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Ngo LT, Chaudhari P, Wang WK, Tseng YT, Kuo PL, Huang CJ, Chiang CY, Chau LK, Huang TT. Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay. ACS Sens 2024; 9:4207-4215. [PMID: 39088458 DOI: 10.1021/acssensors.4c01194] [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] [Indexed: 08/03/2024]
Abstract
β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.
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Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pallavi Chaudhari
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Wei-Kai Wang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, College of Medicine, National Cheng Kung University Hospital, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, 1 Yida Rd., Yanchao District, Kaohsiung City 82445, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, 300 Zhongda Rd., Zhongli District, Taoyuan City 320, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung Pei Rd., Chung-Li City 32023, Taiwan
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
- Center for Nano Bio-Detection, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Tze-Ta Huang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Stomatology, College of Medicine and Hospital, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
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Anton-Păduraru DT, Azoicăi AN, Trofin F, Mîndru DE, Murgu AM, Bocec AS, Iliescu Halițchi CO, Ciongradi CI, Sȃrbu I, Iliescu ML. Diagnosing Cystic Fibrosis in the 21st Century-A Complex and Challenging Task. Diagnostics (Basel) 2024; 14:763. [PMID: 38611676 PMCID: PMC11012009 DOI: 10.3390/diagnostics14070763] [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: 03/04/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Cystic fibrosis (CF) is a chronic and potentially life-threatening condition, wherein timely diagnosis assumes paramount significance for the prompt initiation of therapeutic interventions, thereby ameliorating pulmonary function, addressing nutritional deficits, averting complications, mitigating morbidity, and ultimately enhancing the quality of life and extending longevity. This review aims to amalgamate existing knowledge to provide a comprehensive appraisal of contemporary diagnostic modalities pertinent to CF in the 21st century. Deliberations encompass discrete delineations of each diagnostic modality and the elucidation of potential diagnostic quandaries encountered in select instances, as well as the delineation of genotype-phenotype correlations germane to genetic counseling endeavors. The synthesis underscores that, notwithstanding the availability and strides in diagnostic methodologies, including genetic assays, the sweat test (ST) retains its position as the preeminent diagnostic standard for CF, serving as a robust surrogate for CFTR functionality. Prospective clinical investigations in the realm of CF should be orchestrated with the objective of discerning novel diagnostic modalities endowed with heightened specificity and sensitivity.
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Affiliation(s)
- Dana-Teodora Anton-Păduraru
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
| | - Alice Nicoleta Azoicăi
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
| | - Felicia Trofin
- Department of Preventive Medicine and Interdisciplinarity—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania
| | - Dana Elena Mîndru
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
| | - Alina Mariela Murgu
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
| | - Ana Simona Bocec
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
| | - Codruța Olimpiada Iliescu Halițchi
- Department of Mother and Child Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania; (D.-T.A.-P.); (A.N.A.); (D.E.M.); (A.M.M.); (A.S.B.); (C.O.I.H.)
| | - Carmen Iulia Ciongradi
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
- 2nd Department of Surgery, Pediatric Surgery and Orthopedics, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania
| | - Ioan Sȃrbu
- “Sf.Maria” Children Emergency Hospital, 700309 Iaṣi, Romania; (C.I.C.); (I.S.)
- 2nd Department of Surgery, Pediatric Surgery and Orthopedics, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania
| | - Maria Liliana Iliescu
- Department of Preventive Medicine and Interdisciplinarity—Public Health and Health Management, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaṣi, Romania;
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Abedalthagafi M, Bawazeer S, Fawaz RI, Heritage AM, Alajaji NM, Faqeih E. Non-invasive prenatal testing: a revolutionary journey in prenatal testing. Front Med (Lausanne) 2023; 10:1265090. [PMID: 38020177 PMCID: PMC10666054 DOI: 10.3389/fmed.2023.1265090] [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: 07/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) is a pioneering technique that has consistently advanced the field of prenatal testing to detect genetic abnormalities and conditions with the aim of decreasing the incidence and prevalence of inherited conditions. NIPT remains a method of choice for common autosomal aneuploidies, mostly trisomy 21, and several monogenic disorders. The advancements in gene sequencing techniques have expanded the panel of conditions where NIPT could be offered. However, basic research on the impact of several genetic conditions lags behind the methods of detection of these sequence aberrations, and the impact of the expansion of NIPT should be carefully considered based on its utility. With interest from commercial diagnostics and a lack of regulatory oversight, there remains a need for careful validation of the predictive values of different tests offered. NIPT comes with many challenges, including ethical and economic issues. The scientific evidence, technical feasibility, and clinical benefit of NIPT need to be carefully investigated before new tests and developments are translated into clinical practice. Moreover, the implementation of panel expansion of NIPT should accompany expert genetic counseling pre- and post-testing.
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Affiliation(s)
- Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA, United States
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Shahad Bawazeer
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | - Nouf M. Alajaji
- Department of Maternal Fetal Medicine, Women's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
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Faldynová L, Walczysková S, Černá D, Kudrejová M, Hilscherová Š, Kaniová R, Širůčková S. Non-invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an "in-house" target enrichment next generation sequencing-Solution for non-centralized NIPT laboratory? Prenat Diagn 2023; 43:1320-1332. [PMID: 37602788 DOI: 10.1002/pd.6421] [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: 05/24/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVE Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities. METHOD From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods. RESULTS The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant. CONCLUSION The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.
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Affiliation(s)
- Lucie Faldynová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Sylwia Walczysková
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Dita Černá
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Monika Kudrejová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Šárka Hilscherová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Romana Kaniová
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Simona Širůčková
- Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
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Gonsalves Z, Klugman S. Noninvasive Prenatal Screening for Single-Gene Disorders. Clin Obstet Gynecol 2023; 66:629-635. [PMID: 37650672 DOI: 10.1097/grf.0000000000000795] [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
Single-gene disorders (SGDs), also known as monogenic disorders, are caused by pathogenic variants at individual loci. Prenatal cell-free DNA screening for SGDs has been investigated for decades. Detecting paternal and de novo variants may be somewhat straightforward, whereas detecting maternally inherited variants poses a significant challenge. Although commercially available in both high-risk and low-risk patients, many limitations exist. The use of SGDs is not supported by professional medical societies.
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Affiliation(s)
- Zenobia Gonsalves
- Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, New York
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Carrier Screening Programs for Cystic Fibrosis, Fragile X Syndrome, Hemoglobinopathies and Thalassemia, and Spinal Muscular Atrophy: A Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2023; 23:1-398. [PMID: 37637488 PMCID: PMC10453298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Background We conducted a health technology assessment to evaluate the safety, effectiveness, and cost-effectiveness of carrier screening programs for cystic fibrosis (CF), fragile X syndrome (FXS), hemoglobinopathies and thalassemia, and spinal muscular atrophy (SMA) in people who are considering a pregnancy or who are pregnant. We also evaluated the budget impact of publicly funding carrier screening programs, and patient preferences and values. Methods We performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Cochrane Risk of Bias tool and the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We performed a systematic economic literature search and conducted cost-effectiveness analyses comparing preconception or prenatal carrier screening programs to no screening. We considered four carrier screening strategies: 1) universal screening with standard panels; 2) universal screening with a hypothetical expanded panel; 3) risk-based screening with standard panels; and 4) risk-based screening with a hypothetical expanded panel. We also estimated the 5-year budget impact of publicly funding preconception or prenatal carrier screening programs for the given conditions in Ontario. To contextualize the potential value of carrier screening, we spoke with 22 people who had sought out carrier screening. Results We included 107 studies in the clinical evidence review. Carrier screening for CF, hemoglobinopathies and thalassemia, FXS, and SMA likely results in the identification of couples with an increased chance of having an affected pregnancy (GRADE: Moderate). Screening likely impacts reproductive decision-making (GRADE: Moderate) and may result in lower anxiety among pregnant people, although the evidence is uncertain (GRADE: Very low).We included 21 studies in the economic evidence review, but none of the study findings were directly applicable to the Ontario context. Our cost-effectiveness analyses showed that in the short term, preconception or prenatal carrier screening programs identified more at-risk pregnancies (i.e., couples that tested positive) and provided more reproductive choice options compared with no screening, but were associated with higher costs. While all screening strategies had similar values for health outcomes, when comparing all strategies together, universal screening with standard panels was the most cost-effective strategy for both preconception and prenatal periods. The incremental cost-effectiveness ratios (ICERs) of universal screening with standard panels compared with no screening in the preconception period were $29,106 per additional at-risk pregnancy detected and $367,731 per affected birth averted; the corresponding ICERs in the prenatal period were about $29,759 per additional at-risk pregnancy detected and $431,807 per affected birth averted.We estimated that publicly funding a universal carrier screening program in the preconception period over the next 5 years would require between $208 million and $491 million. Publicly funding a risk-based screening program in the preconception period over the next 5 years would require between $1.3 million and $2.7 million. Publicly funding a universal carrier screening program in the prenatal period over the next 5 years would require between $128 million and $305 million. Publicly funding a risk-based screening program in the prenatal period over the next 5 years would require between $0.8 million and $1.7 million. Accounting for treatment costs of the screened health conditions resulted in a decrease in the budget impact of universally provided carrier screening programs or cost savings for risk-based programs.Participants value the perceived potential positive impact of carrier screening programs such as medical benefits from early detection and treatment, information for reproductive decision-making, and the social benefit of awareness and preparation. There was a strong preference expressed for thorough, timely, unbiased information to allow for informed reproductive decision-making. Conclusions Carrier screening for CF, FXS, hemoglobinopathies and thalassemia, and SMA is effective at identifying at-risk couples, and test results may impact preconception and reproductive decision-making.The cost-effectiveness and budget impact of carrier screening programs are uncertain for Ontario. Over the short term, carrier screening programs are associated with higher costs, and also higher chances of detecting at-risk pregnancies compared with no screening. The 5-year budget impact of publicly funding universal carrier screening programs is larger than that of risk-based programs. However, accounting for treatment costs of the screened health conditions results in a decrease in the total additional costs for universal carrier screening programs or in cost savings for risk-based programs.The people we spoke with who had sought out carrier screening valued the potential medical benefits of early detection and treatment, particularly the support and preparation for having a child with a potential genetic condition.
