, CA, United States
- PetDx, The Center for Novel Therapeutics, La Jolla, CA, United States
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Zhang M, Tang J, Li J, Wang C, Wei R, Fang Y, Zhu J. Value of noninvasive prenatal testing in the detection of rare fetal autosomal abnormalities. Eur J Obstet Gynecol Reprod Biol 2023; 284:5-11. [PMID: 36905803 DOI: 10.1016/j.ejogrb.2023.03.002] [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: 08/12/2022] [Revised: 02/08/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023]
Abstract
OBJECTIVES To evaluate the value of noninvasive prenatal testing (NIPT) in the screening of rare autosomal abnormalities and provide further support for the clinical application of NIPT. STUDY DESIGN A total of 81,518 pregnant women who underwent NIPT at the Anhui Maternal and Child Health Hospital between May 2018 and March 2022 were selected. The high-risk samples were analyzed using amniotic fluid karyotype and chromosome microarray analysis (CMA), and the pregnancy outcomes were followed up. RESULTS NIPT detected 292 cases (0.36%) with rare autosomal abnormalities among the 81,518 cases sampled. Of these, 140 (0.17%) showed rare autosomal trisomies (RATs), and 102 of these patients agreed to undergo invasive testing. Five cases were true positives, with a positive predictive value (PPV) of 4.90%. Copy number variants (CNV) were detected in 152 samples of the total cases (0.19%), and 95 of the patients involved agreed to the use of CMA. Twenty-nine of these cases were confirmed to be true positive, with a PPV of 30.53%. Detailed follow-up information was obtained in 81 cases from 97 patients with false-positive results for RATs. Thirty-seven of these cases (45.68%) had adverse perinatal outcomes, with a higher incidence of small for gestational age (SGA), intrauterine growth retardation (IUGR), and preterm birth (PTB). CONCLUSIONS NIPT is not recommended for screening for RATs. However, considering that positive results are associated with an increased risk of IUGR and PTB, additional fetal ultrasound examination should be performed to monitor fetal growth. In addition, NIPT has a reference value in screening for CNVs, especially pathogenic CNVs, but a comprehensive analysis of prenatal diagnosis combined with ultrasound and family history is still needed.
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Affiliation(s)
- Miaomiao Zhang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China; Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Junxiang Tang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jingran Li
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Rong Wei
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Yuqin Fang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China; Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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20
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Acreman ML, Bussolaro S, Raymond YC, Fantasia I, Rolnik DL, Da Silva Costa F. The predictive value of prenatal cell-free DNA testing for rare autosomal trisomies: a systematic review and meta-analysis. Am J Obstet Gynecol 2023; 228:292-305.e6. [PMID: 36027954 DOI: 10.1016/j.ajog.2022.08.034] [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] [Received: 06/08/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The diagnostic accuracy of cell-free fetal DNA in screening for rare autosomal trisomies is uncertain. We conducted a systematic review and meta-analysis aiming to determine the predictive value of cell-free DNA in screening for rare autosomal trisomies. DATA SOURCES PubMed, Embase, and Web of Science were searched from inception to January 2022. STUDY ELIGIBILITY CRITERIA All studies that reported on the diagnostic accuracy of cell-free DNA in the detection of rare autosomal trisomies were included. Case series were included if they contained at least 10 cases with diagnostic test results or postnatal genetic testing. METHODS Study appraisal was completed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Statistical analysis was performed using random-effects meta-analysis of double-arcsine transformed proportions of confirmed results in the fetus out of the positive tests to obtain a pooled estimate of the positive predictive value. RESULTS The search identified 7553 studies, of which 1852 were duplicates. After screening 5701 titles and abstracts, 380 studies proceeded to the full-text screen; 206 articles were retrieved for data extraction, of which another 175 articles were excluded. A total of 31 studies, with a total of 1703 women were included for analysis. The pooled positive predictive value of cell-free DNA for the diagnosis of rare autosomal trisomies was 11.46% (95% confidence interval, 7.80-15.65). Statistical heterogeneity was high (I2=82%). Sensitivity analysis restricted to 5 studies at low risk of bias demonstrated a pooled positive predictive value of 9.13% (95% confidence interval, 2.49-18.76). There were insufficient data to provide accurate ascertainment of sensitivity and specificity because most studies only offered confirmatory tests to women with high-risk results. CONCLUSION The positive predictive value of cell-free DNA in diagnosing rare autosomal trisomies is approximately 11%. Clinicians should provide this information when offering cell-free DNA for screening of conditions outside of common autosomal trisomies.
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Affiliation(s)
- Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Queensland, Australia.
| | - Sofia Bussolaro
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Yvette C Raymond
- Department of Obstetrics and Gynaecology, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
| | - Ilaria Fantasia
- Obstetrics and Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
| | - Fabricio Da Silva Costa
- Maternal Foetal Medicine Unit, Gold Coast University Hospital and School of Medicine, Griffith University, Gold Coast, Australia
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21
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Prenatal Diagnosis of Uniparental Disomy in Cases of Rare Autosomal Trisomies Detected Using Noninvasive Prenatal Test: A Case of Prader-Willi Syndrome. Diagnostics (Basel) 2023; 13:diagnostics13040580. [PMID: 36832068 PMCID: PMC9955094 DOI: 10.3390/diagnostics13040580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Rare autosomal trisomies (RATs) other than common aneuploidies can be detected using noninvasive prenatal testing (NIPT). However, conventional karyotyping is insufficient for evaluating diploid fetuses with uniparental disomy (UPD) due to trisomy rescue. Using the diagnostic process for Prader-Willi syndrome (PWS), we aim to describe the need for additional prenatal diagnostic testing for confirming UPD in fetuses diagnosed with RATs via NIPT and its clinical implications. NIPT was performed using the massively parallel sequencing (MPS) method, and all pregnant women with RATs underwent amniocentesis. After confirming the normal karyotype, short tandem repeat (STR) analysis, methylation-specific PCR (MS-PCR), and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were performed to detect UPD. Overall, six cases were diagnosed with RATs. There was a suspicion of trisomies of chromosomes 7, 8, and 15 in two cases each. However, these cases were confirmed to have a normal karyotype using amniocentesis. In one of six cases, PWS caused by maternal UPD 15 was diagnosed using MS-PCR and MS-MLPA. We propose that in cases where RAT is detected by NIPT, UPD should be considered following trisomy rescue. Even if amniocentesis confirms a normal karyotype, UPD testing (such as MS-PCR and MS-MLPA) should be recommended for accurate assessment, as an accurate diagnosis can lead to appropriate genetic counseling and improved overall pregnancy management.
