1
|
Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
Collapse
Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| |
Collapse
|
2
|
Smeekens SP, Timmermans R, Westra D, Gilissen C, Faas BHW. Detection of DNA Contamination in Prenatal Samples from Whole Exome Sequencing Data. Clin Chem 2024:hvae068. [PMID: 38863407 DOI: 10.1093/clinchem/hvae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/16/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Maternal cell contamination (MCC) in prenatal samples poses a risk for misdiagnosis, and therefore, testing for contamination is necessary during genetic analysis of prenatal specimens. MCC testing is currently performed as a method separate from the diagnostic method. With the increasing application of whole exome sequencing (WES) in prenatal diagnosis, we sought to develop a method to estimate the level of contamination from WES data, aiming to eliminate the need for a separate MCC test. METHODS To investigate the impact of MCC on the distribution of the variant allele fraction in WES data, contamination was both simulated in silico and artificially induced. Subsequently, a bioinformatic WES contamination method was developed and validated by comparing its performance to that of the gold standard (short tandem repeat [STR]) MCC test, validated for detecting ≥5% contamination. Finally, post-implementation performance was monitored for a 15-month period. RESULTS During validation, 270 prenatal samples underwent analysis with both WES and the gold standard test. In 259 samples, the results were concordant (248 not contaminated, 11 contaminated with both tests). In 11 samples, contamination was only detected in WES data (2 of which contained ≥5% contamination with WES, which is above the detection limit of the gold standard test). The data of the post-implementation evaluation on 361 samples, of which 68 were contaminated, were in line with the validation data. CONCLUSIONS Contamination can reliably be detected in WES data, rendering a separate contamination test unnecessary for the majority of samples.
Collapse
Affiliation(s)
- Sanne P Smeekens
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Raoul Timmermans
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, the Netherlands
| | - Brigitte H W Faas
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| |
Collapse
|
3
|
Weller K, Westra D, Peters NCJ, Wilke M, Van Opstal D, Feenstra I, van Drongelen J, Eggink AJ, Diderich KEM, DeKoninck PLJ. Exome sequencing in fetuses with congenital diaphragmatic hernia in a nationwide cohort. Prenat Diagn 2024. [PMID: 38862387 DOI: 10.1002/pd.6622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
OBJECTIVE To evaluate the diagnostic yield of exome sequencing (ES) in fetuses and neonates with prenatally detected congenital diaphragmatic hernia (CDH) and normal copy number variant (CNV) analysis. METHODS We conducted a retrospective cohort study of prenatally diagnosed CDH cases seen between 2019 and 2022. All cases who underwent prenatal or postnatal genetic testing were reviewed. The results from the ES analysis that identified pathogenic or likely pathogenic single nucleotide variants are described. RESULTS In total, 133 fetuses with CDH were seen, of whom 98 (74%) had an isolated CDH and 35 (26%) had a complex CDH (associated structural anomalies) on prenatal examination. ES was performed in 68 cases, and eight pathogenic or likely pathogenic variants were found, accounting for a 12% diagnostic yield (10% [5/50] in isolated cases and 17% [3/18] in complex CDH). CONCLUSIONS In 12% of fetuses and neonates with CDH and normal CNV analysis results, pathogenic or likely pathogenic variants were identified with ES. These data indicate that there is a substantial diagnostic yield when offering ES in prenatally detected CDH, both in complex and isolated cases.
Collapse
Affiliation(s)
- Katinka Weller
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nina C J Peters
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris van Drongelen
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alex J Eggink
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Philip L J DeKoninck
- Department of Obstetrics and Gynecology, Division of Obstetrics and Fetal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
4
|
Makhamreh MM, Shivashankar K, Araji S, Critchlow E, O'Brien BM, Wodoslawsky S, Berger SI, Al-Kouatly HB. RASopathies are the most common set of monogenic syndromes identified by exome sequencing for nonimmune hydrops fetalis: A systematic review and meta-analysis. Am J Med Genet A 2024; 194:e63494. [PMID: 38156365 DOI: 10.1002/ajmg.a.63494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
RASopathies are a group of malformation syndromes known to lead to nonimmune hydrops fetalis (NIHF) in severe presentations. Pathogenic variants can be de novo or parentally inherited. Despite being a known frequent presentation, the fraction of monogenic NIHF cases due to RASopathies is limited in the literature. Also, the specific parental contribution of RASopathies to NIHF is not well described. Our objective was to review pooled exome sequencing (ES) diagnostic yield of RASopathies for NIHF and to determine the parental contribution of RASopathy to NIHF. We performed a systematic review of prenatal ES studies from January 1, 2000 to August 1, 2022. Thirty-six studies met inclusion criteria. Cases with RASopathy gene variants were reviewed. NIHF cases were further classified as isolated or non-isolated. Thirty-six ES studies including 46 pregnancies with NIHF and a diagnosed RASopathy were reviewed. Forty-four diagnostic variants and 2 variants of uncertain significance in 12 RASopathy genes were identified. Expanding on what was previously published, a total of 506 NIHF cases were extracted with 191 cases yielding a positive diagnosis by ES. The overall rate of RASopathy diagnosis in clinically diagnosed NIHF cases was 9% (44/506). The rate of RASopathy diagnosis among NIHF cases with positive genetic diagnosis by ES was 23% (44/191). Of the 46 cases identified, 13 (28%) variants were parentally inherited; specifically, 5/13 (38%) maternal, 3/13 (23%) paternal, 2/13 (15%) biparental, and 3/13 (23%) unspecified. Majority of NIHF cases 29/46 (63%) were isolated. Among NIHF cases with positive ES diagnoses, RASopathy diagnostic yield by ES was 23%. NIHF secondary to RASopathies was parentally inherited in 28% of cases. Most cases of NIHF due to RASopathy were isolated, with no prenatal detection of associated anomalies.
Collapse
Affiliation(s)
- Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Sarah Araji
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Mississippi, Jackson, Mississippi, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Barbara M O'Brien
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research and Rare Disease Institute, Children's National Medical Center, Washington, DC, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
5
|
Rogers A, De Jong L, Waters W, Rawlings LH, Simons K, Gao S, Soubrier J, Kenyon R, Lin M, King R, Lawrence DM, Muller P, Leblanc S, McGregor L, Sallevelt SCEH, Liebelt J, Hardy TSE, Fletcher JM, Scott HS, Kulkarni A, Barnett CP, Kassahn KS. Extending the new era of genomic testing into pregnancy management: A proposed model for Australian prenatal services. Aust N Z J Obstet Gynaecol 2024. [PMID: 38577897 DOI: 10.1111/ajo.13814] [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: 11/12/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Trio exome sequencing can be used to investigate congenital abnormalities identified on pregnancy ultrasound, but its use in an Australian context has not been assessed. AIMS Assess clinical outcomes and changes in management after expedited genomic testing in the prenatal period to guide the development of a model for widespread implementation. MATERIALS AND METHODS Forty-three prospective referrals for whole exome sequencing, including 40 trios (parents and pregnancy), two singletons and one duo were assessed in a tertiary hospital setting with access to a state-wide pathology laboratory. Diagnostic yield, turn-around time (TAT), gestational age at reporting, pregnancy outcome, change in management and future pregnancy status were assessed for each family. RESULTS A clinically significant genomic diagnosis was made in 15/43 pregnancies (35%), with an average TAT of 12 days. Gestational age at time of report ranged from 16 + 5 to 31 + 6 weeks (median 21 + 3 weeks). Molecular diagnoses included neuromuscular and skeletal disorders, RASopathies and a range of other rare Mendelian disorders. The majority of families actively used the results in pregnancy decision making as well as in management of future pregnancies. CONCLUSIONS Rapid second trimester prenatal genomic testing can be successfully delivered to investigate structural abnormalities in pregnancy, providing crucial guidance for current and future pregnancy management. The time-sensitive nature of this testing requires close laboratory and clinical collaboration to ensure appropriate referral and result communication. We found the establishment of a prenatal coordinator role and dedicated reporting team to be important facilitators. We propose this as a model for genomic testing in other prenatal services.
Collapse
Affiliation(s)
- Alice Rogers
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Lucas De Jong
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Wendy Waters
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Lesley H Rawlings
- Genomics Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Keryn Simons
- Genomics Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Song Gao
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Julien Soubrier
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Rosalie Kenyon
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Ming Lin
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Rob King
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - David M Lawrence
- ACRF SA Cancer Genome Facility, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peter Muller
- Maternal Fetal Medicine Service (MFMS), Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Shannon Leblanc
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Lesley McGregor
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Suzanne C E H Sallevelt
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Jan Liebelt
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Tristan S E Hardy
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Repromed, Monash IVF, Adelaide, South Australia, Australia
| | - Janice M Fletcher
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Abhi Kulkarni
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Karin S Kassahn
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Technology Advancement Unit, Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| |
Collapse
|
6
|
Blayney GV, Laffan E, Jacob PA, Baptiste CD, Gabriel H, Sparks TN, Yaron Y, Norton ME, Diderich K, Wang Y, Chong K, Chitayat D, Saini N, Aggarwal S, Pauta M, Borrell A, Gilmore K, Chandler NJ, Allen S, Vora N, Noor A, Monaghan C, Kilby MD, Wapner RJ, Chitty LS, Mone F. Monogenic conditions and central nervous system anomalies: A prospective study, systematic review and meta-analysis. Prenat Diagn 2024; 44:422-431. [PMID: 38054560 PMCID: PMC11044826 DOI: 10.1002/pd.6466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
OBJECTIVES Determine the incremental diagnostic yield of prenatal exome sequencing (pES) over chromosome microarray (CMA) or G-banding karyotype in fetuses with central nervous system (CNS) abnormalities. METHODS Data were collected via electronic searches from January 2010 to April 2022 in MEDLINE, Cochrane, Web of Science and EMBASE. The NHS England prenatal exome cohort was also included. Incremental yield was calculated as a pooled value using a random-effects model. RESULTS Thirty studies were included (n = 1583 cases). The incremental yield with pES for any CNS anomaly was 32% [95%CI 27%-36%; I2 = 72%]. Subgroup analysis revealed apparent incremental yields in; (a) isolated CNS anomalies; 27% [95%CI 19%-34%; I2 = 74%]; (b) single CNS anomaly; 16% [95% CI 10%-23%; I2 = 41%]; (c) more than one CNS anomaly; 31% [95% Cl 21%-40%; I2 = 56%]; and (d) the anatomical subtype with the most optimal yield was Type 1 malformation of cortical development, related to abnormal cell proliferation or apoptosis, incorporating microcephalies, megalencephalies and dysplasia; 40% (22%-57%; I2 = 68%). The commonest syndromes in isolated cases were Lissencephaly 3 and X-linked hydrocephalus. CONCLUSIONS Prenatal exome sequencing provides a high incremental diagnostic yield in fetuses with CNS abnormalities with optimal yields in cases with multiple CNS anomalies, particularly those affecting the midline, posterior fossa and cortex.