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Nguyen HM, Lindsay C, Baradaran M, Guertin JR, Nshimyumukiza L, Soukkhaphone B, Reinharz D. Development of a discrete choice experiment questionnaire to elicit preferences by pregnant women and policymakers for the expansion of non-invasive prenatal screening. PLoS One 2023; 18:e0287653. [PMID: 37352239 PMCID: PMC10289448 DOI: 10.1371/journal.pone.0287653] [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: 10/12/2022] [Accepted: 06/10/2023] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVE An instrument for measuring intervention preferences applicable to both patients and policymakers would make it possible to better confront the needs of the supply and demand sides of the health care system. This study aimed to develop a discrete choice experiments (DCE) questionnaire to elicit the preferences of patients and policymakers. The instrument was specifically developed to estimate preferences for new conditions to be added to a screening program for fetal chromosomal anomalies. METHODS A DCE development study was conducted. The methods employed included a literature review, a qualitative study (based on individual semi-structured interviews, consultations, and a focus group discussion) with pregnant women and policymakers, and a pilot project with 33 pregnant women to validate the first version of the instrument and test the feasibility of its administration. RESULTS An initial list of 10 attributes was built based on a literature review and the qualitative research components of the study. Five attributes were built based on the responses provided by the participants from both groups. Eight attributes were consensually retained. A pilot project performed on 33 pregnant women led to a final instrument containing seven attributes: 'conditions to be screened', 'test performance', 'moment at gestational age to obtain the test result', 'degree of test result certainty to the severity of the disability', 'test sufficiency', 'information provided from test result', and 'cost related to the test'. CONCLUSION It is possible to reach a consensus on the construction of a DCE instrument intended to be administered to pregnant women and policymakers. However, complete validation of the consensual instrument is limited because there are too few voting members of health technology assessment agencies committees to statistically ascertain the relevance of the attributes and their levels.
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Affiliation(s)
- Hung Manh Nguyen
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
| | - Carmen Lindsay
- Centre de Recherche du CHU de Québec, Université Laval, Québec, Canada
| | - Mohammad Baradaran
- Département de Génie Électrique et de Génie Informatique, Université Laval, Québec, Canada
| | - Jason Robert Guertin
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
- Centre de Recherche du CHU de Québec, Université Laval, Québec, Canada
| | - Leon Nshimyumukiza
- Institut national D’excellence en Santé et en Services Sociaux, Québec, Canada
- Faculté des Sciences Infirmières, Université Laval, Québec, Canada
| | | | - Daniel Reinharz
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
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Jeppesen LD, Lildballe DL, Hatt L, Hedegaard J, Singh R, Toft CLF, Schelde P, Pedersen AS, Knudsen M, Vogel I. Noninvasive prenatal screening for cystic fibrosis using circulating trophoblasts: Detection of the 50 most common disease-causing variants. Prenat Diagn 2023; 43:3-13. [PMID: 36447355 PMCID: PMC10107343 DOI: 10.1002/pd.6276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
OBJECTIVES Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders. Prenatal or preconception CF screening is offered in some countries. A maternal blood sample in early pregnancy can provide circulating trophoblasts and offers a DNA source for genetic analysis of both the mother and the fetus. This study aimed to develop a cell-based noninvasive prenatal test (NIPT) to screen for the 50 most common CF variants. METHODS Blood samples were collected from 30 pregnancies undergoing invasive diagnostics and circulating trophoblasts were harvested in 27. Cystic fibrosis testing was conducted using two different methods: by fragment length analysis and by our newly developed NGS-based CF analysis. RESULTS In all 27 cases, cell-based NIPT provided a result using both methods in agreement with the invasive test result. CONCLUSION This study shows that cell-based NIPT for CF screening provides a reliable result without the need for partner- and proband samples.
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Affiliation(s)
- Line Dahl Jeppesen
- ARCEDI, Vejle, Denmark.,Center for Fetal Diagnostics, Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Dorte Launholt Lildballe
- Center for Fetal Diagnostics, Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | - Christian Liebst Frisk Toft
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark
| | | | - Anders Sune Pedersen
- ARCEDI, Vejle, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- ARCEDI, Vejle, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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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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Li YQ, Tan GJ, Zhou YQ. Digital PCR and its applications in noninvasive prenatal testing. Brief Funct Genomics 2022; 21:376-386. [PMID: 35923115 DOI: 10.1093/bfgp/elac024] [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: 02/14/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
In the past decade, digital PCR (dPCR), as a new nucleic acid absolute quantification technology, has been widely used in clinical research. dPCR does not rely on the standard curve and has a higher tolerance to inhibitors. Therefore, it is more accurate than quantitative real-time PCR (qPCR) for the absolute quantification of target sequences. In this article, we aim to review the application of dPCR in noninvasive prenatal testing (NIPT). We focused on the progress of dPCR in screening and identifying fetal chromosome aneuploidies and monogenic mutations. We introduced some common strategies for dPCR in NIPT and analyzed the advantages and disadvantages of different methods. In addition, we compared dPCR with qPCR and next-generation sequencing, respectively, and described their superiority and shortcomings in clinical applications. Finally, we envisaged what the future of dPCR might be in NIPT. Although dPCR can provide reproducible results with improved accuracy due to the digital detection system, it is essential to combine the merits of dPCR and other molecular techniques to achieve more effective and accurate prenatal diagnostic strategies.
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Affiliation(s)
- Yue-Qi Li
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Gong-Jun Tan
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Yu-Qiu Zhou
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
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11
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Pacault M, Verebi C, Lopez M, Vaucouleur N, Orhant L, Deburgrave N, Leturcq F, Vidaud D, Girodon E, Bienvenu T, Nectoux J. Non-invasive prenatal diagnosis of single gene disorders by paternal mutation exclusion: 3 years of clinical experience. BJOG 2022; 129:1879-1886. [PMID: 35486001 DOI: 10.1111/1471-0528.17201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 12/24/2021] [Accepted: 01/22/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Cell-free fetal DNA (cffDNA) analysis is performed routinely for aneuploidy screening, RhD genotyping or sex determination. Although applications to single gene disorders (SGD) are being rapidly developed worldwide, only a few laboratories offer cffDNA testing routinely as a diagnosis service for this indication. In a previous report, we described a standardised protocol for non-invasive exclusion of paternal variant in SGD. Three years later, we now report our clinical experience with the protocol. DESIGN Descriptive study. SETTING Multi-centre French. POPULATION Indications for referral included pregnancies at risk of 25% or 50% of paternally inherited SGD, and pregnancies associated with an increased risk of SGD due to a de novo variant, either from strongly suggestive ultrasound findings or from a possible parental germinal mosaicism in the context of a previously affected child. METHODS Non-invasive prenatal diagnosis was performed using custom assays for droplet digital PCR. Feasibility, diagnostic performance and turn-around time were evaluated. RESULTS Mean time for a new assay design and validation was evaluated at 14 days, and mean result reporting time was 6 days. All referred pathogenic variants could be targeted except one located in a complex genomic region. A result was obtained for every 198 referrals except two. CONCLUSION This service was successfully implemented as a routine laboratory practice. It has been widely adopted by French clinicians and patients for paternal variant exclusion in various disorders.
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Affiliation(s)
- Mathilde Pacault
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Maureen Lopez
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Nicolas Vaucouleur
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Lucie Orhant
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Nathalie Deburgrave
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - France Leturcq
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Dominique Vidaud
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Emmanuelle Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
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12
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Zhong LPW, Chiu RWK. The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment. Annu Rev Genomics Hum Genet 2022; 23:413-425. [PMID: 35316613 DOI: 10.1146/annurev-genom-110821-113411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for single-gene disorders. The development of a spectrum of approaches to analyze cell-free DNA in maternal circulation, including relative mutation dosage, relative haplotype dosage, and size-based methods, has expanded the scope of noninvasive prenatal testing to sex-linked and autosomal recessive disorders. Cell-free fetal DNA analysis for several of the more prevalent single-gene disorders has recently been introduced into clinical service. This article reviews the analytical approaches currently available and discusses the extent of the clinical implementation of noninvasive prenatal testing for single-gene disorders. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lilian Pok Wa Zhong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
| | - Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; ,
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13
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Toft CLF, Diemer T, Ingerslev HJ, Pedersen IS, Adrian SW, Kesmodel US. Patients' choices and opinions on chorionic villous sampling and non-invasive alternatives for prenatal testing following preimplantation genetic testing for hereditary disorders: A cross-sectional questionnaire study. Prenat Diagn 2022; 42:212-225. [PMID: 34997771 DOI: 10.1002/pd.6088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The aim of this study was to investigate choices of and reasoning behind chorionic villous sampling and opinions on non-invasive prenatal testing among women and men achieving pregnancy following preimplantation genetic testing (PGT) for hereditary disorders. METHODS A questionnaire was electronically submitted to patients who had achieved a clinical pregnancy following PGT at the Center for Preimplantation Genetic Testing, Aalborg University Hospital, Denmark, between 2017 and 2020. RESULTS Chorionic villous sampling was declined by approximately half of the patients. The primary reason for declining was the perceived risk of miscarriage due to the procedure. Nine out of 10 patients responded that they would have opted for a non-invasive prenatal test if it had been offered. Some patients were not aware that the nuchal translucency scan offered to all pregnant women in the early second trimester only rarely provides information on the hereditary disorder for which PGT was performed. CONCLUSION Improved counseling on the array of prenatal tests and screenings available might be required to assist patients in making better informed decisions regarding prenatal testing. Non-invasive prenatal testing is welcomed by the patients and will likely increase the number of patients opting for confirmatory prenatal testing following PGT for hereditary disorders.