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22
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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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23
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Clinical, Cytogenetic and Molecular Cytogenetic Outcomes of Cell-Free DNA Testing for Rare Chromosomal Anomalies. Genes (Basel) 2022; 13:genes13122389. [PMID: 36553656 PMCID: PMC9777917 DOI: 10.3390/genes13122389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. This study focuses on the confirmatory and follow-up data of cases with positive cfDNA testing for RCAs and cases with screen-negative results in a series of 912 consecutive cases that underwent invasive testing following cfDNA testing. Chorion villus sampling (CVS), amniocentesis (AS), fetal blood sampling, and term placenta samples were investigated using classical cytogenetic and molecular cytogenetic techniques. Out of 593 screen-positive results, 504 (85%) were for common aneuploidies, 40 (6.7%) for rare autosomal trisomies (RATs), and 49 (8.3%) for structural chromosome anomalies (SAs). Of the screen-positives for RATs, 20 cases were evaluated only in fetal tissue, and confined placental mosaicism (CPM) could not be excluded. Among cases with definitive results (n = 20), the rates of true positives, placental mosaics, and false positives were 35%, 45%, and 10%, respectively. Among screen-positives for SAs, 32.7% were true positives. The confirmation rate was higher for duplications than deletions (58.3% vs. 29.4%). The rate of chromosomal abnormality was 10.9% in the group of 256 screen-negatives with pathological ultrasound findings. This study provides further data to assess the efficiency of expanded cfDNA testing for RATs and SAs. The test efficiency for cfDNA seems to be higher for duplications than for deletions, which is evidence of the role of expert ultrasound in identifying pregnancies at increased risk for chromosome anomalies, even in pregnancies with screen-negatives. Furthermore, we discussed the efficiency of CVS vs. AC in screen-positives for RATs.
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24
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Hu R, Huang W, Zhou W, Luo X, Ren C, Huang H, Hou Y, Guo L, He W, Lu J. Phenotypic findings and pregnancy outcomes of fetal rare autosomal aneuploidies detected using chromosomal microarray analysis. Hum Genomics 2022; 16:64. [PMID: 36457118 PMCID: PMC9714082 DOI: 10.1186/s40246-022-00438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Aneuploidies are the most common chromosomal abnormality and the main genetic cause of adverse pregnancy outcomes. Since numerous studies have focused on common trisomies, relatively little is known about the association between phenotypic findings and rare autosomal aneuploidies (RAAs). We conducted a retrospective study of 48,904 cases for chromosomal microarray analysis in a large tertiary referral center and reported the overall frequencies, clinical manifestations, and outcomes of prenatal RAAs. RESULTS A total of 90 RAAs were detected, of which 83 cases were mosaic trisomies and 7 were non-mosaic trisomies. Chromosomes 16, 22, and 9 were identified as the major chromosomes involving RAAs. The four predominant indications for prenatal diagnosis in our RAA cases were RAA-positive in noninvasive prenatal screening, advanced maternal age, ultrasound abnormalities, and high-risk for serum prenatal screening. Cardiovascular defects were the most frequently observed structural abnormalities, followed by musculoskeletal anomalies. Increased nuchal translucency and persistent left superior vena cava, the major soft marker abnormalities involved, were also observed in our RAA cases. Clinical outcomes were available for all RAAs, with 63 induced abortions and 27 live births recorded. CONCLUSIONS Variable phenotypes and outcomes were observed, which were highly heterogeneous in cases of prenatal RAAs. Thus, a cautious and comprehensive strategy should be implemented during prenatal counseling for RAAs.
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Affiliation(s)
- Rong Hu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weiwei Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weining Zhou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Xiaohui Luo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Congmian Ren
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Huajie Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Yaping Hou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Li Guo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Wei He
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Jian Lu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
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25
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Lannoo L, van Straaten K, Breckpot J, Brison N, De Catte L, Dimitriadou E, Legius E, Peeters H, Parijs I, Tsuiko O, Vancoillie L, Vermeesch JR, Van Buggenhout G, Van Den Bogaert K, Van Calsteren K, Devriendt K. Rare autosomal trisomies detected by non-invasive prenatal testing: an overview of current knowledge. Eur J Hum Genet 2022; 30:1323-1330. [PMID: 35896702 PMCID: PMC9712527 DOI: 10.1038/s41431-022-01147-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/15/2022] [Accepted: 06/30/2022] [Indexed: 12/16/2022] Open
Abstract
Non-invasive prenatal testing has been introduced for the detection of Trisomy 13, 18, and 21. Using genome-wide screening also other "rare" autosomal trisomies (RATs) can be detected with a frequency about half the frequency of the common trisomies in the large population-based studies. Large prospective studies and clear clinical guidelines are lacking to provide adequate counseling and management to those who are confronted with a RAT as a healthcare professional or patient. In this review we reviewed the current knowledge of the most common RATs. We compiled clinical relevant parameters such as incidence, meiotic or mitotic origin, the risk of fetal (mosaic) aneuploidy, clinical manifestations of fetal mosaicism for a RAT, the effect of confined placental mosaicism on placental function and the risk of uniparental disomy (UPD). Finally, we identified gaps in the knowledge on RATs and highlight areas of future research. This overview may serve as a first guide for prenatal management for each of these RATs.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | | | - Jeroen Breckpot
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Luc De Catte
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | | | - Eric Legius
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Olga Tsuiko
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | | | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, Division Woman and Child, University Hospitals Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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26
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Genome-Wide Cell-Free DNA Test for Fetal Chromosomal Abnormalities and Variants: Unrestricted Versus Restricted Reporting. Diagnostics (Basel) 2022; 12:diagnostics12102439. [PMID: 36292129 PMCID: PMC9600475 DOI: 10.3390/diagnostics12102439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
This study aimed to compare the screening performance of genome-wide cfDNA testing for chromosomal abnormalities between two periods where additional findings were reported and not reported. Data were obtained from consecutive pregnant women with a singleton pregnancy at ≥10 weeks who requested cfDNA testing during 2015–2019. The performance of screening of the cfDNA test was determined by calculating the concordance rate, detection rate, and false-positive rate. Data from 3981 women were included. The no-result rates were similar between the two reporting periods (2.04% vs. 2.08%). Concordance rates for trisomy 21 and 18 were 100% and 100%, respectively. There were two cases tested high risk for trisomy 13, with a concordance rate of 0%. In total, 12 cases were high risk for any sex chromosome aneuploidy with an overall concordance of 75%, and 15 cases tested high risk for any rare autosomal trisomy, with a 13.3% concordance rate. The detection rates for trisomy 21 and 18 were 100% and 100%, respectively. For any SCA, the detection rate was 90%. For the two reporting periods, the combined false-positive rates were 0.93% and 0.17%, which were significantly different (p = 0.002). Restricting the reporting of additional findings from genome-wide cfDNA analysis has reduced the false-positive rate but without a reduction in the no-result rate.
