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Allen SK, Doyle S. Chapter 2: Non-invasive prenatal diagnosis. Best Pract Res Clin Obstet Gynaecol 2024; 97:102544. [PMID: 39255551 DOI: 10.1016/j.bpobgyn.2024.102544] [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: 06/04/2024] [Revised: 06/21/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024]
Abstract
Non-invasive prenatal diagnosis of monogenic disorders is becoming integrated into routine clinical care for many indications. This is carried out by testing cell-free DNA extracted from the plasma portion of a maternal blood sample. The cell-free DNA is low in concentration, and consists of a mixture of maternal and fetally-derived DNA which are not easy to separate. Methods used therefore need to be rapid, sensitive and specific, including real-time PCR, digital PCR and next generation sequencing with complex algorithms. Testing may be required for pregnancies with an increased chance of a monogenic disorder due to family history or carrier status, or where there are specific abnormalities identified by ultrasound scan. In these situations, testing is considered to be diagnostic and therefore does not require confirmation by invasive testing. With increased access to genomic technologies, and more diagnoses for rare disease patients, future demand for NIPD and possibilities during pregnancy will continue.
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Affiliation(s)
- Stephanie K Allen
- Birmingham Women's and Children's NHS Trust, Mindelsohn Way, Edgbaston, Birmingham, B15 2TG, UK.
| | - Samantha Doyle
- The Department of Perinatal Genetics, The National Maternity Hospital, Dublin, 2, Ireland; UCD Perinatal Research Centre, University College Dublin, National Maternity Hospital, Dublin, Ireland.
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2
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Bellair M, Amaral E, Ouren M, Roark C, Kim J, O'Connor A, Soriano A, Schindler ML, Wapner RJ, Stone JL, Tavella N, Merriam A, Perley L, Breman AM, Beaudet AL. Noninvasive single-cell-based prenatal genetic testing: A proof of concept clinical study. Prenat Diagn 2024; 44:304-316. [PMID: 38411249 DOI: 10.1002/pd.6529] [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: 08/16/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
OBJECTIVE To clinically assess a cell-based noninvasive prenatal genetic test using sequence-based copy number analysis of single trophoblasts from maternal blood. METHODS Blood was obtained from 401 (243 + 158) individuals (8-22 weeks) and shipped overnight. Red cells were lysed, and nucleated cells stained for cytokeratin (CK) and CD45 and enriched for positive CK staining. Automated scanning was used to identify and pick single CK+ /CD45- trophoblasts which were subjected to next-generation sequencing. RESULTS Blood was obtained from 243 pregnancies scheduled for CVS or amniocentesis. Luna results were normal for 160 singletons while 15 cases were abnormal (14 aneuploidy and one monozygotic twin with Williams syndrome deletion). The deletion was confirmed in both fetuses. Placental mosaicism occurred in 7 of 236 (3.0%) Luna cases and in 3 of 188 (1.6%) CVS cases (total 4.6%). No scorable trophoblasts were recovered in 32 of 236 usable samples. Additionally, 158 low-risk pregnancies not undergoing CVS/amniocentesis showed normal results in 133 cases. Seven had aneuploidy results, and there were three likely pathogenic deletions/duplications, including one15q11-q13 deletion. CONCLUSION Although the sample size is modest and statistically accurate measures of test performance are not possible, the Luna test detected aneuploidy and deletions/duplications based on concordance with CVS/amniocentesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ronald J Wapner
- Columbia University Irving Medical Center, New York, New York, USA
| | - Joanne L Stone
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicola Tavella
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lauren Perley
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Amy M Breman
- Indiana University School of Medicine, Indianapolis, Indiana, USA
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3
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Maktabi MA, Vossaert L, Van den Veyver IB. Cell-based Noninvasive Prenatal Testing (cbNIPT)-A Review on the Current Developments and Future Prospects. Clin Obstet Gynecol 2023; 66:636-648. [PMID: 37650673 PMCID: PMC10491429 DOI: 10.1097/grf.0000000000000798] [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] [Indexed: 09/01/2023]
Abstract
Considering the diagnostic limitations of cfDNA-based noninvasive prenatal testing (NIPT), scientists have long been interested in isolating and analyzing rare intact fetal and trophoblast cells from maternal blood or endocervical samples to diagnose fetal genetic conditions. These cells may be scarce and difficult to isolate, but they are a direct source of pure fetal genetic material. In this review, we summarize the history of cell-based NIPT, present an updated review on its current developments, evaluate its genetic diagnostic potential, and discuss its future prospects for clinical use.