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Affiliation(s)
- Christian L F Toft
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Tue Diemer
- Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Hans J Ingerslev
- Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark.,Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
| | - Inge S Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Stine W Adrian
- Department of Culture and Learning, Aalborg University, Aalborg, Denmark
| | - Ulrik S Kesmodel
- Center for Preimplantation Genetic Testing, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark.,Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
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14
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De Falco L, Piscopo C, D’Angelo R, Evangelista E, Suero T, Sirica R, Ruggiero R, Savarese G, Di Carlo A, Furino G, Scarpato C, Fico A. Detection of 46, XY Disorder of Sex Development (DSD) Based on Plasma Cell-Free DNA and Targeted Next-Generation Sequencing. Genes (Basel) 2021; 12:genes12121890. [PMID: 34946839 PMCID: PMC8700836 DOI: 10.3390/genes12121890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
Mutations in the HSD17B3 gene cause HSD17B3 deficiency and result in 46, XY Disorders of Sex Development (46, XY DSD). The diagnosis of 46, XY DSD is very challenging and not rarely is confirmed only at older ages, when an affected XY female presents with primary amenorrhea or develops progressive virilization. The patient described in this paper represents a case of discrepancies between non-invasive prenatal testing (NIPT) and ultrasound based fetal sex determination detected during prenatal screening. Exome sequencing was performed on the cell free fetal DNA (cffDNA), amniotic fluid, and the parents. Libraries were generated according to the manufacturer’s protocols using TruSight One Kits (Illumina Inc., San Diego, CA, USA). Sequencing was carried out on NEXT Seq 500 (Illumina) to mean sequencing depth of at least 100×. A panel of sexual disease genes was used in order to search for a causative variant. The finding of a mutation (c.645 A>T, p.Glu215Asp) in HSD17B3 gene in amniotic fluid as well as in cffDNA and both parents supported the hypothesis of the HSD17B3 deficiency. In conclusion, we used clinical exome sequencing and non-invasive prenatal detection, providing a solution for NIPT of a single-gene disorder. Early genetic diagnoses are useful for patients and clinicians, contribute to clinical knowledge of DSD, and are invaluable for genetic counseling of couples contemplating future pregnancies.
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Affiliation(s)
- Luigia De Falco
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
- Correspondence:
| | - Carmelo Piscopo
- Medical and Laboratory Genetic Unit, A. Cardarelli Hospital, 80131 Naples, Italy;
| | - Rossana D’Angelo
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Eloisa Evangelista
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Teresa Suero
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Raffaella Ruggiero
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Antonella Di Carlo
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Giulia Furino
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
| | - Ciro Scarpato
- Ambulatorio Medicina Prenatale, PO S. Giuliano, 80014 Naples, Italy;
| | - Antonio Fico
- AMES, Centro Polidiagnostico Strumentale, 80013 Naples, Italy; (R.D.); (E.E.); (T.S.); (R.S.); (R.R.); (G.S.); (A.D.C.); (G.F.); (A.F.)
- Fondazione Genetica per la Vita Onlus, Via Cuma, 80132 Naples, Italy
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15
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Chen C, Chen M, Zhu Y, Jiang L, Li J, Wang Y, Lu Z, Guo F, Wang H, Peng Z, Yang Y, Sun J. Noninvasive prenatal diagnosis of monogenic disorders based on direct haplotype phasing through targeted linked-read sequencing. BMC Med Genomics 2021; 14:244. [PMID: 34627256 PMCID: PMC8502361 DOI: 10.1186/s12920-021-01091-x] [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: 08/21/2020] [Accepted: 09/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Though massively parallel sequencing has been widely applied to noninvasive prenatal screen for common trisomy, the clinical use of massively parallel sequencing to noninvasive prenatal diagnose monogenic disorders is limited. This study was to develop a method for directly determining paternal haplotypes for noninvasive prenatal diagnosis of monogenic disorders without requiring proband’s samples. Methods The study recruited 40 families at high risk for autosomal recessive diseases. The targeted linked-read sequencing was performed on high molecular weight (HMW) DNA of parents using customized probes designed to capture targeted genes and single-nucleotide polymorphisms (SNPs) distributed within 1Mb flanking region of targeted genes. Plasma DNA from pregnant mothers also underwent targeted sequencing using the same probes to determine fetal haplotypes according to parental haplotypes. The results were further confirmed by invasive prenatal diagnosis. Results Seventy-eight parental haplotypes of targeted gene were successfully determined by targeted linked-read sequencing. The predicted fetal inheritance of variant was correctly deduced in 38 families in which the variants had been confirmed by invasive prenatal diagnosis. Two families were determined to be no-call. Conclusions Targeted linked-read sequencing method demonstrated to be an effective means to phase personal haplotype for noninvasive prenatal diagnosis of monogenic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01091-x.
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Affiliation(s)
- Chao Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yaping Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lu Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhe Lu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fengyu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Hairong Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China. .,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
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16
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Comparing Germany and Israel regarding debates on policy-making at the beginning of life: PGD, NIPT and their paths of routinization. Ethik Med 2021. [DOI: 10.1007/s00481-021-00652-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Definition
The routinization of prenatal diagnosis is the source of bioethical and policy debates regarding choice, autonomy, access, and protection. To understand these debates in the context of cultural diversity and moral pluralism, we compare Israel and Germany, focusing on two recent repro-genetic “hot spots” of such policy-making at the beginning of life: pre-implantation genetic diagnosis (PGD) and non-invasive prenatal genetic testing (NIPT), two cutting-edge repro-genetic technologies that are regulated and viewed very differently in Germany and Israel, reflecting different medicolegal policies as well as public and bioethical considerations.
Arguments
First, we compare policy-making in the context of PGD for HLA (human leukocyte antigen) typing, used to create sibling donors, approved in Israel under specific conditions while prohibited in Germany. Second, we compare policy-making in the context of NIPT, which came under fire in Germany, while in Israel there has been little public debate about it.
Conclusion
Both countries justify their contrasting policies as reflecting a concern for the well-being and care of the embryo/child, thus highlighting different concepts of embryo/child protection, (relational) autonomy, family relations, and the impact of religion and history on the promotion/protection of life. We use the juxtaposition of PGD and NIPT to highlight some inconsistencies in policies concerning the protection of extra- and intra-corporeal embryos. We conclude by drawing on the comparison to show how national variations exist alongside co-evolution.
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17
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Toft CLF, Ingerslev HJ, Kesmodel US, Hatt L, Singh R, Ravn K, Nicolaisen BH, Christensen IB, Kølvraa M, Jeppesen LD, Schelde P, Vogel I, Uldbjerg N, Farlie R, Sommer S, Østergård MLV, Jensen AN, Mogensen H, Kjartansdóttir KR, Degn B, Okkels H, Ernst A, Pedersen IS. Cell-based non-invasive prenatal testing for monogenic disorders: confirmation of unaffected fetuses following preimplantation genetic testing. J Assist Reprod Genet 2021; 38:1959-1970. [PMID: 33677749 PMCID: PMC8417213 DOI: 10.1007/s10815-021-02104-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Proof of concept of the use of cell-based non-invasive prenatal testing (cbNIPT) as an alternative to chorionic villus sampling (CVS) following preimplantation genetic testing for monogenic disorders (PGT-M). METHOD PGT-M was performed by combined testing of short tandem repeat (STR) markers and direct mutation detection, followed by transfer of an unaffected embryo. Patients who opted for follow-up of PGT-M by CVS had blood sampled, from which potential fetal extravillous throphoblast cells were isolated. The cell origin and mutational status were determined by combined testing of STR markers and direct mutation detection using the same setup as during PGT. The cbNIPT results with respect to the mutational status were compared to those of genetic testing of the CVS. RESULTS Eight patients had blood collected between gestational weeks 10 and 13, from which 33 potential fetal cell samples were isolated. Twenty-seven out of 33 isolated cell samples were successfully tested (82%), of which 24 were of fetal origin (89%). This corresponds to a median of 2.5 successfully tested fetal cell samples per case (range 1-6). All fetal cell samples had a genetic profile identical to that of the transferred embryo confirming a pregnancy with an unaffected fetus, in accordance with the CVS results. CONCLUSION These findings show that although measures are needed to enhance the test success rate and the number of cells identified, cbNIPT is a promising alternative to CVS. TRIAL REGISTRATION NUMBER N-20180001.
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Affiliation(s)
- Christian Liebst Frisk Toft
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | | | - Ulrik Schiøler Kesmodel
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
| | | | | | | | | | | | | | | | | | - Ida Vogel
- Department of Clinical Genetic, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus, Denmark
| | - Richard Farlie
- Department of Obstetrics and Gynecology, Viborg Regional Hospital, Viborg, Denmark
| | - Steffen Sommer
- Department of Obstetrics and Gynecology, Horsens Regional Hospital, Horsens, Denmark
| | | | - Ann Nygaard Jensen
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - Helle Mogensen
- Department of Obstetrics and Gynecology, Kolding Regional Hospital, Kolding, Denmark
| | - Kristín Rós Kjartansdóttir
- Molecular Genetics Laboratory, Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | - Birte Degn
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Okkels
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Ernst
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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18
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Gerrish A, Bowns B, Mashayamombe-Wolfgarten C, Young E, Court S, Bott J, McCalla M, Ramsden S, Parks M, Goudie D, Carless S, Clokie S, Cole T, Allen S. Non-Invasive Prenatal Diagnosis of Retinoblastoma Inheritance by Combined Targeted Sequencing Strategies. J Clin Med 2020; 9:jcm9113517. [PMID: 33143217 PMCID: PMC7692133 DOI: 10.3390/jcm9113517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Retinoblastoma, the most common childhood eye cancer, presents in two forms: heritable or sporadic. Heritable retinoblastoma is caused by a germline mutation in the RB1 gene. Early diagnosis of children at risk of inheriting an RB1 mutation is crucial to achieve optimal clinical outcome. Currently, the majority of genetic testing is performed on newborns, which has multiple disadvantages for both families and the healthcare system. We have developed a non-invasive prenatal diagnosis (NIPD) service for retinoblastoma, available from 8 weeks’ gestation, which uses a combination of massively parallel sequencing (MPS) techniques, dependent on the inheritance model. Detection of paternal or suspected de novo RB1 variants is achieved through amplicon-based MPS. NIPD of a fetus at risk of maternal inheritance is performed using capture-based targeted sequencing and relative haplotype dosage analysis. In addition, we show proof of principle of how capture-based sequencing can be used for de novo variants unsuitable for amplicon-based testing. In total, we report the NIPD of 15 pregnancies, results of which show 100% concordance with all postnatal testing performed at the time of publication (n = 12) with remaining pregnancies ongoing. NIPD of retinoblastoma therefore offers a viable alternative to newborn genetic testing.