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27
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Raymond YC, Fernando S, Menezes M, Meagher S, Mol BW, McLennan A, Scott F, Mizia K, Carey K, Fleming G, Rolnik DL. Cell-free DNA screening for rare autosomal trisomies and segmental chromosome imbalances. Prenat Diagn 2022; 42:1349-1357. [PMID: 36068932 PMCID: PMC9826090 DOI: 10.1002/pd.6233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/02/2022] [Accepted: 08/26/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To assess the outcomes of pregnancies at high-risk for rare autosomal trisomies (RATs) and segmental imbalances (SIs) on cell-free DNA (cfDNA) screening. METHOD A retrospective study of women who underwent cfDNA screening between September 2019 and July 2021 at three ultrasound services in Australia. Positive predictive values (PPVs) were calculated using fetal chromosomal analysis. RESULTS Among 23,857 women screened, there were 93 high-risk results for RATs (0.39%) and 82 for SIs (0.34%). The PPVs were 3.8% (3/78, 95% CI 0.8%-10.8%) for RATs and 19.1% (13/68, 95% CI 10.6%-30.5%) for SIs. If fetuses with structural anomalies were also counted as true-positive cases, the PPV for RATS increased to 8.5% (7/82, 95% CI 3.5%-16.8%). Among 85 discordant cases with birth outcomes available (65.4%), discordant positive RATs had a significantly higher proportion of infants born below the 10th and 3rd birthweight percentiles than expected (19.6% (p = 0.022) and 9.8% (p = 0.004), respectively), which was not observed in the SI group (2.9% < 10th (p = 0.168) and 0.0% <3rd (p = 0.305)). CONCLUSION The PPVs for SI and RAT results are low, except when a structural abnormality is also present. Discordant positive RATs are associated with growth restriction.
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Affiliation(s)
- Yvette C. Raymond
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia
| | - Shavi Fernando
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia
| | - Melody Menezes
- Monash Ultrasound for WomenMelbourneVictoriaAustralia,Department of PediatricsThe University of MelbourneMelbourneVictoriaAustralia
| | - Simon Meagher
- Monash Ultrasound for WomenMelbourneVictoriaAustralia
| | - Ben W. Mol
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia,Aberdeen Centre for Women's Health ResearchUniversity of AberdeenAberdeenUK
| | - Andrew McLennan
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia,Discipline of Obstetrics, Gynaecology and NeonatologyThe University of SydneySydneyNew South WalesAustralia
| | - Fergus Scott
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Karen Mizia
- Ultrasound CareSydneyNew South WalesAustralia,Australian National UniversityCanberraAustralia
| | - Karen Carey
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia
| | | | - Daniel Lorber Rolnik
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia
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28
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Mossfield T, Soster E, Menezes M, Agenbag G, Dubois ML, Gekas J, Hardy T, Jurkowska M, Kleinfinger P, Loggenberg K, Marchili P, Sirica R. Multisite assessment of the impact of cell-free DNA-based screening for rare autosomal aneuploidies on pregnancy management and outcomes. Front Genet 2022; 13:975987. [PMID: 36105088 PMCID: PMC9465083 DOI: 10.3389/fgene.2022.975987] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
Cell-free (cf) DNA screening is a noninvasive prenatal screening approach that is typically used to screen for common fetal trisomies, with optional screening for sex chromosomal aneuploidies and fetal sex. Genome-wide cfDNA screening can screen for a wide variety of additional anomalies, including rare autosomal aneuploidies (RAAs) and copy number variants. Here, we describe a multi-cohort, global retrospective study that looked at the clinical outcomes of cases with a high-risk cfDNA screening result for a RAA. Our study cohort included a total of 109 cases from five different sites, with diagnostic outcome information available for 68% (74/109) of patients. Based on confirmatory diagnostic testing, we found a concordance rate of 20.3% for presence of a RAA (15/74) in our study population. Pregnancy outcome was also available for 77% (84/109) of cases in our cohort. Many of the patients experienced adverse pregnancy outcomes, including intrauterine fetal demise, fetal growth restriction, and preterm birth. These adverse outcomes were observed both in patients with fetal or placental confirmation of the presence of a RAA, as well as patients that did not undergo fetal and/or placental diagnostic testing. In addition, we have proposed some suggestions for pregnancy management and counseling considerations for situations where a RAA is noted on a cfDNA screen. In conclusion, our study has shown that genome-wide cfDNA screening for the presence of rare autosomal aneuploidies can be beneficial for both patients and their healthcare practitioners. This can provide a possible explanation for an adverse pregnancy outcome or result in a change in pregnancy management, such as increased monitoring for adverse outcomes.
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Affiliation(s)
| | - Erica Soster
- Labcorp Women’s Health and Genetics, Laboratory Corporation of America, San Diego, CA, United States
| | - Melody Menezes
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | - Jean Gekas
- CHU de Quebec Research and Mother and Child Center, Department of Medical Genetics, University Hospital of Quebec, Laval University, Quebec City, QC, Canada
| | - Tristan Hardy
- Monash IVF Genetics, Monash IVF Group, Richmond, VIC, Australia
| | | | | | | | | | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale, Srl, Naples, Italy
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van Prooyen Schuurman L, Sistermans EA, Van Opstal D, Henneman L, Bekker MN, Bax CJ, Pieters MJ, Bouman K, de Munnik S, den Hollander NS, Diderich KE, Faas BH, Feenstra I, Go AT, Hoffer MJ, Joosten M, Komdeur FL, Lichtenbelt KD, Lombardi MP, Polak MG, Jehee FS, Schuring-Blom H, Stevens SJ, Srebniak MI, Suijkerbuijk RF, Tan-Sindhunata GM, van der Meij KR, van Maarle MC, Vernimmen V, van Zelderen-Bhola SL, van Ravesteyn NT, Knapen MF, Macville MV, Galjaard RJH. Clinical impact of additional findings detected by genome-wide non-invasive prenatal testing: Follow-up results of the TRIDENT-2 study. Am J Hum Genet 2022; 109:1140-1152. [PMID: 35659929 PMCID: PMC9247828 DOI: 10.1016/j.ajhg.2022.04.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/29/2022] [Indexed: 12/17/2022] Open
Abstract
In the TRIDENT-2 study, all pregnant women in the Netherlands are offered genome-wide non-invasive prenatal testing (GW-NIPT) with a choice of receiving either full screening or screening solely for common trisomies. Previous data showed that GW-NIPT can reliably detect common trisomies in the general obstetric population and that this test can also detect other chromosomal abnormalities (additional findings). However, evidence regarding the clinical impact of screening for additional findings is lacking. Therefore, we present follow-up results of the TRIDENT-2 study to determine this clinical impact based on the laboratory and perinatal outcomes of cases with additional findings. Between April 2017 and April 2019, additional findings were detected in 402/110,739 pregnancies (0.36%). For 358 cases, the origin was proven to be either fetal (n = 79; 22.1%), (assumed) confined placental mosaicism (CPM) (n = 189; 52.8%), or maternal (n = 90; 25.1%). For the remaining 44 (10.9%), the origin of the aberration could not be determined. Most fetal chromosomal aberrations were pathogenic and associated with severe clinical phenotypes (61/79; 77.2%). For CPM cases, occurrence of pre-eclampsia (8.5% [16/189] vs 0.5% [754/159,924]; RR 18.5), and birth weight <2.3rd percentile (13.6% [24/177] vs 2.5% [3,892/155,491]; RR 5.5) were significantly increased compared to the general obstetric population. Of the 90 maternal findings, 12 (13.3%) were malignancies and 32 (35.6%) (mosaic) pathogenic copy number variants, mostly associated with mild or no clinical phenotypes. Data from this large cohort study provide crucial information for deciding if and how to implement GW-NIPT in screening programs. Additionally, these data can inform the challenging interpretation, counseling, and follow-up of additional findings.