Collapse
Affiliation(s)
- Gillian V. Blayney
- Fetal Medicine Department, Royal Jubilee Maternity Service, Belfast Health and Social Care Trust, Belfast, UK
| | - Eoghan Laffan
- Department of Radiology, Children’ Health Ireland at Crumlin, Dublin, Ireland
| | | | | | | | - Teresa N. Sparks
- Department of Obstetrics, Gynaecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mary E. Norton
- Department of Obstetrics, Gynaecology & Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
| | - Karin Diderich
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Yiming Wang
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Karen Chong
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Neelam Saini
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam’s Institute of Medical Sciences, Hyderabad, India
| | - Montse Pauta
- Insitut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), BCNatal, Barcelona, Spain
| | - Antoni Borrell
- Insitut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), BCNatal, Barcelona, Spain
| | - Kelly Gilmore
- Department of Obstetrics and Gynaecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, South and Central Genomic Laboratory Hub, Birmingham, UK
| | - Neeta Vora
- Department of Obstetrics and Gynaecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Abdul Noor
- Division of Diagnostic Medical Genetics, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Caitriona Monaghan
- Fetal Medicine Department, Royal Jubilee Maternity Service, Belfast Health and Social Care Trust, Belfast, UK
| | - Mark D. Kilby
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | | | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Fionnuala Mone
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| |
Collapse
|
7
|
McInnes-Dean H, Mellis R, Daniel M, Walton H, Baple EL, Bertoli M, Fisher J, Gajewska-Knapik K, Holder-Espinasse M, Lafarge C, Leeson-Beevers K, McEwan A, Pandya P, Parker M, Peet S, Roberts L, Sankaran S, Smith A, Tapon D, Wu WH, Wynn SL, Chitty LS, Hill M, Peter M. 'Something that helped the whole picture': Experiences of parents offered rapid prenatal exome sequencing in routine clinical care in the English National Health Service. Prenat Diagn 2024; 44:465-479. [PMID: 38441167 DOI: 10.1002/pd.6537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 04/11/2024]
Abstract
OBJECTIVES In October 2020, rapid prenatal exome sequencing (pES) was introduced into routine National Health Service (NHS) care in England. This study aimed to explore parent experiences and their information and support needs from the perspective of parents offered pES and of health professionals involved in its delivery. METHODS In this qualitative study, semi-structured interviews were conducted with 42 women and 6 male partners and 63 fetal medicine and genetic health professionals. Interviews were transcribed verbatim and analysed using thematic analysis. RESULTS Overall views about pES were positive and parents were grateful to be offered the test. Highlighted benefits of pES included the value of the additional information for pregnancy management and planning for future pregnancies. An anxious wait for results was common, often associated with the need to make decisions near to 24 weeks in pregnancy when there are legal restrictions for late termination. Descriptions of dealing with uncertainty were also common, even when results had been returned. Many parents described pES results as informing decision-making around whether or not to terminate pregnancy. Some professionals were concerned that a non-informative result could be overly reassuring and highlighted that careful counselling was needed to ensure parents have a good understanding of what the result means for their pregnancy. Emotional support from professionals was valued; however, some parents felt that post-test support was lacking. CONCLUSION Parents and professionals welcomed the introduction of pES. Results inform parents' decision-making around the termination of pregnancy. When there are no diagnostic findings or uncertain findings from pES, personalised counselling that considers scans and other tests are crucial. Directing parents to reliable online sources of information and providing emotional support throughout could improve their experiences of care.
Collapse
Affiliation(s)
- Hannah McInnes-Dean
- Antenatal Results and Choices, London, UK
- North Thames Genomic Laboratory Hub, 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
| | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, 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
| | - Morgan Daniel
- North Thames Genomic Laboratory Hub, 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
| | - Holly Walton
- Department of Applied Health Research, University College London, London, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Peninsula Clinical Genetics Service, School, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | | | | | - Katarzyna Gajewska-Knapik
- Department of Obstetrics and Gynaecology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muriel Holder-Espinasse
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Caroline Lafarge
- School of Human and Social Sciences, University of West London, London, UK
| | | | - Alec McEwan
- Department of Obstetrics and Gynaecology, Nottingham University Hospitals, Nottingham, UK
| | - Pranav Pandya
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
- Fetal Medicine Unit, University College London Hospitals, London, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| | | | | | - Srividhya Sankaran
- School of Life Course and Population Sciences, Kings College London, St Thomas' Hospital, London, UK
- Department of Women and Children Health, Evelina Women & Children's Hospital Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Audrey Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Dagmar Tapon
- Queen Charlotte's & Chelsea Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Wing Han Wu
- North Thames Genomic Laboratory Hub, 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
| | - Sarah L Wynn
- Unique - Rare Chromosome Disorder Support Group, Oxted, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, 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
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, 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
| | - Michelle Peter
- North Thames Genomic Laboratory Hub, 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
| |
Collapse
|
8
|
Mustafa HJ, Barbera JP, Sambatur EV, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Brewer CJ, Khalil A. Diagnostic yield of exome sequencing in prenatal agenesis of corpus callosum: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:312-320. [PMID: 37519216 DOI: 10.1002/uog.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/25/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES To determine the incremental diagnostic yield of exome sequencing (ES) after negative chromosomal microarray analysis (CMA) in cases of prenatally diagnosed agenesis of the corpus callosum (ACC) and to identify the associated genes and variants. METHODS A systematic search was performed to identify relevant studies published up until June 2022 using four databases: PubMed, SCOPUS, Web of Science and The Cochrane Library. Studies in English reporting on the diagnostic yield of ES following negative CMA in prenatally diagnosed partial or complete ACC were included. Authors of cohort studies were contacted for individual participant data and extended cohorts were provided for two of them. The increase in diagnostic yield with ES for pathogenic/likely pathogenic (P/LP) variants was assessed in all cases of ACC, isolated ACC, ACC with other cranial anomalies and ACC with extracranial anomalies. To identify all reported genetic variants, the systematic review included all ACC cases; however, for the meta-analysis, only studies with ≥ three ACC cases were included. Meta-analysis of proportions was employed using a random-effects model. Quality assessment of the included studies was performed using modified Standards for Reporting of Diagnostic Accuracy criteria. RESULTS A total of 28 studies, encompassing 288 prenatally diagnosed ACC cases that underwent ES following negative CMA, met the inclusion criteria of the systematic review. We classified 116 genetic variants in 83 genes associated with prenatal ACC with a full phenotypic description. There were 15 studies, encompassing 268 cases, that reported on ≥ three ACC cases and were included in the meta-analysis. Of all the included cases, 43% had a P/LP variant on ES. The highest yield was for ACC with extracranial anomalies (55% (95% CI, 35-73%)), followed by ACC with other cranial anomalies (43% (95% CI, 30-57%)) and isolated ACC (32% (95% CI, 18-51%)). CONCLUSIONS ES demonstrated an incremental diagnostic yield in cases of prenatally diagnosed ACC following negative CMA. While the greatest diagnostic yield was observed in ACC with extracranial anomalies and ACC with other central nervous system anomalies, ES should also be considered in cases of isolated ACC. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- H J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Riley Children and Indiana University Health Fetal Center, Indianapolis, IN, USA
| | - J P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - E V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX, USA
| | - G Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST-Papa Giovanni XXIII, Bergamo, Italy
| | - Y Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C D Baptiste
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - R J Wapner
- Obstetrics and Gynecology, Reproductive Genetics, Columbia University Medical Center, New York, NY, USA
| | - C J Brewer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - A Khalil
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| |
Collapse
|
9
|
Senturk L, Gulec C, Sarac Sivrikoz T, Kayserili H, Kalelioglu IH, Avci S, Has R, Coucke P, Kalayci T, Wollnik B, Karaman B, Toksoy G, Symoens S, Yigit G, Yuksel A, Basaran S, Tuysuz B, Altunoglu U, Uyguner ZO. Association of Antenatal Evaluations with Postmortem and Genetic Findings in the Series of Fetal Osteogenesis Imperfecta. Fetal Diagn Ther 2024; 51:285-299. [PMID: 38346409 DOI: 10.1159/000536324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/20/2023] [Indexed: 06/05/2024]
Abstract
INTRODUCTION Counseling osteogenesis imperfecta (OI) pregnancies is challenging due to the wide range of onsets and clinical severities, from perinatal lethality to milder forms detected later in life. METHODS Thirty-eight individuals from 36 families were diagnosed with OI through prenatal ultrasonography and/or postmortem clinical and radiographic findings. Genetic analysis was conducted on 26 genes associated with OI in these subjects that emerged over the past 20 years; while some genes were examined progressively, all 26 genes were examined in the group where no pathogenic variations were detected. RESULTS Prenatal and postnatal observations both consistently showed short limbs in 97%, followed by bowing of the long bones in 89%. Among 32 evaluated cases, all exhibited cranial hypomineralization. Fractures were found in 29 (76%) cases, with multiple bones involved in 18 of them. Genetic associations were disclosed in 27 families with 22 (81%) autosomal dominant and five (19%) autosomal recessive forms, revealing 25 variants in six genes (COL1A1, COL1A2, CREB3L1, P3H1, FKBP10, and IFITM5), including nine novels. Postmortem radiological examination showed variability in intrafamily expression of CREBL3- and P3H1-related OI. CONCLUSION Prenatal diagnosis for distinguishing OI and its subtypes relies on factors such as family history, timing, ultrasound, genetics, and postmortem evaluation.