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Affiliation(s)
- Amy Gerrish
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
- Correspondence:
| | - Benjamin Bowns
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Chipo Mashayamombe-Wolfgarten
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Elizabeth Young
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Samantha Court
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Joshua Bott
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Maureen McCalla
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Simon Ramsden
- Manchester Centre For Genomic Medicine, University of Manchester, St Mary’s Hospital, Manchester Academic Health Science Centre, Manchester M13 9WL, UK;
| | - Michael Parks
- Nonacus Limted, Birmingham Research Park, Birmingham B15 2SQ, UK;
| | - David Goudie
- East of Scotland Regional Genetics Service, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK;
| | - Sue Carless
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Samuel Clokie
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
| | - Stephanie Allen
- West Midlands Regional Genetics Service, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham B15 2TG, UK; (B.B.); (C.M.-W); (E.Y.); (S.C.); (J.B.); (M.M.); (S.C.); (S.C.); (T.C.); (S.A.)
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Mirzaei Gisomi N, Javadi G, Zare Karizi S, Miryounesi M, Keshavarz P. Evaluation of beta-thalassemia in the fetus through cffDNA with multiple polymorphisms as a haplotype in the beta-globin gene. Transfus Clin Biol 2020; 27:243-252. [PMID: 32798758 DOI: 10.1016/j.tracli.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Invasive biopsy during the pregnancy is associated with an abortion risk of approximately 1% for the fetus. Free fetal DNA in maternal plasma is an excellent source of genetic material for prenatal molecular diagnoses. This study was conducted to investigate beta-thalassemia mutation in the fetus through maternal blood with multiple polymorphisms as haplotypes in the beta-globin gene. METHODS In this study, a total of 33 beta-thalassemia carrier (minor) couples were genotyped by ARMS-PCR for IVSII-IG>A mutation. During pregnancy, 10mL of blood was collected from pregnant women, and DNA was extracted by the magnetic bead-based extraction, and fetal DNA was enriched with AMPure XP kit. Five polymorphisms in 4 haplotype groups were evaluated by the Sanger Sequencing method. Finally, results were compared with those of the invasion method. RESULTS Participants in study were 33 couples, mean age of the men was 26±5 years, and mean age of women was 23±4 years, and mean MCV, MCH, HbA2 blood parameters were 62.4±5.3, 19.6±3.1, 4.2±2.1 respectively. A total of 33 fetuses were genotyped for IVSII-IG>A mutation. Nine fetuses were affected, 10 fetuses were normal and 14 fetuses were carrier of beta-thalassemia. Sensitivity and specificity of Sanger Sequencing were equal to 88.8% and 91.6% respectively. Positive and negative predictive values were obtained as 80% and 95.6%, respectively. CONCLUSION Mutational status of the fetus can be assessed by determining inheritance of paternally-derived alleles based on detection of haplotype-associated SNP in maternal plasma. Magnetic-based DNA extraction and fetal DNA enrichment are very simple and easy to perform and have satisfactory accuracy.
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Affiliation(s)
- Nadia Mirzaei Gisomi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Gholamreza Javadi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Shohre Zare Karizi
- Department of biology, faculty of biological sciences, Islamic Azad university, Varamin-Pishva Branch, Varamin, Iran
| | - Mohammad Miryounesi
- Department of medical genetics, Shahid Beheshti university of medical sciences, Tehran, Iran
| | - Parvaneh Keshavarz
- Cellular and molecular research center, faculty of medicine, Guilan university of medical sciences, Rasht, Iran; Medical genetics laboratory, Rasht, Iran.
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20
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How will new genetic technologies, such as gene editing, change reproductive decision-making? Views of high-risk couples. Eur J Hum Genet 2020; 29:39-50. [PMID: 32773775 PMCID: PMC7852899 DOI: 10.1038/s41431-020-00706-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/03/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
Couples at increased risk of having offspring with a specific genetic disorder who want to avoid having an affected child have several reproductive options including prenatal diagnosis (PND) and preimplantation genetic testing (PGT). In the future, non-invasive prenatal diagnosis (NIPD), germline gene editing (GGE) and somatic gene editing (SGE) might become available. This study explores if, and how, availability of new genetic technologies, including NIPD, GGE, SGE, would change reproductive decision-making of high-risk couples. In 2018, semi-structured interviews were conducted with 25 genetically at-risk couples. Couples previously had received genetic counselling for PND and PGT, and in most cases opted for (one of) these techniques, at one Dutch Clinical Genetics Center between 2013 and 2017. Considerations participants mentioned regarding the hypothetical use of NIPD, GGE and SGE, seem similar to considerations regarding PND and PGT and are reflected in underlying concepts. These include safety and burden for mother and child, and moral considerations. Couples generally favoured NIPD over PND as this would be safe and enables earlier diagnosis. Increased opportunities of having a 'healthy' embryo and less embryo disposal were considerations in favour of GGE. Some regarded GGE as unsafe and feared slippery slope scenarios. Couples were least favourable towards SGE compared to choosing for a genetic reproductive technology, because of the perceived burden for the affected offspring. With the possibly growing number of technological options, understanding high risk couples' perspectives can assist in navigating the reproductive decision-making process. Counsellors should be prepared to counsel on more and complex reproductive options.
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21
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Non-invasive prenatal diagnosis and screening for monogenic disorders. Eur J Obstet Gynecol Reprod Biol 2020; 253:320-327. [PMID: 32907778 DOI: 10.1016/j.ejogrb.2020.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Cell-free fetal DNA (cffDNA) can be detected in the maternal circulation from 4 weeks gestation, and is present with cell-free maternal DNA at a level of between 5 % and 20 %. Cell-free DNA (cfDNA) can be extracted from a maternal blood sample and, although it is not possible to separate the fetal from the maternal cfDNA, it has enabled non-invasive prenatal diagnosis (NIPD) without the associated miscarriage risk that accompanies invasive testing. NIPD for monogenic diseases was first reported in 2000 and since then there have been many proof of principle studies showing how analysis of cfDNA can provide a definitive diagnosis early in pregnancy for a wide range of single gene diseases. Testing for a number of these diseases has been available in the UK National Health Service (NHS) since 2012. This review highlights the main techniques that are being used for NIPD and discusses the technical limitations of the methods, as well as the advances that are being made to overcome some of the issues. NIPD is technologically challenging for a number of reasons. Firstly, because it requires the detection of low level fetal variants in a high maternal background. For de novo and paternally-inherited variants this has been achieved through the use of techniques such as next-generation sequencing (NGS) and digital PCR to detect variants in the cffDNA that are not present in the maternal cfDNA. However, for maternally-inherited variants this is much more challenging and relies on dosage-based techniques to detect small differences in the levels of mutant and wild-type alleles. Alongside the technical advances that are making NIPD more widely available in both the public healthcare and commercial settings, it is crucial that we continue to monitor the social and ethical impact to ensure that patients are being offered safe and accurate testing.
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22
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Scotchman E, Chandler NJ, Mellis R, Chitty LS. Noninvasive Prenatal Diagnosis of Single-Gene Diseases: The Next Frontier. Clin Chem 2020; 66:53-60. [PMID: 31843868 DOI: 10.1373/clinchem.2019.304238] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cell-free fetal DNA (cffDNA) is present in the maternal blood from around 4 weeks gestation and makes up 5%-20% of the total circulating cell-free DNA (cfDNA) in maternal plasma. Presence of cffDNA has allowed development of noninvasive prenatal diagnosis (NIPD) for single-gene disorders. This can be performed from 9 weeks gestation and offers a definitive diagnosis without the miscarriage risk associated with invasive procedures. One of the major challenges is distinguishing fetal mutations in the high background of maternal cfDNA, and research is currently focusing on the technological advances required to solve this problem. CONTENT Here, we review the literature to describe the current status of NIPD for monogenic disorders and discuss how the evolving methodologies and technologies are expected to impact this field in both the commercial and public healthcare setting. SUMMARY NIPD for single-gene diseases was first reported in 2000 and took 12 years to be approved for use in a public health service. Implementation has remained slow but is expected to increase as this testing becomes cheaper, faster, and more accurate. There are still many technical and analytical challenges ahead, and it is vital that discussions surrounding the ethical and social impact of NIPD take account of the considerations required to implement these services safely into the healthcare setting, while keeping up with the technological advances.