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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Lin Y, Hu P, Li H, Luo C, Liang D, Xu Z. Pregnancy outcomes of rare autosomal trisomies results in non-invasive prenatal screening: clinical follow-up data from a single tertiary centre. J Cell Mol Med 2022; 26:2251-2258. [PMID: 35174956 PMCID: PMC8995450 DOI: 10.1111/jcmm.17245] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
This study was performed to assess the association between detection of rare autosomal trisomies (RATs) by non-invasive prenatal screening (NIPS) and adverse pregnancy outcomes. We retrospectively analyzed women with high-risk RATs results from January 2014 to December 2020. The women's clinical information was collected, and their pregnancy outcomes were compared with those of women with low-risk results. In total, 151 (0.24%) RATs results were reported among 62,752 NIPS examinations. Sixty-five women chose to undergo amniocentesis for confirmation, which revealed 3 cases of true fetal mosaicism for RATs and a positive predictive value of 4.6% (3/65). Among the 139 women with available outcomes, 26 (18.7%) had a preterm birth, 10 (7.2%) underwent pregnancy termination because of fetal defects and 5 (3.6%) had miscarriages. Interestingly, compared with the control group, pregnancies in which NIPS revealed trisomy 16 (T16), T22, T9 and T2 were at higher risk of adverse outcomes, including preterm birth, miscarriage and ultrasound abnormalities. However, the risk of adverse outcomes was comparable between the control group and pregnancies with positive results of T7, T3, T8 and T20. In summary, the risk of adverse pregnancy outcomes was higher in women with specific RATs-positive NIPS results. Pregnancies with T16, T22, T9 and T2 results, even if false-positive, should be considered high-risk pregnancies.
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Affiliation(s)
- Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Chunyu Luo
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
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Dap M, Caffin L, Perdriolle-Galet E, Bonnet C, Morel O. Is Cell-free fetal DNA testing a safe option for women in a high-risk population after combined first-trimester testing? J Gynecol Obstet Hum Reprod 2022; 51:102329. [PMID: 35114410 DOI: 10.1016/j.jogoh.2022.102329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/23/2022] [Accepted: 01/30/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Our study aimed to examine the relevance of cell-free fetal DNA (cfDNA) testing on the screening of chromosomal defects and the issue of pregnancies in patients with a risk over 1:50 after the first-trimester combined test. METHODS This is a retrospective monocentric study. We included all consecutive patients with a singleton pregnancy between January 2015 and December 2020 attending our fetal medicine centre because the estimated risk for trisomy 21 after the first-trimester combined screening was over 1:50. The patients could either choose to have invasive testing or cell-free DNA testing. We collected data about the patient, the tests results (cfDNA, karyotype) and the pregnancy outcome (born alive, medical termination, miscarriage or intrauterine fetal death). RESULTS We included 98 patients with an estimated risk for trisomy 21 over 1:50. We found a total of 14 major chromosomal abnormalities (14/98; 14.3%), of which: thirteen trisomies 21 and one triploidy 69, XXY. A cfDNA testing was chosen by 34 (34/98; 34.7%) patients. Among the pathological results of invasive testing, 5 (5/64; 7.8%) couldn't be targeted by cfDNA testing. Two of them were placental mosaicism, one a triploidy 69, XXY, and two defects inherited from a parent and considered benign. There was no miscarriage linked to an invasive test in the population study. CONCLUSION In our monocentric cohort, a third of the patients choose cfDNA in a case of a risk over 1:50 after combined testing. Even if this cohort is too small to draw definitive conclusions, cfDNA could be safe in a high-risk population after combined testing. None of the chromosomal abnormalities found at the karyotype and non-detectable by cfDNA was a loss of information that impacted pregnancy follow-up. Further study could explore the input of Genome-Wide cfDNA and chromosomal micro-array in this population.
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Affiliation(s)
- Matthieu Dap
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France; Department of fetopathology and placental pathology, CHRU of Nancy, Nancy, France.
| | - Lucie Caffin
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France
| | | | - Céline Bonnet
- Department of Genetics, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Olivier Morel
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France; Inserm, Diagnostic and Interventional Adaptive Imaging, University of Lorraine, Nancy, France
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Harasim T, Neuhann T, Behnecke A, Stampfer M, Holinski-Feder E, Abicht A. Initial Clinical Experience with NIPT for Rare Autosomal Aneuploidies and Large Copy Number Variations. J Clin Med 2022; 11:jcm11020372. [PMID: 35054066 PMCID: PMC8777675 DOI: 10.3390/jcm11020372] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE Amniocentesis, chorionic villi sampling and first trimester combined testing are able to screen for common trisomies 13, 18, and 21 and other atypical chromosomal anomalies (ACA). The most frequent atypical aberrations reported are rare autosomal aneuploidies (RAA) and copy number variations (CNV), which are deletions or duplications of various sizes. We evaluated the clinical outcome of non-invasive prenatal testing (NIPT) results positive for RAA and large CNVs to determine the clinical significance of these abnormal results. METHODS Genome-wide NIPT was performed on 3664 eligible patient samples at a single genetics center. For patients with positive NIPT reports, the prescribing physician was asked retrospectively to provide clinical follow-up information using a standardized questionnaire. RESULTS RAAs and CNVs (>7 Mb) were detected in 0.5%, and 0.2% of tested cases, respectively. Follow up on pregnancies with an NIPT-positive result for RAA revealed signs of placental insufficiency or intra-uterine death in 50% of the cases and normal outcome at the time of birth in the other 50% of cases. We showed that CNV testing by NIPT allows for the detection of unbalanced translocations and relevant maternal health conditions. CONCLUSION NIPT for aneuploidies of all autosomes and large CNVs of at least 7 Mb has a low "non-reportable"-rate (<0.2%) and allows the detection of additional conditions of clinical significance.
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Scott F, Menezes M, Smet ME, Carey K, Hardy T, Fullston T, Rolnik DL, McLennan A. Reply. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:128-129. [PMID: 34985816 DOI: 10.1002/uog.24819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- F Scott
- Sydney Ultrasound for Women, Sydney, NSW, Australia
- University of New South Wales, Sydney, Australia
| | - M Menezes
- Monash Ultrasound for Women, Melbourne, Australia
| | - M E Smet
- Sydney Ultrasound for Women, Sydney, NSW, Australia
- Department of Obstetrics and Gynaecology, Westmead Hospital, Sydney, Australia
| | - K Carey
- Sydney Ultrasound for Women, Sydney, NSW, Australia
| | - T Hardy
- Repromed, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
| | | | - D L Rolnik
- Monash Ultrasound for Women, Melbourne, Australia
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
| | - A McLennan
- Sydney Ultrasound for Women, Sydney, NSW, Australia
- University of Sydney, Sydney, Australia
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Nowakowska BA, Pankiewicz K, Nowacka U, Niemiec M, Kozłowski S, Issat T. Genetic Background of Fetal Growth Restriction. Int J Mol Sci 2021; 23:ijms23010036. [PMID: 35008459 PMCID: PMC8744929 DOI: 10.3390/ijms23010036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/19/2021] [Indexed: 12/14/2022] Open
Abstract
Fetal growth restriction (FGR) is one of the most formidable challenges in present-day antenatal care. Pathological fetal growth is a well-known factor of not only in utero demise in the third trimester, but also postnatal morbidity and unfavorable developmental outcomes, including long-term sequalae such as metabolic diseases, diabetic mellitus or hypertension. In this review, the authors present the current state of knowledge about the genetic disturbances responsible for FGR diagnosis, divided into fetal, placental and maternal causes (including preeclampsia), as well as their impact on prenatal diagnostics, with particular attention on chromosomal microarray (CMA) and noninvasive prenatal testing technique (NIPT).