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Affiliation(s)
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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4
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Chang L, Jiao H, Chen J, Wu G, Liu P, Li R, Guo J, Long W, Tang X, Lu B, Xu H, Wu H. Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases. Life Sci Alliance 2023; 6:e202201761. [PMID: 36810160 PMCID: PMC9947115 DOI: 10.26508/lsa.202201761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemophilia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases.
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Affiliation(s)
- Liang Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Haining Jiao
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiucheng Chen
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Guanlin Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jianying Guo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Wenqing Long
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojian Tang
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingjie Lu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Haibin Xu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Han Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
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5
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Guibourdenche J, Leguy MC, Pidoux G, Hebert-Schuster M, Laguillier C, Anselem O, Grangé G, Bonnet F, Tsatsaris V. Biochemical Screening for Fetal Trisomy 21: Pathophysiology of Maternal Serum Markers and Involvement of the Placenta. Int J Mol Sci 2023; 24:ijms24087669. [PMID: 37108840 PMCID: PMC10146970 DOI: 10.3390/ijms24087669] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
It is now well established that maternal serum markers are often abnormal in fetal trisomy 21. Their determination is recommended for prenatal screening and pregnancy follow-up. However, mechanisms leading to abnormal maternal serum levels of such markers are still debated. Our objective was to help clinicians and scientists unravel the pathophysiology of these markers via a review of the main studies published in this field, both in vivo and in vitro, focusing on the six most widely used markers (hCG, its free subunit hCGβ, PAPP-A, AFP, uE3, and inhibin A) as well as cell-free feto-placental DNA. Analysis of the literature shows that mechanisms underlying each marker's regulation are multiple and not necessarily directly linked with the supernumerary chromosome 21. The crucial involvement of the placenta is also highlighted, which could be defective in one or several of its functions (turnover and apoptosis, endocrine production, and feto-maternal exchanges and transfer). These defects were neither constant nor specific for trisomy 21, and might be more or less pronounced, reflecting a high variability in placental immaturity and alteration. This explains why maternal serum markers can lack both specificity and sensitivity, and are thus restricted to screening.
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Affiliation(s)
- Jean Guibourdenche
- Hormonologie CHU Cochin AP-HP, 75014 Paris, France
- Faculté de Santé, Université Paris Cité, 75014 Paris, France
- FHU Préma, 75014 Paris, France
| | | | | | | | - Christelle Laguillier
- Hormonologie CHU Cochin AP-HP, 75014 Paris, France
- Faculté de Santé, Université Paris Cité, 75014 Paris, France
- UMR-S1139, 75014 Paris, France
| | - Olivia Anselem
- FHU Préma, 75014 Paris, France
- Maternité Port Royal CHU Cochin AP-HP, 75014 Paris, France
| | - Gilles Grangé
- FHU Préma, 75014 Paris, France
- Maternité Port Royal CHU Cochin AP-HP, 75014 Paris, France
| | - Fidéline Bonnet
- Hormonologie CHU Cochin AP-HP, 75014 Paris, France
- Faculté de Santé, Université Paris Cité, 75014 Paris, France
| | - Vassilis Tsatsaris
- Faculté de Santé, Université Paris Cité, 75014 Paris, France
- FHU Préma, 75014 Paris, France
- Maternité Port Royal CHU Cochin AP-HP, 75014 Paris, France
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Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility. Heliyon 2023; 9:e13923. [PMID: 36879971 PMCID: PMC9984859 DOI: 10.1016/j.heliyon.2023.e13923] [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: 07/10/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.