Collapse
Affiliation(s)
- Leyli Senturk
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Cagri Gulec
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Tugba Sarac Sivrikoz
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hulya Kayserili
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | - Ibrahim Halil Kalelioglu
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sahin Avci
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | - Recep Has
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Paul Coucke
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tugba Kalayci
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Birsen Karaman
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Institute of Child Health, Department of Pediatric Basic Sciences, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Guven Toksoy
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Gokhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Atil Yuksel
- Division of Perinatology, Department of Obstetrics and Gynecology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Seher Basaran
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Medical School, Istanbul, Turkey
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| |
Collapse
|
10
|
Marouane A, Neveling K, Deden AC, van den Heuvel S, Zafeiropoulou D, Castelein S, van de Veerdonk F, Koolen DA, Simons A, Rodenburg R, Westra D, Mensenkamp AR, de Leeuw N, Ligtenberg M, Matthijsse R, Pfundt R, Kamsteeg EJ, Brunner HG, Gilissen C, Feenstra I, de Boode WP, Yntema HG, van Zelst-Stams WAG, Nelen M, Vissers LELM. Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease. Front Genet 2024; 14:1304520. [PMID: 38259611 PMCID: PMC10800954 DOI: 10.3389/fgene.2023.1304520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Rapid exome sequencing (rES) has become the first-choice genetic test for critically ill patients, mostly neonates, young infants, or fetuses in prenatal care, in time-sensitive situations and when it is expected that the genetic test result may guide clinical decision making. The implementation of rES has revolutionized medicine by enabling timely identification of genetic causes for various rare diseases. The utilization of rES has increasingly been recognized as an essential diagnostic tool for the identification of complex and undiagnosed genetic disorders. Methods: We conducted a retrospective evaluation of our experiences with rES performed on 575 critically ill patients from various age groups (prenatal to adulthood), over a four-year period (2016-2019). These patients presented with a wide spectrum of rare diseases, including but not limited to neurological disorders, severe combined immune deficiency, and cancer. Results: During the study period, there was a significant increase in rES referrals, with a rise from a total of two referrals in Q1-2016 to 10 referrals per week in Q4-2019. The median turnaround time (TAT) decreased from 17 to 11 days in the period 2016-2019, with an overall median TAT of 11 days (IQR 8-15 days). The overall diagnostic yield for this cohort was 30.4%, and did not significantly differ between the different age groups (e.g. adults 22.2% vs children 31.0%; p-value 0.35). However, variability in yield was observed between clinical entities: craniofacial anomalies yielded 58.3%, while for three clinical entities (severe combined immune deficiency, aneurysm, and hypogonadotropic hypogonadism) no diagnoses were obtained. Discussion: Importantly, whereas clinical significance is often only attributed to a conclusive diagnosis, we also observed impact on clinical decision-making for individuals in whom no genetic diagnosis was established. Hence, our experience shows that rES has an important role for patients of all ages and across the broad spectrum of rare diseases to impact clinical outcomes.
Collapse
Affiliation(s)
- Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - A. Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frank van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - David A. Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Richard Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dineke Westra
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| | - Arjen R. Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marjolijn Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Rene Matthijsse
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem P. de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children’s Hospital, Nijmegen, Netherlands
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
11
|
Mehollin-Ray AR, Stover S, Cassady CI, Zhang B, Calvo-Garcia M, Kline-Fath B. Using MRI-derived observed-to-expected total fetal lung volume to predict lethality in fetal skeletal dysplasia. Pediatr Radiol 2024; 54:43-48. [PMID: 38052986 DOI: 10.1007/s00247-023-05825-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Pulmonary hypoplasia is the primary cause of perinatal death in lethal skeletal dysplasias. The antenatal ultrasound correlates for lethality are indirect, measuring the thorax (thoracic circumference, TC) or femur compared to the abdomen (TC/AC, FL/AC). A single study has correlated lethality with the observed-to-expected total lung volume (O/E-TFLV) on fetal MRI in 23 patients. OBJECTIVE Our aim was to define a cutoff value to predict lethality more specifically using MRI-derived O/E-TFLV. MATERIALS AND METHODS Two large fetal center databases were searched for fetuses with skeletal dysplasia and MRI; O/E-TFLV was calculated. Ultrasound measures were included when available. Each was evaluated as a continuous variable against lethality (stillbirth or death in the first month of life). Logistic regression and receiver operating characteristic (ROC) curve analyses evaluated the prediction ability. AUC, sensitivity, and specificity were calculated. P < 0.05 was considered statistically significant. RESULTS A total of 80 fetuses met inclusion criteria. O/E-TFLV < 0.49 was a significant risk factor in predicting lethality, with sensitivity and specificity of 0.63 and 0.93, respectively, and an AUC of 0.81 (P < 0.001). FL/AC < 0.129 was also a strong variable with sensitivity, specificity, and AUC of 0.73, 0.88, and 0.78, respectively (P < 0.001). TC/AC and TC percentile were not significant risk factors for lethality. An O/E-TFLV of < 0.38 defines a specificity for lethality at 1.00. CONCLUSION MRI-derived O/E-TFLV and US-derived FL/AC are significant predictors of lethality in fetuses with skeletal dysplasia. When prognosis is uncertain after ultrasound, calculation of MRI-derived O/E-TFLV may provide additional useful information for prognosis and delivery planning.
Collapse
Affiliation(s)
- Amy R Mehollin-Ray
- Department of Radiology and Imaging Sciences, Division of Pediatric Radiology, Emory University School of Medicine, 1405 Clifton Rd NE, Atlanta, GA, 30322, USA.
- E. B. Singleton Department of Radiology, Texas Children's Hospital, Houston, TX, USA.
| | - Samantha Stover
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher I Cassady
- E. B. Singleton Department of Radiology, Texas Children's Hospital, Houston, TX, USA
- Department of Radiology, Starship Children's Hospital, Auckland, New Zealand
| | - Bin Zhang
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Maria Calvo-Garcia
- Department of Radiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Beth Kline-Fath
- Department of Radiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| |
Collapse
|
12
|
Diderich KEM, Klapwijk JE, van der Schoot V, van den Born M, Wilke M, Joosten M, Stuurman KE, Hoefsloot LH, Van Opstal D, Brüggenwirth HT, Srebniak MI. The role of a multidisciplinary team in managing variants of uncertain clinical significance in prenatal genetic diagnosis. Eur J Med Genet 2023; 66:104844. [PMID: 37709011 DOI: 10.1016/j.ejmg.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Although in general prenatal exome sequencing only reports (likely) pathogenic variants, in some cases a variant of uncertain significance (VUS) is disclosed. The aims of this retrospective study were to evaluate the types of VUS that have been reported to prospective parents, possible reclassification and to design a standard flow chart to determine which types of VUS could be considered for reporting in prenatal settings. Furthermore, we investigated what the crucial elements are to facilitate rapid management of uncertain results in a prenatal setting. MATERIAL AND METHODS We reviewed exome results from 451 pregnancies performed in 2019-2021. We analyzed which factors that were taken into account by the multidisciplinary team (MDT) contributed towards decision making on reporting VUS after prenatal exome sequencing. RESULTS In 9/451 (2%) pregnancies tested with exome sequencing using a broad panel analysis a VUS was reported. After birth 3/9 VUS could be reclassified to likely pathogenic variants based on new clinical follow up data. We considered reporting VUS in genes: 1) matching the fetal phenotype, 2) associated with a severe disorder when a functional test is available or 3) possibly associated with a disorder where early post-partum diagnosis and treatment are crucial for a better prognosis. Two flowcharts were designed to guide first the laboratory specialist and then the MDT in decisions on reporting VUS. The crucial elements that enabled timely decisions on VUS disclosure were regular meetings, appropriate expertise, professional connections with other experts and psychological safety within the MDT. CONCLUSION In this study three out of nine VUS could be re-classified as likely pathogenic after clinical follow-up. In order to protect pregnant couples from the burden of uncertain results, the genetic professionals have to take the responsibility to limit the reporting of VUS. This can be done not only by automated filtering of data, by following professional guidelines and by building standardized decision flows, but also by discussing individual cases considering personal situations and the involved disease and by sharing professional experience and responsibility in a multidisciplinary prenatal team setting.
Collapse
Affiliation(s)
- Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.
| | - Jasmijn E Klapwijk
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Hennie T Brüggenwirth
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Malgorzata I Srebniak
- Department of Clinical Genetics, Erasmus MC, Dr Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| |
Collapse
|
13
|
Mustafa HJ, Sambatur EV, Barbera JP, Pagani G, Yaron Y, Baptiste CD, Wapner RJ, Khalil A. Diagnostic yield with exome sequencing in prenatal severe bilateral ventriculomegaly: a systematic review and meta-analysis. Am J Obstet Gynecol MFM 2023; 5:101048. [PMID: 37311485 DOI: 10.1016/j.ajogmf.2023.101048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
OBJECTIVE This study aimed to determine the incremental diagnostic yield of prenatal exome sequencing after negative chromosomal microarray analysis results in prenatally diagnosed bilateral severe ventriculomegaly or hydrocephalus; another objective was to categorize the associated genes and variants. DATA SOURCES A systematic search was performed to identify relevant studies published until June 2022 using 4 databases (Cochrane Library, Web of Science, Scopus, and MEDLINE). STUDY ELIGIBILITY CRITERIA Studies in English reporting on the diagnostic yield of exome sequencing following negative chromosomal microarray analysis results in cases of prenatally diagnosed bilateral severe ventriculomegaly were included. METHODS Authors of cohort studies were contacted for individual participant data, and 2 studies provided their extended cohort data. The incremental diagnostic yield of exome sequencing was assessed for pathogenic/likely pathogenic findings in cases of: (1) all severe ventriculomegaly; (2) isolated severe ventriculomegaly (as the only cranial anomaly); (3) severe ventriculomegaly with other cranial anomalies; and (4) nonisolated severe ventriculomegaly (with extracranial anomalies). To be able to identify all reported genetic associations, the systematic review portion was not limited to any minimal severe ventriculomegaly case numbers; however, for the synthetic meta-analysis, we included studies with ≥3 severe ventriculomegaly cases. Meta-analysis of proportions was done using a random-effects model. Quality assessment of the included studies was performed using the modified STARD (Standards for Reporting of Diagnostic Accuracy Studies) criteria. RESULTS A total of 28 studies had 1988 prenatal exome sequencing analyses performed following negative chromosomal microarray analysis results for various prenatal phenotypes; this included 138 cases with prenatal bilateral severe ventriculomegaly. We categorized 59 genetic variants in 47 genes associated with prenatal severe ventriculomegaly along with their full phenotypic description. There were 13 studies reporting on ≥3 severe ventriculomegaly cases, encompassing 117 severe ventriculomegaly cases that were included in the synthetic analysis. Of all the included cases, 45% (95% confidence interval, 30-60) had positive pathogenic/likely pathogenic exome sequencing results. The highest yield was for nonisolated cases (presence of extracranial anomalies; 54%; 95% confidence interval, 38-69), followed by severe ventriculomegaly with other cranial anomalies (38%; 95% confidence interval, 22-57) and isolated severe ventriculomegaly (35%; 95% confidence interval, 18-58). CONCLUSION There is an apparent incremental diagnostic yield of prenatal exome sequencing following negative chromosomal microarray analysis results in bilateral severe ventriculomegaly. Although the greatest yield was found in cases of nonisolated severe ventriculomegaly, consideration should also be given to performing exome sequencing in cases of isolated severe ventriculomegaly as the only brain anomaly identified on prenatal imaging.