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Affiliation(s)
- Beata Anna Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211 Warsaw, Poland;
- Correspondence: (B.A.N.); (K.P.); Tel.: +48-22-3277131 (B.A.N.); +48-22-3277044 (K.P.)
| | - Katarzyna Pankiewicz
- Department of Obstetrics and Gynecology, Institute of Mother and Child in Warsaw, Kasprzaka 17a, 01-211 Warsaw, Poland; (U.N.); (S.K.); (T.I.)
- Correspondence: (B.A.N.); (K.P.); Tel.: +48-22-3277131 (B.A.N.); +48-22-3277044 (K.P.)
| | - Urszula Nowacka
- Department of Obstetrics and Gynecology, Institute of Mother and Child in Warsaw, Kasprzaka 17a, 01-211 Warsaw, Poland; (U.N.); (S.K.); (T.I.)
| | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211 Warsaw, Poland;
| | - Szymon Kozłowski
- Department of Obstetrics and Gynecology, Institute of Mother and Child in Warsaw, Kasprzaka 17a, 01-211 Warsaw, Poland; (U.N.); (S.K.); (T.I.)
| | - Tadeusz Issat
- Department of Obstetrics and Gynecology, Institute of Mother and Child in Warsaw, Kasprzaka 17a, 01-211 Warsaw, Poland; (U.N.); (S.K.); (T.I.)
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Peng H, Yang J, Wang D, Guo F, Hou Y, Yin A. Outcomes of pregnancies with trisomy 16 mosaicism detected by NIPT: a series of case reports. Mol Cytogenet 2021; 14:44. [PMID: 34544454 PMCID: PMC8454120 DOI: 10.1186/s13039-021-00559-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 11/12/2022] Open
Abstract
Background Trisomy 16 (T16) is thought to be the most frequent chromosome abnormality at conception, which is often associated with a high risk of abnormal outcomes. Methods A retrospective analysis of 14 cases with high risk of T16 by noninvasive prenatal testing (NIPT) was conducted. All cases in the analysis involved prenatal diagnosis, karyotyping and chromosomal microarray analysis. Case reports NIPT detected 12 cases of T16 and 2 cases of T16 mosaicism. Prenatal diagnosis confirmed 5 true positive cases and 9 false positive cases. Among the 5 true positive cases, 3 cases had ultrasound abnormalities. All of the 9 false positive cases continued their pregnancies. The newborns who were from these 9 false positive cases except 1 case (case 7) had low birth weights (< 2.5 kg) and there were also 2 premature deliveries. Conclusion NIPT serves as a fast and early prenatal screening method, giving clues to chromosome abnormalities and providing guidance for managing pregnancy. Confined placental mosaicism in 16 pregnancies may be at higher risk for preterm delivery.
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Affiliation(s)
- Haishan Peng
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Jiexia Yang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Dongmei Wang
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Fangfang Guo
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Yaping Hou
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China
| | - Aihua Yin
- Prenatal Diagnosis Centre, Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, 521-523 Xingnan Road, Guangzhou, 511442, Guangdong, China.
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Srebniak MI, Jehee FS, Joosten M, Boter M, de Valk WG, van der Helm R, Sistermans EA, Voorhoeve E, Bhola S, Hoffer MJV, den Hollander N, Macville MVE, Van Opstal D. Non-invasive prenatal diagnosis for translocation carriers-YES please or NO go? Acta Obstet Gynecol Scand 2021; 100:2036-2043. [PMID: 34472080 DOI: 10.1111/aogs.14256] [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: 05/04/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The presence of an unbalanced familial translocation can be reliably assessed in the cytotrophoblast of chorionic villi. However, carriers of a balanced translocation often decline invasive testing. This study aimed to investigate whether an unbalanced translocation can also be diagnosed in cell free DNA by whole-genome non-invasive prenatal screening (NIPS). MATERIAL AND METHODS Pregnant women carrying a fetus with an unbalanced familial translocation, for whom NIPS as well as microarray data were available, were included in this retrospective assessment. NIPS was performed in the course of the TRIDENT study. RESULTS In 12 cases, both NIPS and microarray data were available. In 10 of 12 cases the unbalanced translocation was correctly identified by NIPS without prior knowledge on parental translocation. One was missed because the fetal fraction was too low. One was missed because of technical restrictions in calling 16p gains. CONCLUSIONS This study supports the hypothesis that routine NIPS may be used for prenatal diagnosis of unbalanced inheritance of familial translocations, especially with prior knowledge of the translocation allowing focused examination of the involved chromosomal regions. Our study showed that routine shallow sequencing designed for aneuploidy detection in cell free DNA may be sufficient for higher resolution NIPS, if specialized copy number software is used and if sufficient fetal fraction is present.
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Affiliation(s)
| | - Fernanda S Jehee
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Walter G de Valk
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Shama Bhola
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Soster E, Boomer T, Hicks S, Caldwell S, Dyr B, Chibuk J, Almasri E. Three years of clinical experience with a genome-wide cfDNA screening test for aneuploidies and copy-number variants. Genet Med 2021; 23:1349-1355. [PMID: 33731879 PMCID: PMC8257487 DOI: 10.1038/s41436-021-01135-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Pregnant women have unprecedented choices for prenatal screening and testing. Cell-free DNA (cfDNA) offers the option to screen for aneuploidy of all chromosomes and genome-wide copy-number variants (CNVs), expanding screening beyond the common trisomies ("traditional" cfDNA). We sought to review the utilization trends and clinical performance characteristics of a commercially available genome-wide cfDNA test, with a subset having available diagnostic testing outcomes. METHODS Retrospective analysis of 55,517 samples submitted for genome-wide cfDNA screening at a commercial laboratory, assessing indications, demographics, results, and performance. The cohort was broken into three "testing years"' to compare trends. RESULTS Indications shifted over time, with a decrease in referrals for ultrasound findings (22.0% to 12.0%) and an increase in no known high-risk indication (3.0% to 16.6%). Of the positive results, 25% would be missed with traditional cfDNA screening. High sensitivity and specificity were observed with a positive predictive value (PPV) of 72.6% for genome-wide CNVs and 22.4% for rare autosomal trisomies (RATs). CONCLUSION A broader patient population is utilizing genome-wide cfDNA, yet positivity rates and the contribution of genome-wide events have remained stable at approximately 5% and 25%, respectively. Test performance in a real-world clinical population shows high PPVs in those CNVs tested, with diagnostic outcomes in over 40% of positive cases.