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Blagowidow N, Nowakowska B, Schindewolf E, Grati FR, Putotto C, Breckpot J, Swillen A, Crowley TB, Loo JCY, Lairson LA, Óskarsdóttir S, Boot E, Garcia-Minaur S, Cristina Digilio M, Marino B, Coleman B, Moldenhauer JS, Bassett AS, McDonald-McGinn DM. Prenatal Screening and Diagnostic Considerations for 22q11.2 Microdeletions. Genes (Basel) 2023; 14:160. [PMID: 36672900 PMCID: PMC9858737 DOI: 10.3390/genes14010160] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 01/11/2023] Open
Abstract
Diagnosis of a chromosome 22q11.2 microdeletion and its associated deletion syndrome (22q11.2DS) is optimally made early. We reviewed the available literature to provide contemporary guidance and recommendations related to the prenatal period. Indications for prenatal diagnostic testing include a parent or child with the 22q11.2 microdeletion or suggestive prenatal screening results. Definitive diagnosis by genetic testing of chorionic villi or amniocytes using a chromosomal microarray will detect clinically relevant microdeletions. Screening options include noninvasive prenatal screening (NIPS) and imaging. The potential benefits and limitations of each screening method should be clearly conveyed. NIPS, a genetic option available from 10 weeks gestational age, has a 70-83% detection rate and a 40-50% PPV for most associated 22q11.2 microdeletions. Prenatal imaging, usually by ultrasound, can detect several physical features associated with 22q11.2DS. Findings vary, related to detection methods, gestational age, and relative specificity. Conotruncal cardiac anomalies are more strongly associated than skeletal, urinary tract, or other congenital anomalies such as thymic hypoplasia or cavum septi pellucidi dilatation. Among others, intrauterine growth restriction and polyhydramnios are additional associated, prenatally detectable signs. Preconception genetic counselling should be offered to males and females with 22q11.2DS, as there is a 50% risk of transmission in each pregnancy. A previous history of a de novo 22q11.2 microdeletion conveys a low risk of recurrence. Prenatal genetic counselling includes an offer of screening or diagnostic testing and discussion of results. The goal is to facilitate optimal perinatal care.
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Affiliation(s)
- Natalie Blagowidow
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD 21204, USA
| | - Beata Nowakowska
- Cytogenetic Laboratory, Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17a, 01-211 Warsaw, Poland
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment and the 22q and You Center, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Francesca Romana Grati
- R&D Department, Menarini Biomarkers Singapore, Via Giuseppe di Vittorio 21/b3, 40013 Castel Maggiore, Italy
| | - Carolina Putotto
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome (Italy), Viale del Policlinico 155, 00161 Roma, Italy
| | - Jeroen Breckpot
- Center for Human Genetics, Herestraat 49, 3000 Leuven, Belgium
| | - Ann Swillen
- Center for Human Genetics, Herestraat 49, 3000 Leuven, Belgium
| | - Terrence Blaine Crowley
- Division of Human Genetics, The 22q and You Center, and Clinical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Joanne C. Y. Loo
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Lauren A. Lairson
- Division of Human Genetics, The 22q and You Center, and Clinical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sólveig Óskarsdóttir
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Department of Paediatrics, Queen Silva Children’s Hospital, 416 50 Gothenburg, Sweden
| | - Erik Boot
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON M5G 2C4, Canada
- Advisium’s Heeren Loo, Berkenweg 11, 3818 LA Amersfoort, The Netherlands
- Department of Psychiatry and Neuropsychology, Maastricht University, 6211 LK Maastricht, The Netherlands
| | - Sixto Garcia-Minaur
- Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, 28046 Madrid, Spain
| | | | - Bruno Marino
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome (Italy), Viale del Policlinico 155, 00161 Roma, Italy
| | - Beverly Coleman
- Center for Fetal Diagnosis and Treatment and the 22q and You Center, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Radiology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie S. Moldenhauer
- Center for Fetal Diagnosis and Treatment and the 22q and You Center, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Obstetrics, Gynecology, and Surgery, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON M5G 2C4, Canada
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, and Department of Psychiatry, University of Toronto, Toronto, ON M5S 2S1, Canada
- Division of Cardiology, Department of Medicine, and Centre for Mental Health, and Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2N2, Canada
| | - Donna M. McDonald-McGinn
- Division of Human Genetics, The 22q and You Center, and Clinical Genetics Center, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185 Roma, Italy
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Doffini A, Forcato C, Mangano C, Lattuada D, Aversa R, Maranta C, Giovannone ED, Buson G, Bolognesi C, Maiocchi R, Dori M, Jamal L, Ahmad RB, Yeo GSH, Yeo TW, Saragozza S, Silipigni R, Serafini M, Biondi A, Perego S, Vergani P, Ferrazzi E, Ricciardi-Castagnoli P, Musci TJ, Grati FR. Isolation of single circulating trophoblasts from maternal circulation for noninvasive fetal copy number variant profiling. Prenat Diagn 2023; 43:14-27. [PMID: 36443901 PMCID: PMC10107339 DOI: 10.1002/pd.6275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To develop a multi-step workflow for the isolation of circulating extravillous trophoblasts (cEVTs) by describing the key steps enabling a semi-automated process, including a proprietary algorithm for fetal cell origin genetic confirmation and copy number variant (CNV) detection. METHODS Determination of the limit of detection (LoD) for submicroscopic CNV was performed by serial experiments with genomic DNA and single cells from Coriell cell line biobank with known imbalances of different sizes. A pregnancy population of 372 women was prospectively enrolled and blindly analyzed to evaluate the current workflow. RESULTS An LoD of 800 Kb was demonstrated with Coriell cell lines. This level of resolution was confirmed in the clinical cohort with the identification of a pathogenic CNV of 800 Kb, also detected by chromosomal microarray. The mean number of recovered cEVTs was 3.5 cells per sample with a significant reverse linear trend between gestational age and cEVT recovery rate and number of recovered cEVTs. In twin pregnanices, evaluation of zygosity, fetal sex and copy number profiling was performed in each individual cell. CONCLUSION Our semi-automated methodology for the isolation and single-cell analysis of cEVTS supports the feasibility of a cell-based noninvasive prenatal test for fetal genomic profiling.