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Affiliation(s)
- Elizabeth Scotchman
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Natalie J Chandler
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Rhiannon Mellis
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lyn S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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23
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Mellis R, Chandler N, Jenkins L, Chitty LS. The role of sonographic phenotyping in delivering an efficient noninvasive prenatal diagnosis service for FGFR3-related skeletal dysplasias. Prenat Diagn 2020; 40:785-791. [PMID: 32227640 DOI: 10.1002/pd.5687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/11/2020] [Accepted: 03/07/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVES To evaluate the diagnostic yield of noninvasive prenatal diagnosis (NIPD) for FGFR3-related skeletal dysplasias and assess the accuracy of referrals based on sonographic findings to inform guidelines for referral. METHODS We retrospectively reviewed laboratory and referral records from 2012 to 2018 to ascertain all NIPD tests performed using our next generation sequencing panel to detect FGFR3 mutations. We calculated the diagnostic yield of the test overall and when sub-divided according to the phenotypic features identified on ultrasound before testing. Pregnancy outcomes were ascertained wherever possible from referring centers. RESULTS Of 335 tests, 261 were referred because of sonographic findings, of which 80 (31.3%) had a mutation. The diagnostic yield when short limbs were the only abnormal sonographic feature reported was 17.9% (30/168), increasing to 48.9% (23/47) in the presence of one, and 82.6% (19/23) in the presence of two or more characteristic features in addition to short limbs. CONCLUSIONS Accurate sonographic phenotyping can maximise the diagnostic yield of NIPD in fetuses suspected to have FGFR3-related skeletal dysplasias. We suggest that clear guidelines for referral are necessary to increase benefits, decrease costs by preventing unnecessary NIPD, and potentially allow first-line broader spectrum testing for fetuses where the aetiology may be more heterogeneous.
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Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, United Kingdom
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Lucy Jenkins
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, United Kingdom
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24
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Provenzano A, Palazzo V, Reho P, Pagliazzi A, Marozza A, Farina A, Zuffardi O, Giglio S. Noninvasive prenatal diagnosis in a family at risk for Fraser syndrome. Prenat Diagn 2020; 40:905-908. [DOI: 10.1002/pd.5700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/06/2020] [Accepted: 04/04/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Aldesia Provenzano
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio"University of Florence Florence Italy
| | - Viviana Palazzo
- Medical Genetics UnitMeyer Children's University Hospital Florence Italy
| | - Paolo Reho
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio"University of Florence Florence Italy
| | - Angelica Pagliazzi
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio"University of Florence Florence Italy
| | | | - Antonio Farina
- Division of Obstetrics and Prenatal Medicine, Department of Medicine and Surgery (DIMEC), Sant'Orsola‐Malpighi HospitalUniversity of Bologna Bologna Italy
| | - Orsetta Zuffardi
- Unit of Medical Genetics, Department of Molecular MedicineUniversity of Pavia Pavia Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences "Mario Serio"University of Florence Florence Italy
- Medical Genetics UnitMeyer Children's University Hospital Florence Italy
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25
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Chandler NJ, Ahlfors H, Drury S, Mellis R, Hill M, McKay FJ, Collinson C, Hayward J, Jenkins L, Chitty LS. Noninvasive Prenatal Diagnosis for Cystic Fibrosis: Implementation, Uptake, Outcome, and Implications. Clin Chem 2019; 66:207-216. [DOI: 10.1373/clinchem.2019.305011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/09/2019] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Noninvasive prenatal diagnosis (NIPD) for monogenic disorders has a high uptake by families. Since 2013, our accredited public health service laboratory has offered NIPD for monogenic disorders, predominantly for de novo or paternally dominantly inherited mutations. Here we describe the extension of this service to include definitive NIPD for a recessive condition, cystic fibrosis (CF).
METHODS
Definitive NIPD for CF was developed using next-generation sequencing. Validation was performed on 13 cases from 10 families before implementation. All cases referred for CF NIPD were reviewed to determine turnaround times, genotyping results, and pregnancy outcomes.
RESULTS
Of 38 referrals, 36 received a result with a mean turnaround of 5.75 days (range, 3–11 days). Nine cases were initially inconclusive, with 3 reported unaffected because the low-risk paternal allele was inherited and 4 cases in which the high-risk paternal allele was inherited, receiving conclusive results following repeat testing. One case was inconclusive owing to a paternal recombination around the mutation site, and one case was uninformative because of no heterozygosity. Before 2016, 3 invasive referrals for CF were received annually compared with 38 for NIPD in the 24 months since offering a definitive NIPD service.
CONCLUSIONS
Timely and accurate NIPD for definitive prenatal diagnosis of CF is possible in a public health service laboratory. The method detects recombinations, and the service is well-received as evidenced by the significant increase in referrals. The bioinformatic approach is gene agnostic and will be used to expand the range of conditions tested for.
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Affiliation(s)
- Natalie J Chandler
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Helena Ahlfors
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Suzanne Drury
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Rhiannon Mellis
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Melissa Hill
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Fiona J McKay
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Claire Collinson
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Jane Hayward
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Lucy Jenkins
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Lyn S Chitty
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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26
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Han L, Chen C, Guo F, Ye J, Peng Z, Qiu W, Wang Y, Li W, Zhang H, Liang L, Wang Y, Wang H, Ji X, Sun J, Gu X. Noninvasive prenatal diagnosis of cobalamin C (cblC) deficiency through target region sequencing of cell-free DNA in maternal plasma. Prenat Diagn 2019; 40:324-332. [PMID: 31697851 DOI: 10.1002/pd.5601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to validate the feasibility of haplotype-based noninvasive prenatal diagnosis (NIPD) of cobalamin C (cblC) deficiency. METHOD This method includes three steps: First, targeted sequencing was performed on 21 families affected by cblC deficiency (including the couples and probands). Second, parental haplotypes linked with the pathogenic variant were determined using the genotypes of trios. Then, the fetal haplotypes were inferred through a parental haplotype assisted hidden Markov model (HMM). The NIPD results were confirmed by using the invasive procedures. RESULTS Twenty-one fetal genotypes were successfully inferred by NIPD including three compound heterozygotes with cblC deficiency, nine heterozygote carriers of cblC deficiency, and nine normal fetuses. The NIPD results were confirmed using the invasive procedures with 100% concordant rate. CONCLUSION This result has shown that haplotype-based NIPD of cblC deficiency has high concordant rate and indicated potential clinical utility as a pregnancy diagnosis method for high-risk carrier couples.
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Affiliation(s)
- Lianshu Han
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Jun Ye
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wenjuan Qiu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Huiwen Zhang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanhuan Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Ji
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Xuefan Gu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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27
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Krstić N, Običan SG. Current landscape of prenatal genetic screening and testing. Birth Defects Res 2019; 112:321-331. [PMID: 31633301 DOI: 10.1002/bdr2.1598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
Abstract
Pregnant patients should be offered the option of prenatal genetic screening and diagnostic testing. The type of screening and testing offered to a patient may depend on various factors including but not limited to age, family history, fetal findings, exposures, and patient preferences. Prenatal screening is available for a variety of genetic conditions including aneuploidy, congenital abnormalities, and carrier status. Diagnostic testing options include karyotype, prenatal microarray, as well as next-generation sequencing. The various options differ in methodology, accuracy, timing and indication for testing, and information they provide. Given that the technologies related to prenatal testing are rapidly evolving and improving, the array of available screening and testing modalities are increasing. This article reviews the current offerings in prenatal screening and diagnosis.
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Affiliation(s)
- Nevena Krstić
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida
| | - Sarah G Običan
- Department of Obstetrics and Gynecology, University of South Florida, Morsani College of Medicine, Tampa, Florida
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28
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Chen M, Chen C, Li Y, Yuan Y, Lai Z, Guo F, Wang Y, Huang X, Li S, Wu R, Peng Z, Sun J, Chen D. Haplotype-Based noninvasive prenatal diagnosis for duchenne muscular dystrophy: A pilot study in South China. Eur J Obstet Gynecol Reprod Biol 2019; 240:15-22. [PMID: 31207536 DOI: 10.1016/j.ejogrb.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To explore the accuracy and feasibility of noninvasive prenatal diagnosis (NIPD) for Duchenne Muscular Dystrophy (DMD) based on the haplotype approach. METHODS We recruited singleton pregnancies at-risk of DMD at 12-25 weeks of gestation from 17 families who all had a proband child affected by DMD. We have identified the pathogenic mutations in probands and their mothers by multiplex ligation-dependent probe amplification (MLPA). To construct parental haplotypes, we performed captured sequencing on genomic DNA from parents and probands. The integration analysis of parental haplotypes and targeted sequencing results of maternal plasma DNA were used to infer the fetal haplotype and genotypes in the DMD gene. Fetal DMD genotypes were further confirmed by invasive prenatal diagnosis. RESULT We have successfully performed the haplotype-based NIPD in all recruited families. Ten fetuses were identified as normal, including four female and six male fetuses. Four female fetuses were carriers, and the other three male fetuses were affected by DMD with exons 49-52 deletion, exons 8-37 deletion and c.628 G > T mutation, respectively. The results of NIPD were consistent with those of invasive diagnosis. CONCLUSION Haplotype-based NIPD for DMD by targeted sequencing is promising and has the potential for clinical application.
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Affiliation(s)
- Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Yingting Li
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Zhengfei Lai
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China
| | | | - Shiquan Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China; BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Renhua Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China; Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan 430074, China.
| | - Dunjin Chen
- Department of Fetal Medicine and Prenatal Diagnosis, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, 510150, China; Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China; Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, China.
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Rabinowitz T, Polsky A, Golan D, Danilevsky A, Shapira G, Raff C, Basel-Salmon L, Matar RT, Shomron N. Bayesian-based noninvasive prenatal diagnosis of single-gene disorders. Genome Res 2019; 29:428-438. [PMID: 30787035 PMCID: PMC6396420 DOI: 10.1101/gr.235796.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 01/23/2019] [Indexed: 12/04/2022]
Abstract
In the last decade, noninvasive prenatal diagnosis (NIPD) has emerged as an effective procedure for early detection of inherited diseases during pregnancy. This technique is based on using cell-free DNA (cfDNA) and fetal cfDNA (cffDNA) in maternal blood, and hence, has minimal risk for the mother and fetus compared with invasive techniques. NIPD is currently used for identifying chromosomal abnormalities (in some instances) and for single-gene disorders (SGDs) of paternal origin. However, for SGDs of maternal origin, sensitivity poses a challenge that limits the testing to one genetic disorder at a time. Here, we present a Bayesian method for the NIPD of monogenic diseases that is independent of the mode of inheritance and parental origin. Furthermore, we show that accounting for differences in the length distribution of fetal- and maternal-derived cfDNA fragments results in increased accuracy. Our model is the first to predict inherited insertions–deletions (indels). The method described can serve as a general framework for the NIPD of SGDs; this will facilitate easy integration of further improvements. One such improvement that is presented in the current study is a machine learning model that corrects errors based on patterns found in previously processed data. Overall, we show that next-generation sequencing (NGS) can be used for the NIPD of a wide range of monogenic diseases, simultaneously. We believe that our study will lead to the achievement of a comprehensive NIPD for monogenic diseases.