Collapse
Affiliation(s)
- Hiba J Mustafa
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Indiana University School of Medicine, Indianapolis, IN (Dr Mustafa); Fetal Center at Riley Children's Health, Indiana University Health, Indianapolis, IN (Dr Mustafa).
| | - Enaja V Sambatur
- Research Division, Houston Center for Maternal Fetal Medicine, Houston, TX (Ms Sambatur)
| | - Julie P Barbera
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA (Ms Barbera)
| | - Giorgio Pagani
- Maternal Fetal Medicine Unit, Department of Obstetrics and Gynecology, ASST Papa Giovanni XXIII, Bergamo, Italy (Dr Pagani)
| | - Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetics Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel (Dr Yaron); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel (Dr Yaron)
| | - Caitlin D Baptiste
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Ronald J Wapner
- Division of Women's Genetics, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY (Drs Baptiste and Wapner)
| | - Asma Khalil
- Fetal Medicine Unit, St George's Hospital, St George's University of London, London, United Kingdom (Dr Khalil); Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom (Dr Khalil)
| |
Collapse
|
14
|
Diderich KEM, Klapwijk JE, van der Schoot V, Brüggenwirth HT, Joosten M, Srebniak MI. Challenges and Pragmatic Solutions in Pre-Test and Post-Test Genetic Counseling for Prenatal Exome Sequencing. Appl Clin Genet 2023; 16:89-97. [PMID: 37216148 PMCID: PMC10198275 DOI: 10.2147/tacg.s411185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) and prenatal exome sequencing (pES). However, together with increased numbers of diagnoses made, the need to manage challenging findings such as variants of unknown significance (VUS) and incidental findings (IF) also increased. We have summarized the current guidelines and recommendations and we have shown current solutions used in our tertiary center in the Netherlands. We discuss four of the most common clinical situations: fetus with normal pES results, fetus with a pathogenic finding explaining the fetal phenotype, fetus with a variant of uncertain clinical significance fitting the phenotype and fetus with a variant leading to an incidental diagnosis. Additionally, we reflect on solutions in order to facilitate genetic counseling in an NGS-era.
Collapse
Affiliation(s)
| | | | | | | | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | | |
Collapse
|
15
|
Olde Keizer RACM, Marouane A, Kerstjens-Frederikse WS, Deden AC, Lichtenbelt KD, Jonckers T, Vervoorn M, Vreeburg M, Henneman L, de Vries LS, Sinke RJ, Pfundt R, Stevens SJC, Andriessen P, van Lingen RA, Nelen M, Scheffer H, Stemkens D, Oosterwijk C, van Amstel HKP, de Boode WP, van Zelst-Stams WAG, Frederix GWJ, Vissers LELM. Rapid exome sequencing as a first-tier test in neonates with suspected genetic disorder: results of a prospective multicenter clinical utility study in the Netherlands. Eur J Pediatr 2023:10.1007/s00431-023-04909-1. [PMID: 36997769 PMCID: PMC10257607 DOI: 10.1007/s00431-023-04909-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 04/01/2023]
Abstract
The introduction of rapid exome sequencing (rES) for critically ill neonates admitted to the neonatal intensive care unit has made it possible to impact clinical decision-making. Unbiased prospective studies to quantify the impact of rES over routine genetic testing are, however, scarce. We performed a clinical utility study to compare rES to conventional genetic diagnostic workup for critically ill neonates with suspected genetic disorders. In a multicenter prospective parallel cohort study involving five Dutch NICUs, we performed rES in parallel to routine genetic testing for 60 neonates with a suspected genetic disorder and monitored diagnostic yield and the time to diagnosis. To assess the economic impact of rES, healthcare resource use was collected for all neonates. rES detected more conclusive genetic diagnoses than routine genetic testing (20% vs. 10%, respectively), in a significantly shorter time to diagnosis (15 days (95% CI 10-20) vs. 59 days (95% CI 23-98, p < 0.001)). Moreover, rES reduced genetic diagnostic costs by 1.5% (€85 per neonate). CONCLUSION Our findings demonstrate the clinical utility of rES for critically ill neonates based on increased diagnostic yield, shorter time to diagnosis, and net healthcare savings. Our observations warrant the widespread implementation of rES as first-tier genetic test in critically ill neonates with disorders of suspected genetic origin. WHAT IS KNOWN • Rapid exome sequencing (rES) enables diagnosing rare genetic disorders in a fast and reliable manner, but retrospective studies with neonates admitted to the neonatal intensive care unit (NICU) indicated that genetic disorders are likely underdiagnosed as rES is not routinely used. • Scenario modeling for implementation of rES for neonates with presumed genetic disorders indicated an expected increase in costs associated with genetic testing. WHAT IS NEW • This unique prospective national clinical utility study of rES in a NICU setting shows that rES obtained more and faster diagnoses than conventional genetic tests. • Implementation of rES as replacement for all other genetic tests does not increase healthcare costs but in fact leads to a reduction in healthcare costs.
Collapse
Grants
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 843002608, 846002003 ZonMw
- 779257 Horizon 2020 Framework Programme
- 779257 Horizon 2020 Framework Programme
Collapse
Affiliation(s)
- Richelle A C M Olde Keizer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abderrahim Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - A Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | | | - Tinneke Jonckers
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Marieke Vervoorn
- Department of Pediatrics and Neonatology, Máxima Medical Center, Veldhoven, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Lidewij Henneman
- Department of Human Genetics and Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Linda S de Vries
- Department of Neonatology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Richard J Sinke
- Department of Genetics, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Peter Andriessen
- Department of Pediatrics, Máxima Medical Center, Veldhoven, Netherlands
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, Netherlands
| | | | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Daphne Stemkens
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | - Cor Oosterwijk
- VSOP - National Patient Alliance for Rare and Genetic Diseases, Soest, Netherlands
| | | | - Willem P de Boode
- Department of Neonatology, Radboud University Medical Center, Radboud Institute for Health Sciences, Amalia Children's Hospital, Nijmegen, Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands.
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Genetics, Utrecht University Medical Center, Utrecht, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.
| |
Collapse
|
16
|
Poljak B, Agarwal U, Alfirevic Z, Allen S, Canham N, Higgs J, Kaelin Agten A, Khalil A, Roberts D, Mone F, Navaratnam K. Prenatal exome sequencing and impact on perinatal outcome: cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 61:339-345. [PMID: 36508432 DOI: 10.1002/uog.26141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVES First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation. METHODS This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next-generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ-square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0. RESULTS In total, 72 cases were identified and two-thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one-third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19-34) days vs 14 days (IQR, 10-15 days); P < 0.0001). CONCLUSIONS This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- B Poljak
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - U Agarwal
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - Z Alfirevic
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
- Harris-Wellbeing Research Centre, University of Liverpool, Liverpool, UK
| | - S Allen
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - N Canham
- Clinical Genetics Department, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - J Higgs
- Clinical Genetics Department, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - A Kaelin Agten
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - A Khalil
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, University of London, London, UK
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
| | - D Roberts
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Navaratnam
- Fetal Medicine Unit, Liverpool Women's Hospital NHS Foundation Trust, Liverpool, UK
- Harris-Wellbeing Research Centre, University of Liverpool, Liverpool, UK
| |
Collapse
|
17
|
Al-Kouatly HB, Shivashankar K, Mossayebi MH, Makhamreh M, Critchlow E, Gao Z, Fasehun LK, Alkuraya FS, Ryan EE, Hegde M, Wodoslawsky S, Hughes J, Berger SI. Diagnostic yield from prenatal exome sequencing for non-immune hydrops fetalis: A systematic review and meta-analysis. Clin Genet 2023; 103:503-512. [PMID: 36757664 DOI: 10.1111/cge.14309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Non-immune hydrops fetalis (NIHF) has multiple genetic etiologies diagnosable by exome sequencing (ES). We evaluated the yield of prenatal ES for NIHF, and the contribution of additional clinical findings and history. Systematic review was performed with PROSPERO tag 232951 using CINAHL, PubMed, and Ovid MEDLINE from January 1, 2000 through December 1, 2021. Selected studies performed ES to augment standard prenatal diagnostic approaches. Cases meeting a strict NIHF phenotype were tabulated with structured data imputed from papers or requested from authors. Genetic variants and diagnostic outcomes were harmonized across studies using current ACMG and ClinGen variant classification guidelines. Thirty-one studies reporting 445 NIHF cases had a 37% (95% CI: 32%-41%) diagnostic rate. There was no significant difference between isolated NIHF and NIHF with fetal malformations or between recurrent and simplex cases. Diagnostic rate was higher for consanguineous than non-consanguineous cases. Disease categories included RASopathies (24%), neuromuscular (21%), metabolic (17%), lymphatic (13%), other syndromes (9%), cardiovascular (5%), hematologic (2%), skeletal (2%), and other categories (7%). Inheritance patterns included recessive (55%), dominant (41%), and X-linked (4%). ES should be considered in the diagnostic workup of NIHF with and without associated ultrasound findings regardless of history of recurrence or consanguinity.
Collapse
Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Matthew H Mossayebi
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Luther-King Fasehun
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Erin E Ryan
- Genomic Data / Genetic Counseling, GeneDx, Gaithersburg, Maryland, USA
| | - Madhuri Hegde
- Global Lab Services, PerkinElmer Genomics, Atlanta, Georgia, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joel Hughes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
| |
Collapse
|
18
|
Vaz FM, Jamal Y, Barto R, Gelb MH, DeBarber AE, Wevers RA, Nelen MR, Verrips A, Bootsma AH, Bouva MJ, Kleise N, van der Zee W, He T, Salomons GS, Huidekoper HH. Newborn screening for Cerebrotendinous Xanthomatosis: A retrospective biomarker study using both flow-injection and UPLC-MS/MS analysis in 20,000 newborns. Clin Chim Acta 2023; 539:170-174. [PMID: 36529270 PMCID: PMC10387442 DOI: 10.1016/j.cca.2022.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Cerebrotendinous Xanthomatosis (CTX) is a treatable disorder of bile acid synthesis caused by deficiency of 27-sterol hydroxylase -encoded by CYP27A1- leading to gastrointestinal and progressive neuropsychiatric symptoms. Biochemically, CTX is characterized by accumulation of the bile alcohol cholestanetetrol glucuronide (GlcA-tetrol) and the deficiency of tauro-chenodeoxycholic acid (t-CDCA) and tauro-trihydroxycholestanoic acid (t-THCA). MATERIALS AND METHODS To ascertain the feasibility of CTX newborn screening (NBS) we performed a study with deidentified Dutch dried blood spots using reagents and equipment that is frequently used in NBS laboratories. 20,076 deidentified newborn blood spots were subjected to flow-injection (FIA)-MS/MS and UPLC-MS/MS analysis to determine the concentration of GlcA-tetrol and calculate the GlcA-tetrol/t-CDCA and t-THCA/GlcA-tetrol ratios. RESULTS Using UPLC-MS/MS analysis both GlcA-tetrol concentration and/or metabolite ratios GlcA-tetrol/t-CDCA proved to be informative biomarkers; newborn DBS results did not overlap with those of the CTX patients. For FIA-MS/MS, GlcA-tetrol also was an excellent marker but when using the combination of the GlcA-tetrol/t-CDCA and t-THCA/GlcA-tetrol ratios also did not yield any screen positives. CONCLUSION Newborn screening for CTX using only metabolite ratios following the measurement of three CTX biomarkers is possible using either FIA-MS/MS or UPLC-MS/MS, which paves the way for introduction of CTX NBS.