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Affiliation(s)
- Anna Doffini
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Claudio Forcato
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Chiara Mangano
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Debora Lattuada
- Department of Woman Child and Neonate, Obstetrics Unit, Fondazione IRCCS, Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Roberta Aversa
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Chiara Maranta
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Emilia D Giovannone
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Genny Buson
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Chiara Bolognesi
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Rebecca Maiocchi
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Martina Dori
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Liyana Jamal
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Raidah B Ahmad
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - George S H Yeo
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Tai Wai Yeo
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Silvia Saragozza
- Research and Development, Cytogenetics and Molecular Genetics, TOMA Advanced Biomedical Assays S.p.A., Impact Lab, Busto Arsizio, Italy
| | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marta Serafini
- Centro Ricerca M. Tettamanti, Department of Pediatrics, University of Milano-Bicocca, Monza, Italy
| | - Andrea Biondi
- Centro Ricerca M. Tettamanti, Department of Pediatrics, University of Milano-Bicocca, Monza, Italy
| | - Sofia Perego
- Department of Obstetrics and Gynecology, MBBM Foundation Onlus at San Gerardo Hospital, Monza, Italy
| | - Patrizia Vergani
- Department of Obstetrics and Gynecology, MBBM Foundation Onlus at San Gerardo Hospital, Monza, Italy
| | - Enrico Ferrazzi
- Department of Woman Child and Neonate, Obstetrics Unit, Fondazione IRCCS, Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Thomas J Musci
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore
| | - Francesca Romana Grati
- A. Menarini Biomarkers Singapore Pte Ltd, R&D department, Singapore, Singapore.,Research and Development, Cytogenetics and Molecular Genetics, TOMA Advanced Biomedical Assays S.p.A., Impact Lab, Busto Arsizio, Italy
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9
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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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Liehr T, Harutyunyan T, Williams H, Weise A. Non-Invasive Prenatal Testing in Germany. Diagnostics (Basel) 2022; 12:2816. [PMID: 36428876 PMCID: PMC9689121 DOI: 10.3390/diagnostics12112816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
In the short 10 years following the introduction of non-invasive prenatal testing (NIPT), it has been adapted in many countries around the world as a standard screening test. In this review, this development was analyzed with a special focus on Germany. As a result, it can be stated that all known advantages of NIPT apart from "compensating for having no access to centers offering invasive diagnostics" are valid for Germany. In addition, following a review of the international literature, all documented issues with NIPT are also observed in Germany. However, the German Gene Diagnostics Act (GenDG) addresses a number of these issues, for example, the regulations by GenDG hamper induced abortions, based exclusively on an abnormal NIPT result. At the same time, GenDG has created new problems, as a possible collusion between the "right not to know with regard to parts of the examination result" may occur, or that the sex of the fetus must not be reported to the pregnant woman before the 12th week of gestation. Main conclusions drawn are that appropriate training and the continuing education of the physicians providing NIPT-related counseling are needed, as well as the provision of balanced and comprehensive information for the pregnant woman or the couple that is imperative.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0001, Armenia
| | | | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, 07747 Jena, Germany
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Feresin A, Stampalija T, Cappellani S, Bussani R, Faletra F, Murru F, Ulivi S, Suergiu S, Savarese P, Pedicini A, Policicchio M, Ruggiero R, Bosio B, Savarese G, Ardisia C. Case Report: Two cases of apparent discordance between non-invasive prenatal testing (NIPT) and amniocentesis resulting in feto-placental mosaicism of trisomy 21. Issues in diagnosis, investigation and counselling. Front Genet 2022; 13:982508. [PMID: 36386832 PMCID: PMC9642548 DOI: 10.3389/fgene.2022.982508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