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Affiliation(s)
- Tom Rabinowitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Avital Polsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - David Golan
- Faculty of Industrial Engineering and Management, Technion, Haifa, 3200003, Israel
| | - Artem Danilevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Guy Shapira
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Chen Raff
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.,Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, 4941494, Israel
| | - Reut Tomashov Matar
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, 4941494, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
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Noninvasive paternal exclusion testing for cystic fibrosis in the first five to eight weeks of gestation. Sci Rep 2018; 8:15941. [PMID: 30374031 PMCID: PMC6205998 DOI: 10.1038/s41598-018-34396-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Prenatal genetic testing is not generally applicable to the very early stages of pregnancy (prior to week 8 gestation), a time period that is crucial to pregnant couples with high risk for transmission of genetic disease to their fetus. Therefore, we developed a new ultra-sensitive targeted next generation sequencing method for noninvasive haplotype-based paternal allele exclusion testing of the cystic fibrosis-associated gene, CFTR. This new method was compared to a conventional library prep and sequencing analysis method and all test results were validated by amniotic fluid testing at later stages of pregnancy. Out of 7 enrolled couples, who provided at least two blood samples (at least one week apart) for noninvasive CFTR testing, a result was obtained for 6 fetuses. Using the new hypersensitive method, all six couples (100%) received a correct diagnosis for the paternal allele as opposed to 3/6 (50%) when tested with the conventional strategy. Among 4 couples who provided just one early pregnancy blood draw for analysis, diagnosis was possible in one fetus, but only using the ultra-sensitive method. Thus, we describe a novel noninvasive CFTR screening method which demonstrates unprecedented fetal allele typing accuracy in the earliest stages of pregnancy.
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Mellis R, Chandler N, Chitty LS. Next-generation sequencing and the impact on prenatal diagnosis. Expert Rev Mol Diagn 2018; 18:689-699. [PMID: 29962246 DOI: 10.1080/14737159.2018.1493924] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The advent of affordable and rapid next-generation sequencing has been transformative for prenatal diagnosis. Sequencing of cell-free DNA in maternal plasma has enabled the development of not only a highly sensitive screening test for fetal aneuploidies, but now definitive noninvasive prenatal diagnosis for monogenic disorders at an early gestation. Sequencing of fetal exomes offers broad diagnostic capability for pregnancies with unexpected fetal anomalies, improving the yield and accuracy of diagnoses and allowing better counseling for parents. The challenge now is to translate these approaches into mainstream use in the clinic. Areas covered: Here, the authors review the current literature to describe the technologies available and how these have evolved. The opportunities and challenges at hand, including considerations for service delivery, counseling, and development of ethical guidelines, are discussed. Expert commentary: As technology continues to advance, future developments may be toward noninvasive fetal whole exome or whole genome sequencing and a universal method for noninvasive prenatal diagnosis without the need to sequence both parents or an affected proband. Expansion of cell-free fetal DNA analysis to include the transcriptome and the methylome is likely to yield clinical benefits for monitoring other pregnancy-related pathologies such as preeclampsia and intrauterine growth restriction.
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Affiliation(s)
- Rhiannon Mellis
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK
| | - Natalie Chandler
- b North Thames NHS Regional Genetics Service , Great Ormond Street NHS Foundation Trust , London , UK
| | - Lyn S Chitty
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK.,c Genetics and Genomic Medicine , UCL Great Ormond Street Institute of Child Health , London , UK
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Bergougnoux A, Taulan-Cadars M, Claustres M, Raynal C. Current and future molecular approaches in the diagnosis of cystic fibrosis. Expert Rev Respir Med 2018; 12:415-426. [PMID: 29580110 DOI: 10.1080/17476348.2018.1457438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Cystic Fibrosis is among the first diseases to have general population genetic screening tests and one of the most common indications of prenatal and preimplantation genetic diagnosis for single gene disorders. During the past twenty years, thanks to the evolution of diagnostic techniques, our knowledge of CFTR genetics and pathophysiological mechanisms involved in cystic fibrosis has significantly improved. Areas covered: Sanger sequencing and quantitative methods greatly contributed to the identification of more than 2,000 sequence variations reported worldwide in the CFTR gene. We are now entering a new technological age with the generalization of high throughput approaches such as Next Generation Sequencing and Droplet Digital PCR technologies in diagnostics laboratories. These powerful technologies open up new perspectives for scanning the entire CFTR locus, exploring modifier factors that possibly influence the clinical evolution of patients, and for preimplantation and prenatal diagnosis. Expert commentary: Such breakthroughs would, however, require powerful bioinformatics tools and relevant functional tests of variants for analysis and interpretation of the resulting data. Ultimately, an optimal use of all those resources may improve patient care and therapeutic decision-making.
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Affiliation(s)
- Anne Bergougnoux
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France.,b EA 7402 , Université de Montpellier , Montpellier , France
| | | | | | - Caroline Raynal
- a Laboratoire de Génétique Moléculaire , Centre Hospitalier Universitaire de Montpellier , Montpellier , France
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Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23:94-101. [PMID: 29305293 DOI: 10.1016/j.siny.2017.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.
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Griffin B, Edwards S, Chitty LS, Lewis C. Clinical, social and ethical issues associated with non-invasive prenatal testing for aneuploidy. J Psychosom Obstet Gynaecol 2018. [PMID: 28635528 DOI: 10.1080/0167482x.2017.1286643] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Non-invasive prenatal testing (NIPT), based on analysis of cell-free foetal DNA, is rapidly becoming a preferred method to screen for chromosomal aneuploidy with the technology now available in over 90 countries. This review provides an up-to-date discussion of the key clinical, social and ethical implications associated with this revolutionary technology. Stakeholders are positive about a test that is highly accurate, safe, can be perfomed early in pregnancy, identifies affected pregnancies that might otherwise have been missed and reduces the need for invasive testing. Nevertheless, professional societies currently recommend it as an advanced screening test due to the low false positive rate (FPR). Despite the practical and psychological benefits, a number of concerns have been raised which warrant attention. These include the potential for routinisation of testing and subsequent impact on informed decision-making, an "easy" blood test inadvertently contributing to women feeling pressured to take the test, fears NIPT will lead to less tolerance and support for those living with Down syndrome and the heightened expectation of having "perfect babies". These issues can be addressed to some extent through clinician education, patient information and establishing national and international consensus in the development of comprehensive and regularly updated guidelines. As the number of conditions we are able to test for non-invasively expands it will be increasingly important to ensure pre-test counselling can be delivered effectively supported by knowledgeable healthcare professionals.
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Affiliation(s)
- Blanche Griffin
- a North East Thames Regional Genetics Service , Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK
| | - Samantha Edwards
- a North East Thames Regional Genetics Service , Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK
| | - Lyn S Chitty
- a North East Thames Regional Genetics Service , Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK.,b Genetics and Genomic Medicine , UCL Institute of Child Health and Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK
| | - Celine Lewis
- a North East Thames Regional Genetics Service , Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK.,b Genetics and Genomic Medicine , UCL Institute of Child Health and Great Ormond Street Hospital for Children NHS Foundation Trust , London , UK
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Jenkins LA, Deans ZC, Lewis C, Allen S. Delivering an accredited non-invasive prenatal diagnosis service for monogenic disorders and recommendations for best practice. Prenat Diagn 2018; 38:44-51. [PMID: 29266293 DOI: 10.1002/pd.5197] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Lucy A. Jenkins
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Zandra C. Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine; Royal Infirmary of Edinburgh; Edinburgh UK
| | - Celine Lewis
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Great Ormond Street Institute of Child Health; London UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's NHS Foundation Trust; Birmingham UK
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Camunas-Soler J, Lee H, Hudgins L, Hintz SR, Blumenfeld YJ, El-Sayed YY, Quake SR. Noninvasive Prenatal Diagnosis of Single-Gene Disorders by Use of Droplet Digital PCR. Clin Chem 2018; 64:336-345. [DOI: 10.1373/clinchem.2017.278101] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022]
Abstract
Abstract
BACKGROUND
Prenatal diagnosis in pregnancies at risk of single-gene disorders is currently performed using invasive methods such as chorionic villus sampling and amniocentesis. This is in contrast with screening for common aneuploidies, for which noninvasive methods with a single maternal blood sample have become standard clinical practice.
METHODS
We developed a protocol for noninvasive prenatal diagnosis of inherited single-gene disorders using droplet digital PCR from circulating cell-free DNA (cfDNA) in maternal plasma. First, the amount of cfDNA and fetal fraction is determined using a panel of TaqMan assays targeting high-variability single-nucleotide polymorphisms. Second, the ratio of healthy and diseased alleles in maternal plasma is quantified using TaqMan assays targeting the mutations carried by the parents. Two validation approaches of the mutation assay are presented.
RESULTS
We collected blood samples from 9 pregnancies at risk for different single-gene disorders, including common conditions and rare metabolic disorders. We measured cases at risk of hemophilia, ornithine transcarbamylase deficiency, cystic fibrosis, β-thalassemia, mevalonate kinase deficiency, acetylcholine receptor deficiency, and DFNB1 nonsyndromic hearing loss. We correctly differentiated affected and unaffected pregnancies (2 affected, 7 unaffected), confirmed by neonatal testing. We successfully measured an affected pregnancy as early as week 11 and with a fetal fraction as low as 3.7% (0.3).