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Rosner M, Kolbe T, Hengstschläger M. Fetomaternal microchimerism and genetic diagnosis: On the origins of fetal cells and cell-free fetal DNA in the pregnant woman. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108399. [PMID: 34893150 DOI: 10.1016/j.mrrev.2021.108399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
During pregnancy several types of fetal cells and fetal stem cells, including pregnancy-associated progenitor cells (PAPCs), traffic into the maternal circulation. Whereas they also migrate to various maternal organs and adopt the phenotype of the target tissues to contribute to regenerative processes, fetal cells also play a role in the pathogenesis of maternal diseases. In addition, cell-free fetal DNA (cffDNA) is detectable in the plasma of pregnant women. Together they constitute the well-known phenomenon of fetomaternal microchimerism, which inspired the concept of non-invasive prenatal testing (NIPT) using maternal blood. An in-depth knowledge concerning the origins of these fetal cells and cffDNA allows a more comprehensive understanding of the biological relevance of fetomaternal microchimerism and has implications for the ongoing expansion of resultant clinical applications.
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Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Kolbe
- Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria; Department IFA Tulln, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria.
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Abstract
PURPOSE OF REVIEW Cell-free DNA-based noninvasive prenatal testing (cfDNA-based NIPT) using maternal blood is highly sensitive for detecting fetal trisomies. However, false-positive and false-negative results can occur, which prevents NIPT from being a diagnostic test. Fetoplacental mosaicism is one of the main reasons for discordant test results. It is therefore important to understand this phenomenon to enable more comprehensive and appropriate genetic counselling. The present review aims to summarize the current knowledge of fetoplacental mosaicism ascertained during cfDNA-based NIPT and refers to the development of recent analytical pipelines for its detection during pregnancy. RECENT FINDINGS Publications are emerging demonstrating that genome-wide approaches to analyzing cfDNA can detect chromosomal aneuploidy other than the common trisomies. Despite the high accuracy of current cfDNA-based NIPT, a substantial number of false-positive and false-negative test results remain. Biological causes, such as fetal or (confined) placental mosaicism have been identified using advanced bioinformatics algorithms. Fetoplacental mosaicism can occur as part of normal pregnancy development, hence clinical practice standards recommend confirmation of positive NIPT results with a diagnostic karyotype or microarray study. SUMMARY cfDNA-based NIPT for fetal chromosomal aneuploidies is not diagnostic because of false-positive and false-negative test results. Recently, novel algorithms have been described that identify pregnancies with an increased risk of fetoplacental mosaicism. Reporting the presence of fetoplacental mosaicism during pregnancy can influence risk estimation and improve genetic counseling.
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Pertile MD, Flowers N, Vavrek D, Andrews D, Kalista T, Craig A, Deciu C, Duenwald S, Meier K, Bhatt S. Performance of a Paired-End Sequencing-Based Noninvasive Prenatal Screening Test in the Detection of Genome-Wide Fetal Chromosomal Anomalies. Clin Chem 2021; 67:1210-1219. [PMID: 34077512 DOI: 10.1093/clinchem/hvab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Noninvasive prenatal tests (NIPTs) detect fetal chromosomal anomalies with high clinical sensitivity and specificity. We examined the performance of a paired-end sequencing-based NIPT in the detection of genome-wide fetal chromosomal anomalies including common trisomies, sex chromosomal aneuploidies (SCA), rare autosomal aneuploidies (RAAs), and partial deletions/duplications ≥7 Mb. METHODS Frozen plasma samples from pregnant women were tested using the VeriSeq NIPT Solution v2 assay. All samples were previously tested with a laboratory-developed NIPT and had known clinical outcomes. Individuals performing the sequencing were blinded to clinical outcome data. Clinical sensitivity and specificity were determined for basic (chromosomes 21, 18, 13, X, and Y) and genome-wide screening modes. RESULTS Of 2335 samples that underwent genome-wide analysis, 28 did not meet QC requirements, resulting in a first-pass assay failure rate of 1.2%. Basic screening analysis, excluding known mosaics, correctly classified 130/130 trisomy 21 samples (sensitivity >99.9%, 95% confidence interval [CI] 97.1%-100%), 41/41 trisomy 18 samples (sensitivity >99.9%, 95% CI 91.4%-100%), and 26/26 trisomy 13 samples (sensitivity >99.9%, 95% CI 87.1%-100%) with 6 false-positive results; specificities ≥99.90% were reported for all 3 trisomies. Concordance for SCAs ranged from 90.5%-100%. Genome-wide screening analysis including known mosaics correctly classified 27/28 RAAs and 20/27 partial deletions/duplications with a specificity of 99.80% for both anomalies, and an overall genome-wide specificity for all anomalies of 99.34%. CONCLUSIONS The VeriSeq NIPT Solution v2 assay enables accurate identification of fetal aneuploidy, allowing detection of genome-wide fetal chromosomal anomalies with high clinical sensitivities and specificities and a low assay failure rate.Clinical Trial Notification [CTN] identification number [ID]: CT-2018-CTN-01585-1 v1, Protocol: NIPT T05 002.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Darcy Vavrek
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Daniel Andrews
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Tasha Kalista
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Andrew Craig
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Cosmin Deciu
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sven Duenwald
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Kristen Meier
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sucheta Bhatt
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
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Yaron Y, Borrell A. Reply: cfDNA testing in recurrent pregnancy loss: a new step in the right way but still raw for the clinical area. Hum Reprod 2021; 36:829-830. [PMID: 33378533 DOI: 10.1093/humrep/deaa360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Antoni Borrell
- BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
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Gou L, Fang Y, Wang N, Zhang M, Liu T, Wang Y, Hu S, Zhang Y, Wu Q, Wang Y, Suo F, Gu M. Clinical management of pregnancies with positive screening results for rare autosomal aneuploidies at a single center. J Int Med Res 2021; 48:300060520966877. [PMID: 33167762 PMCID: PMC7658522 DOI: 10.1177/0300060520966877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objective To review our experiences on clinical management of pregnancies with positive noninvasive prenatal testing (NIPT) results for rare autosomal aneuploidies (RAAs) at a single center. Methods We performed a retrospective study and reviewed data from 18,016 pregnancies undergoing NIPT at a single center in China from March 2017 to February 2020. Depending on the patient’s choice, women with positive screening results for RAAs underwent chromosomal microarray analysis for invasive prenatal diagnosis. Results Thirty-three positive cases for RAAs were identified, with a positive screening rate of 0.18%. The most common RAA was trisomy 7 (33.3%), while trisomies for other chromosomes were less frequent. Monosomies involving chromosomes 16, 14, and 22 were observed. Twenty-eight cases of RAAs underwent invasive diagnosis. Abnormal pregnancy outcomes were observed in four cases, including true fetal mosaicism (n=1), partial uniparental disomy (n=1), miscarriage (n=1), and structural anomalies on ultrasound (n=1). Conclusions RAAs at NIPT might be associated with fetal uniparental disomy, mosaic aneuploidy, and poor pregnancy outcomes, but most positive cases have normal pregnancy outcomes. For RAAs, genetic counseling on the potential risks of abnormal NIPT results, as well as on benefits and limitations of invasive prenatal diagnosis, might help guide clinical management.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuan Fang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Na Wang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Tianya Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yi Wang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yan Zhang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Yifan Wang