Collapse
Affiliation(s)
- Frédéric M Vaz
- Amsterdam UMC Location University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC Location University of Amsterdam, Amsterdam, the Netherlands; United for Metabolic Diseases, the Netherlands.
| | - Youssra Jamal
- Amsterdam UMC Location University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands
| | - Rob Barto
- Amsterdam UMC Location University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands
| | - Michael H Gelb
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Andrea E DeBarber
- University Shared Resource and Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Aad Verrips
- Department of Neurology, Canisius Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Albert H Bootsma
- Amsterdam UMC Location University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands
| | - Marelle J Bouva
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Nick Kleise
- PerkinElmer / Wallac Oy, Mustionkatu 6, 20750 Turku, Finland
| | | | - Tao He
- PerkinElmer / Wallac Oy, Mustionkatu 6, 20750 Turku, Finland
| | - Gajja S Salomons
- Amsterdam UMC Location University of Amsterdam, Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, the Netherlands; Core Facility Metabolomics, Amsterdam UMC Location University of Amsterdam, Amsterdam, the Netherlands; United for Metabolic Diseases, the Netherlands
| | - Hidde H Huidekoper
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands; United for Metabolic Diseases, the Netherlands
| |
Collapse
|
19
|
Liu F, Dai L, Li Z, Yin’s X. Novel variants of NEK9 associated with neonatal arthrogryposis: Two case reports and a literature review. Front Genet 2023; 13:989215. [PMID: 36712877 PMCID: PMC9879004 DOI: 10.3389/fgene.2022.989215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Objective: Pathogenic variants in NEK9 (MIM: 609798) have been identified in patients with lethal congenital contracture syndrome 10 (OMIM: 617022) and arthrogryposis, Perthes disease, and upward gaze palsy (APUG and OMIM: 614262). The shared core phenotype is multiple joint contractures or arthrogryposis. In the present study, three novel variants of NEK9 associated with neonatal arthrogryposis were reported. Methods: The clinical data of two premature infants and their parents were collected. The genomic DNA was extracted from their peripheral blood samples and subjected to trio-whole-exome sequencing (trio-WES) and copy number variation analysis. Results: Using trio-WES, a total of three novel pathogenic variants of NEK9 were detected in the two families. Patient 1 carried compound heterozygous variations of c.717C > A (p. C239*741) and c.2824delA (p.M942Cfs*21), which were inherited from his father and mother, respectively. Patient 2 also carried compound heterozygous variations of c.61G > T (p. E21*959) and c. 2824delA (p. M942Cfs*21), which were inherited from his father and mother, respectively. These variants have not been previously reported in the ClinVar, HGMD, or gnomAD databases. Conclusion: This is the first report about NEK9-related arthrogryposis in neonatal patients. The findings from this study suggest that different types of mutations in NEK9 lead to different phenotypes. Our study expanded the clinical phenotype spectrum and gene spectrum of NEK9-associated arthrogryposis.
Collapse
Affiliation(s)
- Fang Liu
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China,*Correspondence: Fang Liu,
| | - Liying Dai
- Department of Neonatology, Anhui Children’s Hospital, Hefei, China
| | - Zhi Li
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China
| | - Xiaowei Yin’s
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China
| |
Collapse
|
20
|
Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death. Nat Med 2023; 29:180-189. [PMID: 36658419 DOI: 10.1038/s41591-022-02142-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/22/2022] [Indexed: 01/21/2023]
Abstract
Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.
Collapse
|
21
|
The Value of a Comprehensive Genomic Evaluation in Prenatal Diagnosis of Genetic Diseases: A Retrospective Study. Genes (Basel) 2022; 13:genes13122365. [PMID: 36553632 PMCID: PMC9778469 DOI: 10.3390/genes13122365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Currently, there are still many challenges in prenatal diagnosis, such as limited or uncertain fetal phenotyping, variant interpretation, and rapid turnaround times. The aim of this study was to illustrate the value of a comprehensive genomic evaluation in prenatal diagnosis. We retrospectively reviewed 20 fetuses with clinically significant copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) and no further exome sequencing testing in our tertiary center between 2019 and 2020. The residual DNA from the prenatal cases was used for the parallel implementation of CNV sequencing (CNV-seq) and trio-based clinical exome sequencing (trio-CES). CMA revealed 26 clinically significant CNVs (18 deletions and eight duplications) in 20 fetuses, in which five fetuses had two or more CNVs. There were eight fetuses with pathogenic CNVs (e.g., del 1p36), nine fetuses with likely pathogenic CNVs (e.g., dup 22q11.21), and three fetuses with variants of unknown significance (VOUS, e.g., dup 1q21.1q21.2). Trio-CES identified four fetuses with likely pathogenic mutations (SNV/InDels). Of note, a fetus was detected with a maternally inherited hemizygous variant in the SLX4 gene due to a 16p13.3 deletion on the paternal chromosome. The sizes of CNVs detected by CNV-seq were slightly larger than that of the SNP array, and four cases with mosaic CNVs were all identified by CNV-seq. In conclusion, microdeletion/duplication syndromes and monogenic disorders may co-exist in a subject, and CNV deletion may contribute to uncovering additional recessive disease alleles. The application of a comprehensive genomic evaluation (CNVs and SNV/InDels) has great value in the prenatal diagnosis arena. CNV-seq based on NGS technology is a reliable and a cost-effective technique for identifying CNVs.
Collapse
|
22
|
So PL, Hui ASY, Ma TWL, Shu W, Hui APW, Kong CW, Lo TK, Kan ANC, Kan EYL, Chong SC, Chung BHY, Luk HM, Choy KW, Kan ASY, Leung WC. Implementation of Public Funded Genome Sequencing in Evaluation of Fetal Structural Anomalies. Genes (Basel) 2022; 13:2088. [PMID: 36360323 PMCID: PMC9690018 DOI: 10.3390/genes13112088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 08/20/2023] Open
Abstract
With the advancements in prenatal diagnostics, genome sequencing is now incorporated into clinical use to maximize the diagnostic yield following uninformative conventional tests (karyotype and chromosomal microarray analysis). Hong Kong started publicly funded prenatal genomic sequencing as a sequential test in the investigation of fetal structural anomalies in April 2021. The objective of the study was to evaluate the clinical performance and usefulness of this new service over one year. We established a web-based multidisciplinary team to facilitate case selection among the expert members. We retrospectively analyzed the fetal phenotypes, test results, turnaround time and clinical impact in the first 15 whole exome sequencing and 14 whole genome sequencing. Overall, the molecular diagnostic rate was 37.9% (11/29). De novo autosomal dominant disorders accounted for 72.7% (8/11), inherited autosomal recessive disorders for 18.2% (2/11), and inherited X-linked disorders for 9.1% (1/11). The median turnaround time for ongoing pregnancy was 19.5 days (range, 13-31 days). Our study showed an overall clinical impact of 55.2% (16/29), which influenced reproductive decision-making in four cases, guided perinatal management in two cases and helped future family planning in ten cases. In conclusion, our findings support the important role of genome sequencing services in the prenatal diagnosis of fetal structural anomalies in a population setting. It is important to adopt a multidisciplinary team approach to support the comprehensive genetic service.
Collapse
Affiliation(s)
- Po Lam So
- Department of Obstetrics and Gynecology, Tuen Mun Hospital, Hong Kong SAR, China
| | - Annie Shuk Yi Hui
- Department of Obstetrics & Gynaecology, Prince of Wales Hospital, Hong Kong SAR, China
| | - Teresa Wei Ling Ma
- Department of Obstetrics & Gynaecology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Wendy Shu
- Department of Obstetrics & Gynaecology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Amelia Pui Wah Hui
- Department of Obstetrics & Gynaecology, Queen Mary Hospital, Hong Kong SAR, China
| | - Choi Wah Kong
- Department of Obstetrics & Gynaecology, United Christian Hospital, Hong Kong SAR, China
| | - Tsz Kin Lo
- Department of Obstetrics & Gynaecology, Princess Margaret Hospital, Hong Kong SAR, China
| | - Amanda Nim Chi Kan
- Department of Pathology, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Elaine Yee Ling Kan
- Department of Radiology, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Shuk Ching Chong
- Department of Paediatrics, Prince of Wales Hospital, Hong Kong SAR, China
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ho Ming Luk
- Clinical Genetics Service Unit, Hong Kong Children’s Hospital, Hong Kong SAR, China
| | - Kwong Wai Choy
- Prenatal Genetic Diagnosis Centre, Department of Obstetrics & Gynaecology, Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anita Sik Yau Kan
- Prenatal Diagnostic Laboratory, Tsan Yuk Hospital, Hong Kong SAR, China
| | - Wing Cheong Leung
- Department of Obstetrics & Gynaecology, Kwong Wah Hospital, Hong Kong SAR, China
| |
Collapse
|
23
|
Avram CM, Caughey AB, Norton ME, Sparks TN. Cost-Effectiveness of Exome Sequencing versus Targeted Gene Panels for Prenatal Diagnosis of Fetal Effusions and Non-Immune Hydrops Fetalis. Am J Obstet Gynecol MFM 2022; 4:100724. [PMID: 35995366 PMCID: PMC9938838 DOI: 10.1016/j.ajogmf.2022.100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND Although exome sequencing has a greater overall diagnostic yield than targeted gene panels in the evaluation of nonimmune hydrops fetalis and fetal effusions, the cost-effectiveness of this approach is not known. OBJECTIVE This study aimed to evaluate the costs and outcomes of targeted gene panels vs exome sequencing for prenatally diagnosed nonimmune hydrops fetalis and fetal effusions when next-generation sequencing is pursued following nondiagnostic standard nonimmune hydrops fetalis evaluations, including karyotype or chromosomal microarray. STUDY DESIGN A decision-analytical model was designed using TreeAge Pro to compare 10 genetic testing strategies, including a single test only (RASopathy, metabolic, or nonimmune hydrops fetalis-targeted gene panel or exome sequencing), sequential testing (RASopathy panel followed by nonimmune hydrops fetalis panel, metabolic panel followed by nonimmune hydrops fetalis panel, RASopathy panel followed by exome sequencing, metabolic panel followed by exome sequencing, and nonimmune hydrops fetalis panel followed by exome sequencing), and no additional genetic testing. Our theoretical cohort included cases with normal karyotype and/or microarray and excluded cases of alloimmunization and congenital viral infections. As nonimmune hydrops fetalis and fetal effusions can present throughout gestation, whereas pregnancy management options vary depending on gestational age, outcomes were calculated for 3 time intervals: 10 to 18, 18 to 22, and >22 weeks of gestation. The primary outcome was incremental cost per quality-adjusted life year. Additional outcomes included termination of pregnancy, stillbirth, neonatal death, and neonates born with mild, moderate, and severe or profound disease phenotypes. The cost-effectiveness threshold was $100,000 per quality-adjusted life year. RESULTS Among women <18 weeks of gestation, exome sequencing alone was the dominant strategy associated with the lowest costs ($221 million) and the highest quality-adjusted life years (10,288). Strategies with exome sequencing alone or as a sequential test resulted in more terminations but fewer stillbirths, neonatal deaths (NNDs), and affected infants than strategies without exome sequencing. Among women between 18 and 22 weeks of gestation, exome sequencing alone was also associated with the lowest costs ($188 million) and the highest quality-adjusted life years (8734), and similar trends were observed in pregnancy outcomes. Among patients >22 weeks of gestations, when termination was not available, exome sequencing was associated with lower costs ($300 million) and the highest quality-adjusted life years (8492). Exome sequencing was cost-effective up to a cost per test of $50,451 at <18 weeks of gestation, $50,423 at 18 to 22 weeks of gestation, and $9530 at >22 weeks of gestation. Targeted genetic panels and exome sequencing were cost-effective strategies compared with no additional genetic testing. CONCLUSION For cases of nonimmune hydrops fetalis and fetal effusions with nondiagnostic karyotype or microarray, next-generation sequencing was cost-effective compared with a strategy without additional genetic testing. For those that undergo next-generation sequencing, exome sequencing was the cost-effective strategy compared with all other testing strategies using targeted gene panels, leading to lower costs and fewer adverse perinatal outcomes. Exome sequencing was cost-effective in a setting without the option for pregnancy termination. These data supported the routine use of exome sequencing when next-generation sequencing is pursued for establishing a genetic diagnosis underlying otherwise unexplained nonimmune hydrops fetalis and fetal effusions.