CONCLUSIONS
Our method detects single-nucleotide mutations of autosomal recessive diseases as early as the first trimester of pregnancy. This is of importance for metabolic disorders in which early diagnosis can affect management of the disease and reduce complications and anxiety related to invasive testing.
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Affiliation(s)
| | - Hojae Lee
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA
| | - Susan R Hintz
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Yair J Blumenfeld
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
| | - Yasser Y El-Sayed
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Applied Physics, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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Wilson RD, De Bie I, Armour CM, Brown RN, Campagnolo C, Carroll JC, Okun N, Nelson T, Zwingerman R, Audibert F, Brock JA, Brown RN, Campagnolo C, Carroll JC, De Bie I, Johnson JA, Okun N, Pastruck M, Vallée-Pouliot K, Wilson RD, Zwingerman R, Armour C, Chitayat D, De Bie I, Fernandez S, Kim R, Lavoie J, Leonard N, Nelson T, Taylor S, Van Allen M, Van Karnebeek C. Joint SOGC-CCMG Opinion for Reproductive Genetic Carrier Screening: An Update for All Canadian Providers of Maternity and Reproductive Healthcare in the Era of Direct-to-Consumer Testing. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2018; 38:742-762.e3. [PMID: 27638987 DOI: 10.1016/j.jogc.2016.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE This guideline was written to update Canadian maternity care and reproductive healthcare providers on pre- and postconceptional reproductive carrier screening for women or couples who may be at risk of being carriers for autosomal recessive (AR), autosomal dominant (AD), or X-linked (XL) conditions, with risk of transmission to the fetus. Four previous SOGC- Canadian College of Medical Geneticists (CCMG) guidelines are updated and merged into the current document. INTENDED USERS All maternity care (most responsible health provider [MRHP]) and paediatric providers; maternity nursing; nurse practitioner; provincial maternity care administrator; medical student; and postgraduate resident year 1-7. TARGET POPULATION Fertile, sexually active females and their fertile, sexually active male partners who are either planning a pregnancy or are pregnant (preferably in the first trimester of pregnancy, but any gestational age is acceptable). OPTIONS Women and their partners will be able to obtain appropriate genetic carrier screening information and possible diagnosis of AR, AD, or XL disorders (preferably pre-conception), thereby allowing an informed choice regarding genetic carrier screening and reproductive options (e.g., prenatal diagnosis, preimplantation genetic diagnosis, egg or sperm donation, or adoption). OUTCOMES Informed reproductive decisions related to genetic carrier screening and reproductive outcomes based on family history, ethnic background, past obstetrical history, known carrier status, or genetic diagnosis. SOGC REPRODUCTIVE CARRIER SCREENING SUMMARY STATEMENT (2016): Pre-conception or prenatal education and counselling for reproductive carrier screening requires a discussion about testing within the three perinatal genetic carrier screening/diagnosis time periods, which include pre-conception, prenatal, and neonatal for conditions currently being screened for and diagnosed. This new information should be added to the standard reproductive carrier screening protocols that are already being utilized by the most responsible maternity provider through the informed consent process with the patient. (III-A; GRADE low/moderate) SOGC OVERVIEW OF RECOMMENDATIONS QUALITY AND GRADE: There was a strong observational/expert opinion (quality and grade) for the genetic carrier literature with randomized controlled trial evidence being available only for the invasive testing. Both the Canadian Task Force on Preventive Health Care quality and classification and the GRADE evidence quality and grade are provided. EVIDENCE MEDLINE; PubMed; government neonatal screening websites; key words/common reproductive genetic carrier screened diseases/previous SOGC Guidelines/medical academic societies (Society of Maternal-Fetal Medicine [SMFM]; American College of Medical Genetics and Genomics; American College of Obstetricians and Gynecologists [ACOG]; CCMG; Royal College Obstetrics and Gynaecology [RCOG] [UK]; American Society of Human Genetics [ASHG]; International Society of Prenatal Diagnosis [ISPD])/provincial neonatal screening policies and programs; search terms (carrier screening, prenatal screening, neonatal genetic/metabolic screening, cystic fibrosis (CF), thalassemia, hemoglobinopathy, hemophilia, Fragile X syndrome (FXS), spinal muscular atrophy, Ashkenazi Jewish carrier screening, genetic carrier screening protocols, AR, AD, XL). SEARCH PERIOD 10 years (June 2005-September 2015); initial search dates June 30, 2015 and September 15, 2015; completed final search January 4, 2016. Validation of articles was completed by primary authors RD Wilson and I De Bie. BENEFITS, HARMS, AND COST Benefits are to provide an evidenced based reproductive genetic carrier screening update consensus based on international opinions and publications for the use of Canadian women, who are planning a pregnancy or who are pregnant and have been identified to be at risk (personal or male partner family or reproductive history) for the transmission of a clinically significant genetic condition to their offspring with associated morbidity and/or mortality. Harm may arise from having counselling and informed testing of the carrier status of the mother, their partner, or their fetus, as well as from declining to have this counselling and informed testing or from not having the opportunity for counselling and informed testing. Costs will ensue both from the provision of opportunities for counselling and testing, as well as when no such opportunities are offered or are declined and the birth of a child with a significant inherited condition and resulting morbidity/mortality occurs; these comprise not only the health care costs to the system but also the social/financial/psychological/emotional costs to the family. These recommendations are based on expert opinion and have not been subjected to a health economics assessment and local or provincial implementation will be required. GUIDELINE UPDATE This guideline is an update of four previous joint SOGC-CCMG Genetic Screening Guidelines dated 2002, 2006, 2008, and 2008 developed by the SOGC Genetic Committee in collaboration with the CCMG Prenatal Diagnosis Committee (now Clinical Practice Committee). 2016 CARRIER SCREENING RECOMMENDATIONS.
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Chiu EKL, Hui WWI, Chiu RWK. cfDNA screening and diagnosis of monogenic disorders - where are we heading? Prenat Diagn 2018; 38:52-58. [PMID: 29314147 PMCID: PMC5839244 DOI: 10.1002/pd.5207] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022]
Abstract
Cell‐free fetal DNA analysis for non‐invasive prenatal screening of fetal chromosomal aneuploidy has been widely adopted for clinical use. Fetal monogenic diseases have also been shown to be amenable to non‐invasive detection by maternal plasma DNA analysis. A number of recent technological developments in this area has increased the level of clinical interest, particularly as one approach does not require customized reagents per mutation. The mutational status of the fetus can be assessed by determining which parental haplotype that fetus has inherited based on the detection of haplotype‐associated SNP alleles in maternal plasma. Such relative haplotype dosage analysis requires the input of the parental haplotype information for interpretation of the fetal inheritance pattern from the maternal plasma DNA data. The parental haplotype information can be obtained by direct means, reducing the need to infer haplotypes using DNA from other family members. The technique also allows the assessment of complex mutations and has multiplexing capabilities where a number of genes and mutations can be assessed at the same time. These advantages allow non‐invasive prenatal diagnosis of fetal monogenic diseases to be much more scalable. These applications may drive the next wave of clinical adoption of cell‐free fetal DNA testing. © 2018 The Authors Prenatal Diagnosis Published by John Wiley & Sons Ltd What's already known about this topic?
NIPD for some monogenic diseases is now in clinical service. Current NIPD is based on bespoke mutation‐specific assays, or haplotype inference which requires proband DNA.
What does this study add?
The application of universal haplotype‐based NIPD can be extended to most pregnancies at risk for monogenic diseases. The universal protocol circumvents the need for bespoke assays or access to proband DNA.
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Affiliation(s)
- Eunice Ka Long Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
| | - Winnie Wai In Hui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
| | - Rossa Wai Kwun Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
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Xiong L, Barrett AN, Hua R, Ho SSY, Jun L, Chan KCA, Mei Z, Choolani M. Non-invasive prenatal testing for fetal inheritance of maternal β
-thalassaemia mutations using targeted sequencing and relative mutation dosage: a feasibility study. BJOG 2018; 125:461-468. [DOI: 10.1111/1471-0528.15045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 11/26/2022]
Affiliation(s)
- L Xiong
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - AN Barrett
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - R Hua
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - SSY Ho
- Department of Laboratory Medicine; Molecular Diagnosis Centre; National University Hospital; Singapore
| | - L Jun
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - KCA Chan
- Centre for Research into Circulating Fetal Nucleic Acids; Li Ka Shing Institute of Health Sciences; Chinese University of Hong Kong; Shatin New Territories Hong Kong
| | - Z Mei
- Department of Gynaecology & Obstetrics; Nanfang Hospital; Southern Medical University; Guangzhou China
| | - M Choolani
- Department of Obstetrics and Gynaecology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore
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Abstract
PURPOSE OF REVIEW Noninvasive prenatal diagnosis for single gene disorders is coming to fruition in its clinical utility. The presence of cell-free DNA in maternal plasma has been recognized for many years, and a number of applications have developed from this. Noninvasive prenatal diagnosis for single gene disorders has lagged behind due to complexities of technology development, lack of investment and the need for validation samples for rare disorders. RECENT FINDINGS Publications are emerging demonstrating a variety of technical approaches and feasibility of clinical application. Techniques for analysis of cell-free DNA including digital PCR, next-generation sequencing and relative haplotype dosage have been used most often for assay development. Analysis of circulating fetal cells in the maternal blood is still being investigated as a viable alternative and more recently transcervical trophoblast cells. Studies exploring ethical and social issues are generally positive but raise concerns around the routinization of prenatal testing. SUMMARY Further work is necessary to make testing available to all patients with a pregnancy at risk of a single gene disorder, and it remains to be seen if the development of more powerful technologies such as isolation and analysis of single cells will shift the emphasis of noninvasive prenatal diagnosis. As testing becomes possible for a wider range of conditions, more ethical questions will become relevant.