The sequencing of cell-free fetal DNA in the maternal plasma through non-invasive prenatal testing (NIPT) is an accurate genetic screening test to detect the most common fetal aneuploidies during pregnancy. The extensive use of NIPT, as a screening method, has highlighted the limits of the technique, including false positive and negative results. Feto-placental mosaicism is a challenging biological issue and is the most frequent cause of false positive and negative results in NIPT screening, and of discrepancy between NIPT and invasive test results. We are reporting on two cases of feto-placental mosaicism of trisomy 21, both with a low-risk NIPT result, identified by ultrasound signs and a subsequent amniocentesis consistent with a trisomy 21. In both cases, after the pregnancy termination, cytogenetic and/or cytogenomic analyses were performed on the placenta and fetal tissues, showing in the first case a mosaicism of trisomy 21 in both the placenta and the fetus, but a mosaicism in the placenta and a complete trisomy 21 in the fetus in the second case. These cases emphasize the need for accurate and complete pre-test NIPT counselling, as well as to identify situations at risk for a possible false negative NIPT result, which may underestimate a potential pathological condition, such as feto-placental mosaicism or fetal trisomy. Post-mortem molecular autopsy may discriminate between placental, fetal and feto-placental mosaicism, and between complete or mosaic fetal chromosomal anomalies. A multidisciplinary approach in counselling, as well as in the interpretation of biological events, is essential for the clarification of complex cases, such as feto-placental mosaicisms.
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Affiliation(s)
- Agnese Feresin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Tamara Stampalija
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Stefania Cappellani
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Rossana Bussani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Unit of Pathologic Anatomy and Histology, Asugi, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Flora Murru
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Sheila Ulivi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Sarah Suergiu
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | | | | | | | | | - Barbara Bosio
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | | | - Carmela Ardisia
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
- *Correspondence: Carmela Ardisia,
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12
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Crovetti B, Maktabi MA, Erfani H, Panchalee T, Wang Q, Vossaert L, Van den Veyver I. Circulating trophoblast numbers as a potential marker for pregnancy complications. Prenat Diagn 2022; 42:1182-1189. [PMID: 35765264 PMCID: PMC9710861 DOI: 10.1002/pd.6202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/23/2022] [Accepted: 06/23/2022] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To explore the potential of circulating trophoblasts (TBs) as a non-invasive tool to assess placental health and predict obstetric complications. METHODS We retrospectively reviewed maternal characteristics and pregnancy outcomes of 369 women who enrolled in our original cell-based NIPT (cbNIPT) study. The number of circulating TBs recovered from the maternal blood samples was recorded and expressed as fetal cell concentration (FCC). We evaluated if FCC can be used to predict pregnancy outcomes such as hypertensive disorders of pregnancy (HDP), fetal growth restriction, placental abruption, preterm labor, and pregnancy loss. RESULTS Receiver operating characteristic (ROC) analysis was performed to find the best cut off value to classify FCC into a low and high FCC group, and this cut-off point was calculated as 11.1 cells per 100 ml of blood. The adjusted odds ratio (aOR) for the composite morbidity was significantly increased for the high FCC group at an aOR of 1.6. CONCLUSION Circulating TB have the potential of predicting obstetrical complications such as HDP. Future studies, with larger sample sizes, should focus on the study of these cells as a biomarker for placental health and a possible screening or diagnostic tool for fetal genetic conditions.