- Department of Ultrasound, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Suo
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Maosheng Gu
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
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Eggenhuizen GM, Go A, Koster MPH, Baart EB, Galjaard RJ. Confined placental mosaicism and the association with pregnancy outcome and fetal growth: a review of the literature. Hum Reprod Update 2021; 27:885-903. [PMID: 33984128 PMCID: PMC8382909 DOI: 10.1093/humupd/dmab009] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chromosomal mosaicism can be detected in different stages of early life: in cleavage stage embryos, in blastocysts and biopsied cells from blastocysts during preimplantation genetic testing for aneuploidies (PGT-A) and later during prenatal testing, as well as after birth in cord blood. Mosaicism at all different stages can be associated with adverse pregnancy outcomes. There is an onward discussion about whether blastocysts diagnosed as chromosomally mosaic by PGT-A should be considered safe for transfer. An accurate diagnosis of mosaicism remains technically challenging and the fate of abnormal cells within an embryo remains largely unknown. However, if aneuploid cells persist in the extraembryonic tissues, they can give rise to confined placental mosaicism (CPM). Non-invasive prenatal testing (NIPT) uses cell-free (cf) DNA released from the placenta in maternal blood, facilitating the detection of CPM. In literature, conflicting evidence is found about whether CPM is associated with fetal growth restriction (FGR) and/or other pregnancy outcomes. This makes counselling for patients by clinicians challenging and more knowledge is needed for clinical decision and policy making. OBJECTIVE AND RATIONALE The objective of this review is to evaluate the association between CPM and prenatal growth and adverse pregnancy outcomes. All relevant literature has been reviewed in order to achieve an overview on merged results exploring the relation between CPM and FGR and other adverse pregnancy outcomes. SEARCH METHODS The following Medical Subject Headings (MESH) terms and all their synonyms were used: placental, trophoblast, cytotrophoblast, mosaicism, trisomy, fetal growth, birth weight, small for gestational age and fetal development. A search in Embase, PubMed, Medline Ovid, Web of Science, Cochrane Central Register of Controlled Trials (CENTRAL) and Google Scholar databases was conducted. Relevant articles published until 16 July 2020 were critically analyzed and discussed. OUTCOMES There were 823 articles found and screened based on their title/abstract. From these, 213 articles were selected and full text versions were obtained for a second selection, after which 70 publications were included and 328 cases (fetuses) were analyzed. For CPM in eight different chromosomes (of the total 14 analyzed), there was sufficient evidence that birth weight was often below the 5th percentile of fetal growth standards. FGR was reported in 71.7% of CPM cases and preterm birth (<37 weeks of delivery) was reported in 31.0% of cases. A high rate of structural fetal anomalies, 24.2%, in cases with CPM was also identified. High levels of mosaicism in CVS and presence of uniparental disomy (UPD) were significantly associated with adverse pregnancy outcomes. WIDER IMPLICATIONS Based on the literature, the advice to clinicians is to monitor fetal growth intensively from first trimester onwards in case of CPM, especially when chromosome 2, 3, 7, 13, 15, 16 and 22 are involved. In addition to this, it is advised to examine the fetuses thoroughly for structural fetal anomalies and raise awareness of a higher chance of (possibly extreme) premature birth. Despite prematurity in nearly a fifth of cases, the long-term follow-up of CPM life borns seems to be positive. More understanding of the biological mechanisms behind CPM will help in prioritizing embryos for transfer after the detection of mosaicism in embryos through PGT-A.
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Affiliation(s)
- Geerke M Eggenhuizen
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Attie Go
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Maria P H Koster
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Esther B Baart
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands.,Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Robert Jan Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
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Yaron Y, Pauta M, Badenas C, Soler A, Borobio V, Illanes C, Paz-Y-Miño F, Martinez-Portilla R, Borrell A. Maternal plasma genome-wide cell-free DNA can detect fetal aneuploidy in early and recurrent pregnancy loss and can be used to direct further workup. Hum Reprod 2021; 35:1222-1229. [PMID: 32386059 PMCID: PMC7259365 DOI: 10.1093/humrep/deaa073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/15/2020] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Can maternal plasma cell-free DNA (cfDNA) detect chromosomal anomalies in early pregnancy loss (EPL) and recurrent pregnancy loss (RPL)? SUMMARY ANSWER Genome-wide cfDNA testing can serve as an alternative to cytogenetic analysis in products of conception (POCs) in RPLs and can guide further management. WHAT IS KNOWN ALREADY Random chromosomal anomalies are the single most common cause for EPL and RPL. Cytogenetic analysis in POCs may be used to direct management in RPL because the detection of random chromosomal anomalies can eliminate further unwarranted testing. STUDY DESIGN, SIZE, DURATION This was a prospective diagnostic test study from March 2018 to January 2019 of 109 patients experiencing pregnancy loss before 14 weeks gestation at a tertiary-care academic medical center. PARTICIPANTS/MATERIALS, SETTING, METHODS Blood samples were drawn for genome-wide cfDNA testing prior to chorionic villous sampling for cytogenetic analysis of POCs with both short-term cultures (STCs) and long-term cultures (LTCs). Final analysis included 86 patients with non-mosaic cytogenetic results in POCs and available cfDNA results. Aneuploidy detection rates by cfDNA testing and POC cytogenetic analysis were compared. The first 50 samples served as the Training Set to establish pregnancy loss-specific log-likelihood ratio (LLR) thresholds using receiver-operator characteristic (ROC)-like analyses. These were then used for the entire cohort. MAIN RESULTS AND THE ROLE OF CHANCE Seventy-eight samples (71.5%) had results available from both STC and LTC; 12 samples (11%) had a result from STC only, and 7 samples (6.4%) had a result from LTC only. A chromosomal anomaly was detected in 55/86 (64%). The rates of chromosomal anomalies were 61, 72, 73 and 44% in patients undergoing their first, second, third and ≥4th pregnancy losses, respectively. The median cfDNA fetal fraction was 5%. With standard LLR thresholds used for noninvasive prenatal screening, the sensitivity of cfDNA in detecting aneuploidy was 55% (30/55) and with a specificity of 100% (31/31). Using pregnancy loss-specific LLR thresholds, the sensitivity of cfDNA in detecting aneuploidy was 82% (45/55), with a specificity of 90% (28/31). The positive and negative likelihood ratios were 8.46 and 0.20, respectively. Fetal sex was correctly assigned in all cases. LIMITATIONS, REASONS FOR CAUTION Cases with a false-positive result by cfDNA analysis would not receive the indicated RPL workup. Specificity could be improved by using a fetal fraction (FF) cutoff of 4%, but this would result in exclusion of more than a quarter of cases. WIDER IMPLICATIONS OF THE FINDINGS cfDNA-based testing can serve as an alternative to POC cytogenetic analysis and can guide further RPL management: if cfDNA demonstrates aneuploidy, no further action is taken and if no abnormality is detected, the recommended RPL workup is performed. STUDY FUNDING/COMPETING INTEREST(S) Cell-free DNA testing was funded by Illumina, Inc., San Diego, CA. Y.Y. is a member of Illumina’s Clinical Expert Panel and has received travel grants. A.B. has received travel grants from Illumina. All authors have no competing interest to declare.