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Borry P, Favaretto M, Batthyany A, Boey E, Van Tongerloo S, Dooms M, Huys I. Noninvasive prenatal testing: a survey of young (future) parents in Flanders. Per Med 2018; 15:35-43. [DOI: 10.2217/pme-2017-0065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To explore the opinions of young (future) parents toward noninvasive prenatal testing. Materials & methods: A questionnaire was administrated. Results: A total of 1006 surveys were completed by visitors of 40 secondhand clothing fairs spread equally over Flanders (Belgium). The respondents expressed an overall positive opinion toward the use and implementation of a noninvasive prenatal test (NIPT). Most respondents claimed that they would test their unborn child for genetic disorders, even if this was to result in a termination of the pregnancy. Conclusion: The participants agreed nearly unanimously that NIPT must be offered to pregnant women with an increased risk of having a child with a genetic disorder, but they were also positive about extending NIPT screening to all pregnant women.
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Affiliation(s)
- Pascal Borry
- Centre for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Flanders, Belgium
| | - Maddalena Favaretto
- Centre for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Flanders, Belgium
| | - Ann Batthyany
- Department of Clinical Pharmacology & Pharmacotherapy, KU Leuven, Flanders, Belgium
| | - Eline Boey
- Department of Clinical Pharmacology & Pharmacotherapy, KU Leuven, Flanders, Belgium
| | - Sophie Van Tongerloo
- Department of Clinical Pharmacology & Pharmacotherapy, KU Leuven, Flanders, Belgium
| | - Marc Dooms
- Department of Clinical Pharmacology & Pharmacotherapy, KU Leuven, Flanders, Belgium
| | - Isabelle Huys
- Department of Clinical Pharmacology & Pharmacotherapy, KU Leuven, Flanders, Belgium
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Shim SH, Kim JY, Sung SR, Park JE, Shin YJ, Shim SH, Cha DH. Prenatally diagnosed TTN mutation with repeated bilateral club foot by whole exome sequencing. BIOCHIP JOURNAL 2017. [DOI: 10.1007/s13206-017-1309-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Skrzypek H, Hui L. Noninvasive prenatal testing for fetal aneuploidy and single gene disorders. Best Pract Res Clin Obstet Gynaecol 2017; 42:26-38. [DOI: 10.1016/j.bpobgyn.2017.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/21/2017] [Indexed: 01/16/2023]
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Parks M, Court S, Bowns B, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S. Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage. Eur J Hum Genet 2017; 25:416-422. [PMID: 28120840 PMCID: PMC5386415 DOI: 10.1038/ejhg.2016.195] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.
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Affiliation(s)
- Michael Parks
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samantha Court
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Benjamin Bowns
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Siobhan Cleary
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Hewitt
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Fiona MacDonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
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Non-invasive prenatal diagnosis (NIPD) of cystic fibrosis: an optimized protocol using MEMO fluorescent PCR to detect the p.Phe508del mutation. J Cyst Fibros 2016; 16:198-206. [PMID: 28040480 DOI: 10.1016/j.jcf.2016.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/24/2016] [Accepted: 12/11/2016] [Indexed: 01/29/2023]
Abstract
BACKGROUND Analysis of cell-free foetal DNA (cff-DNA) in maternal plasma is very promising for early diagnosis of monogenic diseases; in particular, cystic fibrosis (CF). However, NIPD of single-gene disorders has been limited by the availability of suitable technical platforms and the need to set up patient or disease-specific custom-made approaches. METHODS To make research applications more readily accessible to the clinic, we offer a simple assay combining two independent methods to determine the presence or absence of paternally inherited foetal allele p.Phe508del (the most frequent mutation in CF patients worldwide). The first method detects the presence or absence of a p.Phe508del allele by Mutant Enrichment with 3'-Modified Oligonucleotide PCR coupled to Fragment Length Analysis (MEMO-PCR-FLA). The second method detects the p.Phe508del allele with classical Multiplex Fluorescent PCR including five intragenic and extragenic STR markers of the CFTR locus and a specific SRY sequence. RESULTS We collected 24 plasma samples from 23 women carrying foetuses at risk for CF and tested each sample using both methods. Our new procedures were successfully applied to 10 couples where fathers carried the p.Phe508del mutation and mothers were carrying a different mutation in the CFTR gene. These simple tests provided clear positive or negative results from the maternal plasma of the pregnant women. We confirmed the presence of cff-DNA in the studied samples by the identification of a tri-allelic DNA profile using a miniSTR kit. All results were correlated with chorionic villus sampling or amniocentesis analyses. CONCLUSIONS This NIPD approach, easily set up in any clinical laboratory where prenatal diagnosis is routinely performed, offers many advantages over current methods: it is simple, rapid, and cost-effective. It opens up the possibility for testing a large number of couples with offspring at risk for CF.
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Abstract
The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively. All of these options have benefits and limitations, and genetic counseling has become increasingly complex for providers who are responsible for guiding patients in their decisions about screening and testing before and during pregnancy.
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Affiliation(s)
- Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
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Opinion commune de la SOGC et du CCGM sur le dépistage génétique en contexte de procréation : Mise à jour à l'intention de l'ensemble des prestataires canadiens de soins de santé maternelle et de services en procréation, à l'ère des tests offerts directement aux consommateurs. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2016; 38:763-787.e4. [DOI: 10.1016/j.jogc.2016.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Verhoef TI, Hill M, Drury S, Mason S, Jenkins L, Morris S, Chitty LS. Non-invasive prenatal diagnosis (NIPD) for single gene disorders: cost analysis of NIPD and invasive testing pathways. Prenat Diagn 2016; 36:636-42. [PMID: 27107169 PMCID: PMC6680142 DOI: 10.1002/pd.4832] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 12/29/2022]
Abstract
Objective Evaluate the costs of offering non‐invasive prenatal diagnosis (NIPD) for single gene disorders compared to traditional invasive testing to inform NIPD implementation into clinical practice. Method Total costs of diagnosis using NIPD or invasive testing pathways were compared for a representative set of single gene disorders. Results For autosomal dominant conditions, where NIPD molecular techniques are straightforward, NIPD cost £314 less than invasive testing. NIPD for autosomal recessive and X‐linked conditions requires more complicated technical approaches and total costs were more than invasive testing, e.g. NIPD for spinal muscular atrophy was £1090 more than invasive testing. Impact of test uptake on costs was assessed using sickle cell disorder as an example. Anticipated high uptake of NIPD resulted in an incremental cost of NIPD over invasive testing of £48 635 per 100 pregnancies at risk of sickle cell disorder. Conclusion Total costs of NIPD are dependent upon the complexity of the testing technique required. Anticipated increased demand for testing may have economic implications for prenatal diagnostic services. Ethical issues requiring further consideration are highlighted including directing resources to NIPD when used for information only and restricting access to safe tests if it is not cost‐effective to develop NIPD for rare conditions. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's Already Known About This Topic?Non‐invasive prenatal diagnosis (NIPD) for some single gene disorders has entered clinical practice and NIPD for other conditions is in development. Studies exploring the costs and benefits of implementing NIPD for a range of single gene disorders have not been undertaken.
What Does This Study Add?For single gene disorders where technical approaches are straightforward, NIPD was considerably cheaper than invasive testing, but for conditions that need more technically challenging approaches NIPD was more expensive. The anticipated increase in test uptake following the introduction of NIPD will be a major contributing factor to the cost of a genetic service offering prenatal diagnosis for single gene disorders in clinical practice. Prospective monitoring and audit of uptake following clinical implementation is required to allow full consideration of the economic, social and ethical issues that will arise.
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Affiliation(s)
- Talitha I Verhoef
- Department of Applied Health Research, University College London, London, UK
| | - Melissa Hill
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sarah Mason
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephen Morris
- Department of Applied Health Research, University College London, London, UK
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
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Perlado S, Bustamante-Aragonés A, Donas M, Lorda-Sánchez I, Plaza J, Rodríguez de Alba M. Fetal Genotyping in Maternal Blood by Digital PCR: Towards NIPD of Monogenic Disorders Independently of Parental Origin. PLoS One 2016; 11:e0153258. [PMID: 27078875 PMCID: PMC4831728 DOI: 10.1371/journal.pone.0153258] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/26/2016] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To date, non-invasive prenatal diagnosis (NIPD) of monogenic disorders has been limited to cases with a paternal origin. This work shows a validation study of the Droplet Digital PCR (ddPCR) technology for analysis of both paternally and maternally inherited fetal alleles. For the purpose, single nucleotide polymorphisms (SNPs) were studied with the only intention to mimic monogenic disorders. METHODS NIPD SNP genotyping was performed by ddPCR in 55 maternal plasma samples. In 19 out of 55 cases, inheritance of the paternal allele was determined by presence/absence criteria. In the remaining 36, determination of the maternally inherited fetal allele was performed by relative mutation dosage (RMD) analysis. RESULTS ddPCR exhibited 100% accuracy for detection of paternal alleles. For diagnosis of fetal alleles with maternal origin by RMD analysis, the technology showed an accuracy of 96%. Twenty-nine out of 36 were correctly diagnosed. There was one FP and six maternal plasma samples that could not be diagnosed. DISCUSSION In this study, ddPCR has shown to be capable to detect both paternal and maternal fetal alleles in maternal plasma. This represents a step forward towards the introduction of NIPD for all pregnancies independently of the parental origin of the disease.
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Affiliation(s)
- Sara Perlado
- Department of Genetics, IIS-Fundación Jiménez Díaz UAM, CIBERER, Madrid, Spain
| | | | - Marta Donas
- Department of Genetics, IIS-Fundación Jiménez Díaz UAM, CIBERER, Madrid, Spain
| | | | - Javier Plaza
- Department of Obstetrics & Gynecology, Fundación Jiménez Díaz-IIS, Madrid, Spain
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