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Affiliation(s)
- Brielle Crovetti
- School of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Mohamad Ali Maktabi
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA
| | - Hadi Erfani
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA
| | - Tachjaree Panchalee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Liesbeth Vossaert
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA
| | - Ignatia Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
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13
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Chen Y, Lu L, Zhang Y, Wang F, Ni Y, Wang Q, Ying C. Clinical application of expanded noninvasive prenatal testing for fetal chromosome abnormalities in a cohort of 39,580 pregnancies. Am J Med Genet A 2022; 188:1426-1434. [PMID: 35107205 DOI: 10.1002/ajmg.a.62657] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/02/2022] [Accepted: 01/06/2022] [Indexed: 11/07/2022]
Abstract
The aim of this study was to determine the predictive value of expanded noninvasive prenatal testing (NIPT-plus) for fetal chromosome abnormalities in the second trimester (12-26 weeks). We conducted a retrospective cohort study of 39,580 pregnancies with NIPT-plus. Screening positive cases were diagnosed with karyotyping and single-nucleotide polymorphism array analysis (SNP array)/copy number variation sequencing (CNV-seq) with follow-up. The positive predictive values (PPVs) of trisomy 21, 18, and 13 (T21, T18, and T13), sex chromosome aneuploidies (SCAs), and microdeletion and microduplication syndromes (MMS) by NIPT-plus were recorded. We assessed the predictive value of NIPT-plus based on maternal age and conventional indications. Of 39,580 pregnancies with NIPT-plus, 511 (1.3%) had prenatal screening positive results of fetal chromosome abnormality, of which 87.7% (448/511) had invasive prenatal diagnosis. NIPT-plus performed better in predicting fetal SCAs and chromosome aneuploidies for pregnancies with advanced maternal age (AMA) than young maternal age (YMA). Besides, the PPVs of T21, T13, and chromosome aneuploidies showed an upward trend when comparison was based on maternal age in 5-year subintervals. The termination rates of 45,X, 47,XXX, 47,XXY, and 47,XYY were 100% (11/11), 20.0% (3/15), 91.7% (22/24), and 7.1% (1/14) with postnatal follow-up. Last but not least, the PPV for MMS is 41.7% (30/72), which may have a positive correlation between the size of CNVs. Pregnant women with screen-positive results for common trisomies (T13, T18, and T21) were more willing to conduct invasive prenatal diagnosis compared to those with positive results for SCAs or MMS. However, the current study demonstrated SCAs and MMS had the lowest PPV. This highlights the importance of confirmatory prenatal diagnosis in those patients and the potential impact on genetic counseling and informative decision-making.
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Affiliation(s)
- Yisheng Chen
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Loukaiyi Lu
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Feifei Wang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yinghua Ni
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qiang Wang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Chunmei Ying
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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14
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Alsaffar MM, Hasan M, McStay GP, Sedky M. Digital DNA lifecycle security and privacy: an overview. Brief Bioinform 2022; 23:6518049. [PMID: 35106557 DOI: 10.1093/bib/bbab607] [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: 08/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/14/2022] Open
Abstract
DNA sequencing technologies have advanced significantly in the last few years leading to advancements in biomedical research which has improved personalised medicine and the discovery of new treatments for diseases. Sequencing technology advancement has also reduced the cost of DNA sequencing, which has led to the rise of direct-to-consumer (DTC) sequencing, e.g. 23andme.com, ancestry.co.uk, etc. In the meantime, concerns have emerged over privacy and security in collecting, handling, analysing and sharing DNA and genomic data. DNA data are unique and can be used to identify individuals. Moreover, those data provide information on people's current disease status and disposition, e.g. mental health or susceptibility for developing cancer. DNA privacy violation does not only affect the owner but also affects their close consanguinity due to its hereditary nature. This article introduces and defines the term 'digital DNA life cycle' and presents an overview of privacy and security threats and their mitigation techniques for predigital DNA and throughout the digital DNA life cycle. It covers DNA sequencing hardware, software and DNA sequence pipeline in addition to common privacy attacks and their countermeasures when DNA digital data are stored, queried or shared. Likewise, the article examines DTC genomic sequencing privacy and security.
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Affiliation(s)
- Muhalb M Alsaffar
- Department of Computing, AI and Robotics, School of Digital, Technologies and Arts, Staffordshire University, College Road, ST4 2DE, Staffordshire, United Kingdom
| | | | - Gavin P McStay
- Department of Biological Sciences, School of Health, Science and Wellbeing, Staffordshire University, College Road, Stoke-on-Trent, Staffordshire, ST4 2DE, United Kingdom
| | - Mohamed Sedky
- Department of Computing, AI and Robotics, School of Digital, Technologies and Arts, Staffordshire University, College Road, ST4 2DE, Staffordshire, United Kingdom
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15
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Chitty LS. Non-invasive prenatal testing 10 years on. Prenat Diagn 2021; 41:1187-1189. [PMID: 34418119 DOI: 10.1002/pd.6032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/26/2023]
Affiliation(s)
- Lyn S Chitty
- Great Ormond Street NHS Foundation Trust and the UCL GOS Institute of Child Health, London, UK
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