Collapse
Affiliation(s)
- Carmen M Avram
- Duke University Medical Center, Durham, NC (Carmen M. Avram, MD).
| | - Aaron B Caughey
- Oregon Health & Science University, Portland, OR (Aaron B. Caughey, MD, PhD)
| | - Mary E Norton
- University of California, San Francisco, San Francisco, CA (Mary E. Norton, MD, Teresa N. Sparks, MD, MAS)
| | - Teresa N Sparks
- University of California, San Francisco, San Francisco, CA (Mary E. Norton, MD, Teresa N. Sparks, MD, MAS)
| |
Collapse
|
24
|
Fu F, Li R, Yu Q, Wang D, Deng Q, Li L, Lei T, Chen G, Nie Z, Yang X, Han J, Pan M, Zhen L, Zhang Y, Jing X, Li F, Li F, Zhang L, Yi C, Li Y, Lu Y, Zhou H, Cheng K, Li J, Xiang L, Zhang J, Tang S, Fang P, Li D, Liao C. Application of exome sequencing for prenatal diagnosis of fetal structural anomalies: clinical experience and lessons learned from a cohort of 1618 fetuses. Genome Med 2022; 14:123. [PMID: 36307859 PMCID: PMC9615232 DOI: 10.1186/s13073-022-01130-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. Methods We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. Results A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). Conclusions The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01130-x.
Collapse
|
25
|
Cornthwaite M, Turner K, Armstrong L, Boerkoel C, Chang C, Lehman A, Nikkel SM, Patel MS, Van Allen M, Langlois S. Impact of variation in practice in the prenatal reporting of variants of uncertain significance by commercial laboratories: NEED FOR GREATER ADHERENCE TO PUBLISHED GUIDELINES. Prenat Diagn 2022; 42:1514-1524. [PMID: 36068917 DOI: 10.1002/pd.6232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To evaluate the impact of implementing commercial whole exome sequencing (WES) and targeted gene panel testing in pregnancies with fetal anomalies. METHODS A retrospective chart review of 124 patients with sequencing performed by commercial laboratories. RESULTS The diagnostic yield of WES and panel testing was 21.5% and 26% respectively, based on likely pathogenic (LP) or pathogenic (P) variants. Forty-two per cent of exomes and 32% of panels analyzed had one or more variant of uncertain significance (VUS) reported. A multidisciplinary in depth review of the fetal phenotype, disease phenotype, variant data, and, in some patients, additional prenatal or postnatal investigations increased the diagnostic yield by 5% for exome analysis and 6% for panel analysis. CONCLUSIONS The diagnostic yield of WES and panel testing combined was 23% based on LP and P variants. Although the reporting of VUS contributed to a 5% increase in diagnostic yield for WES and 6% for panels, the large number of VUS reported by commercial laboratories has significant resource implications. Our results support the need for greater adherence to the recommendations on the prenatal reporting of VUS and the importance of a multidisciplinary approach that brings together clinical and laboratory expertise in prenatal genetics and genomics. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- M Cornthwaite
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - K Turner
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - L Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - C Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - C Chang
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - A Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - S M Nikkel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - M S Patel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - M Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - S Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
26
|
Malinowski A, Elsamadicy EA, Turan S. Prenatal diagnosis of a germline variant in TRAF7: Importance of accessibility to prenatal exome sequencing in cases of structural fetal anomalies. Clin Genet 2022; 102:164-165. [PMID: 35684978 DOI: 10.1111/cge.14170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
Diagnosis of a pathogenic germline TRAF7 missense variant (c.1555 C > T, p.L519F) made on a prenatal basis by exome sequencing (ES) performed on chorionic villi. This case highlights the importance of both higher-level prenatal ultrasounds and the accessibility of ES in making genetic diagnoses in making pregnancy management decisions.
Collapse
Affiliation(s)
- Amy Malinowski
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Balitimore, Maryland, USA
| | - Emad A Elsamadicy
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Balitimore, Maryland, USA
| | - Sifa Turan
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Balitimore, Maryland, USA
| |
Collapse
|
27
|
Pauta M, Martinez-Portilla RJ, Borrell A. Diagnostic yield of exome sequencing in fetuses with multisystem malformations: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:715-722. [PMID: 35041238 DOI: 10.1002/uog.24862] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To determine the diagnostic yield of exome sequencing (ES) above that of chromosomal microarray analysis (CMA) or karyotyping in fetuses with multisystem structural anomalies (at least two major anomalies in different anatomical systems). METHOD This was a systematic review conducted in accordance with PRISMA guidelines. Searching PubMed, Web of Knowledge and Cochrane database, we identified studies describing ES, whole-genome and/or next-generation sequencing in fetuses with multisystem malformations. Included were observational studies involving five or more eligible fetuses. A fetus was eligible for inclusion if it had at least two major anomalies of different anatomical systems and a negative CMA or karyotyping result. Only positive variants classified as likely pathogenic or pathogenic determined to be causative of the fetal phenotype were considered. A negative CMA or karyotype result was treated as the reference standard. The diagnostic yield of the primary outcome was calculated by single-proportion analysis using random-effects modeling. A subgroup analysis was performed to compare the diagnostic yield of the solo approach (fetus alone sequenced) with that of the trio approach (fetus and both parents sequenced). RESULTS Seventeen articles with data on ES diagnostic yield, including 694 individuals with multisystem malformations, were identified. Overall, a pathogenic or likely pathogenic variant potentially causative of the fetal phenotype was found in 213 fetuses, giving a 33% (95% CI, 27-40%) incremental yield of ES. A stratified analysis showed similar diagnostic yields of ES using the solo approach (30%; 95% CI, 11-52%) and the trio approach (35%; 95% CI, 26-44%). CONCLUSIONS ES applied in fetuses with multisystem structural anomalies was able to identify a potentially causative gene when CMA or karyotyping had failed to do so in an additional one-third of cases. No differences were observed between the solo and trio approaches for ES. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- M Pauta
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - R J Martinez-Portilla
- Clinical Research Division, Evidence-Based Medicine Department, National Institute of Perinatology, Mexico City, Mexico
| | - A Borrell
- BCNatal, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
28
|
Same performance of exome sequencing before and after fetal autopsy for congenital abnormalities: toward a paradigm shift in prenatal diagnosis? Eur J Hum Genet 2022; 30:967-975. [PMID: 35577939 PMCID: PMC9349205 DOI: 10.1038/s41431-022-01117-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/05/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022] Open
Abstract
Prenatal exome sequencing could be complex because of limited phenotypical data compared to postnatal/portmortem phenotype in fetuses affected by multiple congenital abnormalities (MCA). Here, we investigated limits of prenatal phenotype for ES interpretation thanks to a blindly reanalysis of postmortem ES data using prenatal data only in fetuses affected by MCA and harboring a (likely)pathogenic variant or a variant of unknown significance (VUS). Prenatal ES identified all causative variant previously reported by postmortem ES (22/24 (92%) and 2/24 (8%) using solo-ES and trio-ES respectively). Prenatal ES identified 5 VUS (in four fetuses). Two of them have been previously reported by postmortem ES. Prenatal ES were negative for four fetuses for which a VUS were diagnosed after autopsy. Our study suggests that prenatal phenotype is not a limitation for implementing pES in the prenatal assessment of unsolved MCA to personalize fetal medicine and could influence indication of postmortem examination.
Collapse
|
29
|
Chandler NJ, Scotchman E, Mellis R, Ramachandran V, Roberts R, Chitty LS. Lessons learnt from prenatal exome sequencing. Prenat Diagn 2022; 42:831-844. [PMID: 35506549 PMCID: PMC9325487 DOI: 10.1002/pd.6165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/21/2022] [Accepted: 05/01/2022] [Indexed: 12/27/2022]
Abstract
Background Prenatal exome sequencing (ES) for monogenic disorders in fetuses with structural anomalies increases diagnostic yield. In England there is a national trio ES service delivered from two laboratories. To minimise incidental findings and reduce the number of variants investigated, analysis uses a panel of 1205 genes where pathogenic variants may cause abnormalities presenting prenatally. Here we review our laboratory's early experience developing and delivering ES to identify challenges in interpretation and reporting and inform service development. Methods A retrospective laboratory records review from 01.04.2020 to 31.05.2021. Results Twenty‐four of 116 completed cases were identified as challenging including 13 resulting in difficulties in analysis and reporting, nine where trio inheritance filtering would have missed the diagnosis, and two with no prenatal diagnosis; one due to inadequate pipeline sensitivity, the other because the gene was not on the panel. Two cases with copy number variants identified were not detectable by microarray. Conclusions Variant interpretation requires close communication between referring clinicians, with occasional additional examination of the fetus or parents and communication of evolving phenotypes. Inheritance filtering misses ∼5% of diagnoses. Panel analysis reduces but does not exclude incidental findings. Regular review of published literature is required to identify new reports that may aid classification.