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Affiliation(s)
- Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Sourasky Medical Center, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Montse Pauta
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Celia Badenas
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Anna Soler
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Virginia Borobio
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Carmen Illanes
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Fernanda Paz-Y-Miño
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | | | - Antoni Borrell
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain.,BCNatal, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
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Ge Y, Li J, Zhuang J, Zhang J, Huang Y, Tan M, Li W, Chen J, Zhou Y. Expanded noninvasive prenatal testing for fetal aneuploidy and copy number variations and parental willingness for invasive diagnosis in a cohort of 18,516 cases. BMC Med Genomics 2021; 14:106. [PMID: 33853619 PMCID: PMC8045328 DOI: 10.1186/s12920-021-00955-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/01/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) has been wildly used to screen for common aneuplodies. In recent years, the test has been expanded to detect rare autosomal aneuploidies (RATs) and copy number variations (CNVs). This study was performed to investigate the performance of expanded noninvasive prenatal testing (expanded NIPT) in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RATs), and copy number variations (CNVs) and parental willingness for invasive prenatal diagnosis in a Chinese prenatal diagnosis center. METHODS A total of 24,702 pregnant women were retrospectively analyzed at the Women and Children's Hospital from January 2013 to April 2019, among which expanded NIPT had been successfully conducted in 24,702 pregnant women. The high-risk expanded NIPT results were validated by karyotype analysis and chromosomal microarray analysis. All the tested pregnant women were followed up for pregnancy outcomes. RESULTS Of the 24,702 cases, successful follow-up was conducted in 98.77% (401/446) of cases with common trisomies and SCAs, 91.95% (80/87) of RAT and CNV cases, and 76.25% (18,429/24,169) of cases with low-risk screening results. The sensitivity of expanded NIPT was 100% (95% confidence interval[CI], 97.38-100%), 96.67%(95%CI, 82.78-99.92%), and 100%(95%CI, 66.37-100.00%), and the specificity was 99.92%(95%CI, 99.87-99.96%), 99.96%(95%CI, 99.91-99.98%), and 99.88% (95%CI, 99.82-99.93%) for the detection of trisomies 21, 18, and 13, respectively. Expanded NIPT detected 45,X, 47,XXX, 47,XXY, XYY syndrome, RATs, and CNVs with positive predictive values of 25.49%, 75%, 94.12%, 76.19%, 6.45%, and 50%, respectively. The women carrying fetuses with Trisomy 21/Trisomy 18/Trisomy 13 underwent invasive prenatal diagnosis and terminated their pregnancies at higher rates than those at high risk for SCAs, RATs, and CNVs. CONCLUSIONS Our study demonstrates that the expanded NIPT detects fetal trisomies 21, 18, and 13 with high sensitivity and specificity. The accuracy of detecting SCAs, RATs, and CNVs is still relatively poor and needs to be improved. With a high-risk expanded NIPT result, the women at high risk for common trisomies are more likely to undergo invasive prenatal diagnosis procedures and terminate their pregnancies than those with unusual chromosome abnormalities.
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Affiliation(s)
- Yunsheng Ge
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Jia Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, China
| | - Jian Zhang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yanru Huang
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Meihua Tan
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Wei Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong Province, China
| | - Jiayan Chen
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China
| | - Yulin Zhou
- Prenatal Diagnosis Center, Women and Children's Hospital, School of Medicine, Xiamen University, 10 Zhenhai Road, Xiamen, 361003, Fujian Province, China.
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Christiaens L, Chitty LS, Langlois S. Current controversies in prenatal diagnosis: Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered. Prenat Diagn 2021; 41:1316-1323. [PMID: 33829520 DOI: 10.1002/pd.5943] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 11/11/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on analysis of cell free DNA circulating in the maternal plasma has been available clinically to screen for chromosomal abnormalities since 2011. There is significant evidence to suggest that NIPT has revolutionised prenatal screening for the common trisomies 13, 18, and 21. However, the evidence in favour of its extended use to screen for conditions other than these trisomies remains a topic of debate with no national or international organisation supporting clinical implementation for these indications. In the debate presented here - "Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered" - we will see the pros and cons of screening for a wider range of chromosomal problems. The discussion presented swung the vote from 65% in favour and 35% against before the arguments were voiced to 41% in favour and 59% against. This significant swing in the vote indicates that the majority of our community feel more evidence is required before clinical implementation of extended NIPT.
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Affiliation(s)
- Lieve Christiaens
- Illumina Inc., San Diego, California, USA.,University Hospital of Utrecht, Utrecht, Netherlands
| | - Lyn S Chitty
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H. Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China. Genes (Basel) 2021; 12:478. [PMID: 33806256 PMCID: PMC8067030 DOI: 10.3390/genes12040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information.
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Affiliation(s)
- Yunli Lai
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Genetics and Prenatal Diagnosis Center, The First Affiliation Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Sheng He
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yanqing Tang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Fuben Xu
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yun Chen
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Lintao Meng
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yuli Tao
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Shang Yi
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jiasun Su
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Hongqian Huang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jingsi Luo
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hongwei Wei
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
- Department of Obstetrics and Gynaecology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
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Levy B, Hoffmann ER, McCoy RC, Grati FR. Chromosomal mosaicism: Origins and clinical implications in preimplantation and prenatal diagnosis. Prenat Diagn 2021; 41:631-641. [PMID: 33720449 DOI: 10.1002/pd.5931] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
The diagnosis of chromosomal mosaicism in the preimplantation and prenatal stage is fraught with uncertainty and multiple factors need to be considered in order to gauge the likely impact. The clinical effects of chromosomal mosaicism are directly linked to the type of the imbalance (size, gene content, and copy number), the timing of the initial event leading to mosaicism during embryogenesis/fetal development, the distribution of the abnormal cells throughout the various tissues within the body as well as the ratio of normal/abnormal cells within each of those tissues. Additional factors such as assay noise and culture artifacts also have an impact on the significance and management of mosaic cases. Genetic counseling is an important part of educating patients about the likelihood of having a liveborn with a chromosome abnormality and these risks differ according to the time of ascertainment and the tissue where the mosaic cells were initially discovered. Each situation needs to be assessed on a case-by-case basis and counseled accordingly. This review will discuss the clinical impact of finding mosaicism through: embryo biopsy, chorionic villus sampling, amniocentesis, and noninvasive prenatal testing using cell-free DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francesca R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays, S.p.A. (Impact Lab), Busto Arsizio, Varese, Italy
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50
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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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