What's already known about this topic?
Prenatal exome sequencing (ES) for monogenic disorders in fetuses with structural anomalies is known to increase diagnostic yield Diagnostic prenatal ES services are being embedded into clinical practice internationally
What does this study add?
This study identifies challenges encountered running a diagnostic prenatal ES service including those in variant interpretation and reporting, incidental findings and ethical issues It demonstrates that solely relying on trio inheritance filtering will miss ∼5% of diagnoses Close communication between scientists and referring clinicians is essential to identify evolving phenotypes Regular review of published literature is required to identify new reports that may alter variant classification
Collapse
Affiliation(s)
- Natalie J Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rhiannon Mellis
- North Thames Genomic Laboratory Hub, 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
| | - Vijaya Ramachandran
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rowenna Roberts
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, 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
| |
Collapse
|
30
|
Kucińska-Chahwan A, Roszkowski T, Nowakowska B, Geremek M, Paczkowska M, Bijok J, Massalska D. Extended genetic testing in fetuses with sonographic skeletal system abnormalities. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 59:660-667. [PMID: 34198368 DOI: 10.1002/uog.23722] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES To analyze genetic causes of skeletal system abnormalities diagnosed by prenatal sonography and to establish a diagnostic protocol with regard to extended genetic testing in this group of patients. METHODS This prospective observational cohort study included all singleton pregnancies with a sonographic abnormality of the skeletal system evaluated in a single ultrasound department during a 1-year period (2019). Fetuses underwent routine genetic testing by chromosomal microarray analysis (CMA) supplemented with polyploidy testing, and those with either a normal result or an abnormal result not consistent with the observed phenotype underwent exome sequencing (ES). Interpretation of variants was discussed by a panel of specialists to identify pathogenic/likely pathogenic variants. RESULTS The study group comprised 55 fetuses. A chromosomal abnormality consistent with the observed phenotype was detected in 24 (43.6%) cases. After exclusions, 26 (47.3%) cases underwent further molecular testing by ES, of which 18 (69.2%) were classified as having abnormal ES results, thus increasing the diagnostic yield by a further 18 (32.7%) cases and giving an abnormal genetic test result in 42/55 (76.4%) fetuses overall. Pathogenic or likely pathogenic sequence variants in 14 different genes were detected across 18 fetuses. Seven genes are already listed in the International Skeletal Dysplasia Society Nosology and seven are not typically found to be causal for skeletal dysplasias and are not listed in the Nosology. CONCLUSIONS In fetuses with skeletal system anomalies, chromosomal abnormality was the most common genetic diagnosis. Exome sequencing increased the diagnostic yield over that of CMA and polyploidy testing. Fetuses with skeletal abnormalities should undergo extended genetic testing following routine testing, as many genetic anomalies responsible for skeletal defects may otherwise be missed. © 2021 International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- A Kucińska-Chahwan
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - T Roszkowski
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - B Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - M Geremek
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - M Paczkowska
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - J Bijok
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - D Massalska
- Department of Gynecology Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| |
Collapse
|
31
|
Mellis R, Tapon D, Shannon N, Dempsey E, Pandya P, Chitty LS, Hill M. Implementing a rapid fetal exome sequencing service: What do parents and health professionals think? Prenat Diagn 2022; 42:783-795. [PMID: 35383981 PMCID: PMC9324936 DOI: 10.1002/pd.6140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Prenatal exome sequencing (pES) for the diagnosis of fetal abnormalities is being introduced more widely in clinical practice. Here we explore parents' and professionals' views and experiences of pES, to identify perceived benefits, concerns, and support needs. METHODS Semi-structured interviews were conducted with 11 parents and 20 health professionals (fetal medicine and clinical genetics) with experience of rapid pES prior to implementation in the English National Health Service. Interviews were transcribed verbatim and analysed thematically. RESULTS Parents and professionals were largely positive about pES, emphasising clinical and psychosocial benefits of a timely, definitive diagnosis in pregnancy. Concerns included parental anxiety related to the timing of pES results or uncertain findings, a need for guidelines for case selection and reporting, and ensuring sufficient capacity for counselling, phenotyping and variant interpretation. Professionals were concerned non-genetics professionals may not be equipped to counsel parents on the complexities of pES. CONCLUSION These findings highlight important issues for clinical implementation of pES. Expert counselling is required to enable parents to make informed decisions during a stressful time. To achieve this, professionals need further education and training, and fetal medicine and genetics services must work closely together to ensure parental understanding and appropriate support.
Collapse
Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK,Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Dagmar Tapon
- Queen Charlotte's & Chelsea HospitalImperial College Healthcare NHS TrustLondonUK
| | - Nora Shannon
- Clinical Genetics ServiceNottingham City HospitalNottinghamUK
| | - Esther Dempsey
- South West Thames Regional Genetics ServiceLondonUK,School of Biological and Molecular SciencesSt George's University of LondonLondonUK
| | - Pranav Pandya
- Elizabeth Garrett Anderson Institute for Women's HealthUniversity College LondonLondonUK,Fetal Medicine UnitUniversity College London HospitalsLondonUK
| | - Lyn S. Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK,Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK,Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| |
Collapse
|
32
|
Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
Collapse
|
33
|
Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat Diagn 2022; 42:662-685. [PMID: 35170059 PMCID: PMC9325531 DOI: 10.1002/pd.6115] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022]
Abstract
Objectives We conducted a systematic review and meta‐analysis to determine the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies, where karyotype/chromosomal microarray (CMA) is normal. Methods Following electronic searches of four databases, we included studies with ≥10 structurally abnormal fetuses undergoing ES or whole genome sequencing. The incremental diagnostic yield of ES over CMA/karyotype was calculated and pooled in a meta‐analysis. Sub‐group analyses investigated effects of case selection and fetal phenotype on diagnostic yield. Results We identified 72 reports from 66 studies, representing 4350 fetuses. The pooled incremental yield of ES was 31% (95% confidence interval (CI) 26%–36%, p < 0.0001). Diagnostic yield was significantly higher for cases pre‐selected for likelihood of monogenic aetiology compared to unselected cases (42% vs. 15%, p < 0.0001). Diagnostic yield differed significantly between phenotypic sub‐groups, ranging from 53% (95% CI 42%–63%, p < 0.0001) for isolated skeletal abnormalities, to 2% (95% CI 0%–5%, p = 0.04) for isolated increased nuchal translucency. Conclusion Prenatal ES provides a diagnosis in an additional 31% of structurally abnormal fetuses when CMA/karyotype is non‐diagnostic. The expected diagnostic yield depends on the body system(s) affected and can be optimised by pre‐selection of cases following multi‐disciplinary review to determine that a monogenic cause is likely.
What's already known about this topic?
Prenatal exome sequencing (ES) increases genetic diagnoses in fetuses with structural abnormalities and a normal karyotype and chromosomal microarray. Published diagnostic yields from ES are varied and may be influenced by study size, case selection and fetal phenotype.
What does this study add?
This study provides a comprehensive systematic review of the literature to date and investigates the diagnostic yield of ES for a range of isolated system anomalies, to support clinical decision‐making on how to offer prenatal ES.
Collapse
Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Elizabeth Scotchman
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Lyn S Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| |
Collapse
|
34
|
Marouane A, Olde Keizer RACM, Frederix GWJ, Vissers LELM, de Boode WP, van Zelst-Stams WAG. Congenital anomalies and genetic disorders in neonates and infants: a single-center observational cohort study. Eur J Pediatr 2022; 181:359-367. [PMID: 34347148 PMCID: PMC8760213 DOI: 10.1007/s00431-021-04213-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/21/2021] [Accepted: 07/15/2021] [Indexed: 11/28/2022]
Abstract
Neonates with genetic disorders or congenital anomalies (CA) contribute considerably to morbidity and mortality in neonatal intensive care units (NICUs). The objective of this study is to study the prevalence of genetic disorders in an academic level IV NICU. We retrospective collected and analyzed both clinical and genetic data of all 1444 infants admitted to the NICU of the Radboudumc (October 2013 to October 2015). Data were collected until infants reached at least 2 years of age. A total of 13% (194/1444) of the patients were genetically tested, and 32% (461/1444) had a CA. A total of 37% (72/194) had a laboratory-confirmed genetic diagnosis. In 53%, the diagnosis was made post-neonatally (median age = 209 days) using assays including exome sequencing. Exactly 63% (291/461) of the patients with CA, however, never received genetic testing, despite being clinically similar those who did.Conclusions: Genetic disorders were suspected in 13% of the cohort, but only confirmed in 5%. Most received their genetic diagnosis in the post-neonatal period. Extrapolation of the diagnostic yield suggests that up to 6% of our cohort may have remained genetically undiagnosed. Our data show the need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management. What is Known: • Genetic disorders are suspected in many neonates but only genetically confirmed in a minority. • The presence of a genetic disorder can be easily missed and will often lead to a diagnostic odyssey requiring extensive evaluations, both clinically and genetically. What is New: • Different aspects of the clinical features and uptake of genetic test in a NICU cohort. • The need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management.
Collapse
Affiliation(s)
- A. Marouane
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands
| | - R. A. C. M. Olde Keizer
- Department of Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - G. W. J. Frederix
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands ,Department of Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - L. E. L. M. Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - W. P. de Boode
- Department of Neonatology, Radboudumc Amalia Children’s Hospital, Radboud Institute of Health Sciences, Nijmegen, the Netherlands
| | - W. A. G. van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute of Health Sciences, Nijmegen, The Netherlands
| |
Collapse
|
35
|
Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
Collapse
Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
| |
Collapse
|
36
|
Diagnostic utility of next-generation sequencing-based panel testing in 543 patients with suspected skeletal dysplasia. Orphanet J Rare Dis 2021; 16:412. [PMID: 34627339 PMCID: PMC8501536 DOI: 10.1186/s13023-021-02025-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/17/2021] [Indexed: 12/01/2022] Open
Abstract
Background Skeletal dysplasia is typically diagnosed using a combination of radiographic imaging, clinical examinations, and molecular testing. Identifying a molecular diagnosis for an individual with a skeletal dysplasia can lead to improved clinical care, guide future medical management and treatment, and inform assessment of risk for familial recurrence. The molecular diagnostic utility of multi-gene panel testing using next-generation sequencing (NGS) has not yet been characterized for an unselected population of individuals with suspected skeletal dysplasia. In this study, we retrospectively reviewed patient reports to assess the diagnostic yield, reported variant characteristics, impact of copy number variation, and performance in prenatal diagnostics of panel tests for variants in genes associated with skeletal dysplasia and growth disorders. Results Clinical reports of consecutive patients with a clinical indication of suspected skeletal dysplasia who underwent panel testing were examined. The 543 patients included in the study submitted samples for diagnostic genetic testing with an indication of suspected skeletal dysplasia or growth disorder and received one of three nested panel tests. A molecular diagnosis was established in 42.0% of patients (n = 228/543). Diagnostic variants were identified in 71 genes, nearly half of which (n = 35, 49.3%) contributed uniquely to a molecular diagnosis for a single patient in this cohort. Diagnostic yield was significantly higher among fetal samples (59.0%, n = 52/88) than postnatal samples (38.7%, n = 176/455; z = 3.55, p < 0.001). Diagnostic variants in fetal cases were identified across 18 genes. Thirteen diagnostic CNVs were reported, representing 5.7% of diagnostic findings and ranging in size from 241-bp to whole chromosome aneuploidy. Additionally, 11.4% (36/315) of non-diagnostic patient reports had suspicious variants of unknown significance (VUS), in which additional family studies that provide segregation data and/or functional characterization may result in reclassification to likely pathogenic. Conclusions These findings demonstrate the utility of panel testing for individuals with a suspected skeletal dysplasia or growth disorder, with a particularly high diagnostic yield seen in prenatal cases. Pursuing comprehensive panel testing with high-resolution CNV analysis can provide a diagnostic benefit, given the considerable phenotype overlap amongst skeletal dysplasia conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-02025-7.
Collapse
|
37
|
de Koning MA, Hoffer MJV, Nibbeling EAR, Bijlsma EK, Toirkens MJP, Adama-Scheltema PN, Verweij EJ, Veenhof MB, Santen GWE, Peeters-Scholte CMPCD. Prenatal exome sequencing: A useful tool for the fetal neurologist. Clin Genet 2021; 101:65-77. [PMID: 34611884 PMCID: PMC9297851 DOI: 10.1111/cge.14070] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 01/08/2023]
Abstract
Prenatal exome sequencing (pES) is a promising tool for diagnosing genetic disorders when structural anomalies are detected on prenatal ultrasound. The aim of this study was to investigate the diagnostic yield and clinical impact of pES as an additional modality for fetal neurologists who counsel parents in case of congenital anomalies of the central nervous system (CNS). We assessed 20 pregnancies of 19 couples who were consecutively referred to the fetal neurologist for CNS anomalies. pES had a diagnostic yield of 53% (10/19) with most diagnosed pregnancies having agenesis or hypoplasia of the corpus callosum (7/10). Overall clinical impact was 63% (12/19), of which the pES result aided parental decision making in 55% of cases (6/11), guided perinatal management in 75% of cases (3/4), and was helpful in approving a late termination of pregnancy request in 75% of cases (3/4). Our data suggest that pES had a high diagnostic yield when CNS anomalies are present, although this study is limited by its small sample size. Moreover, pES had substantial clinical impact, which warrants implementation of pES in the routine care of the fetal neurologist in close collaboration with gynecologists and clinical geneticists.
Collapse
Affiliation(s)
- Maayke A de Koning
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Menno J P Toirkens
- Department of Radiology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - E Joanne Verweij
- Department of Obstetrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marieke B Veenhof
- Department of Obstetrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | |
Collapse
|
38
|
Mone F, Eberhardt RY, Hurles ME, Mcmullan DJ, Maher ER, Lord J, Chitty LS, Dempsey E, Homfray T, Giordano JL, Wapner RJ, Sun L, Sparks TN, Norton ME, Kilby MD. Fetal hydrops and the Incremental yield of Next-generation sequencing over standard prenatal Diagnostic testing (FIND) study: prospective cohort study and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:509-518. [PMID: 33847422 PMCID: PMC8487902 DOI: 10.1002/uog.23652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To determine the incremental yield of exome sequencing (ES) over chromosomal microarray analysis (CMA) or karyotyping in prenatally diagnosed non-immune hydrops fetalis (NIHF). METHODS A prospective cohort study (comprising an extended group of the Prenatal Assessment of Genomes and Exomes (PAGE) study) was performed which included 28 cases of prenatally diagnosed NIHF undergoing trio ES following negative CMA or karyotyping. These cases were combined with data from a systematic review of the literature. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov databases were searched electronically (January 2000 to October 2020) for studies reporting on the incremental yield of ES over CMA or karyotyping in fetuses with prenatally detected NIHF. Inclusion criteria for the systematic review were: (i) at least two cases of NIHF undergoing sequencing; (ii) testing initiated based on prenatal ultrasound-based phenotype; and (iii) negative CMA or karyotyping result. The incremental diagnostic yield of ES was assessed in: (i) all cases of NIHF; (ii) isolated NIHF; (iii) NIHF associated with an additional fetal structural anomaly; and (iv) NIHF according to severity (i.e. two vs three or more cavities affected). RESULTS In the extended PAGE study cohort, the additional diagnostic yield of ES over CMA or karyotyping was 25.0% (7/28) in all NIHF cases, 21.4% (3/14) in those with isolated NIHF and 28.6% (4/14) in those with non-isolated NIHF. In the meta-analysis, the pooled incremental yield based on 21 studies (306 cases) was 29% (95% CI, 24-34%; P < 0.00001; I2 = 0%) in all NIHF, 21% (95% CI, 13-30%; P < 0.00001; I2 = 0%) in isolated NIHF and 39% (95% CI, 30-49%; P < 0.00001; I2 = 1%) in NIHF associated with an additional fetal structural anomaly. In the latter group, congenital limb contractures were the most prevalent additional structural anomaly associated with a causative pathogenic variant, occurring in 17.3% (19/110) of cases. The incremental yield did not differ significantly according to hydrops severity. The most common genetic disorders identified were RASopathies, occurring in 30.3% (27/89) of cases with a causative pathogenic variant, most frequently due to a PTPN11 variant (44.4%; 12/27). The predominant inheritance pattern in causative pathogenic variants was autosomal dominant in monoallelic disease genes (57.3%; 51/89), with most being de novo (86.3%; 44/51). CONCLUSIONS Use of prenatal next-generation sequencing in both isolated and non-isolated NIHF should be considered in the development of clinical pathways. Given the wide range of potential syndromic diagnoses and heterogeneity in the prenatal phenotype of NIHF, exome or whole-genome sequencing may prove to be a more appropriate testing approach than a targeted gene panel testing strategy. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- F Mone
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | | | - D J Mcmullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Dempsey
- Molecular and Clinical Sciences, St George's University of London, London, UK
| | - T Homfray
- SW Thames Regional Genetics Department, St George's University Hospitals NHS Foundation Trust, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - L Sun
- Fetal Medicine Unit and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital of Tongji University, Shanghai, China
| | - T N Sparks
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M E Norton
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M D Kilby
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| |
Collapse
|
39
|
Ridnõi K, Muru K, Keernik M, Pajusalu S, Ustav EL, Tammur P, Mölter-Väär T, Kahre T, Šamarina U, Asser K, Szirko F, Reimand T, Õunap K. A two-year prospective study assessing the performance of fetal chromosomal microarray analysis and next-generation sequencing in high-risk pregnancies. Mol Genet Genomic Med 2021; 9:e1787. [PMID: 34486251 PMCID: PMC8580097 DOI: 10.1002/mgg3.1787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/22/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Introduction of cell‐free fetal DNA (cff‐DNA) testing in maternal blood opened possibilities to improve the performance of combined first‐trimester screening (cFTS) in terms of better detection of trisomies and lowering invasive testing rate. The use of new molecular methods, such as chromosomal microarray analysis (CMA) and next‐generation sequencing (NGS), has shown benefits in prenatal diagnosis of chromosomal and genetic diseases, which are not detectable with cff‐DNA screening, but require an invasive procedure. Methods The objective of this study was to evaluate prospectively during two years performance of CMA and NGS in high‐risk pregnancies. Initially, we investigated 14,566 singleton pregnancies with cFTS. A total of 334 high‐risk pregnancies were selected for CMA diagnostic performance evaluation and 28 cases of highly dysmorphic fetuses for NGS analysis. CMA study group was divided into two groups based on the indications for testing; group A patients with high‐risk for trisomies after cFTS, but normal ultrasound and group B patients who met criteria for CMA as a first‐tier diagnostic test. Results The diagnostic yield of CMA was overall 3.6% (1.6% in Group A and 6.0% in Group B). In NGS analysis group, we report diagnostic yield of 17.9%. Conclusion The use of CMA in high‐risk pregnancies is justified and provides relevant clinical information in 3.6% of the cases. NGS analysis in fetuses with multiple anomalies shows promising results, but more investigations are needed for a better understanding of practical applications of this molecular diagnosis method in prenatal settings.
Collapse
Affiliation(s)
- Konstantin Ridnõi
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kai Muru
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Maria Keernik
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Pille Tammur
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Triin Mölter-Väär
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tiina Kahre
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Ustina Šamarina
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Karin Asser
- Radiology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Ferenc Szirko
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| |
Collapse
|
40
|
Castleman JS, Wall E, Allen S, Williams D, Doyle S, Kilby MD. The prenatal exome - a door to prenatal diagnostics? Expert Rev Mol Diagn 2021; 21:465-474. [PMID: 33877000 DOI: 10.1080/14737159.2021.1920398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Prenatal exome sequencing (ES) allows parents the opportunity to obtain arapid molecular diagnosis of monogenic etiology when their fetus is found to have structural anomalies detected on prenatal ultrasound. Such information can improve antenatal and neonatal counseling, decision-making and management, and expand reproductive options in subsequent pregnancies.Areas covered: This review appraises the evidence, from acomprehensive search of bibliographic databases, for the introduction of ES into the fetal medicine care pathway when investigating congenital malformations. The perspectives of clinical geneticists, clinical scientists, fetal medicine specialists, and patients are explored in relation to the novel investigation and the benefits and challenges of its use in ongoing pregnancies with particular reference to UK medical practice.Expert opinion: ES provides agenetic diagnosis for more than 1 in 10 fetuses with structural differences on ultrasound and normal conventional tests (karyotype or chromosomal microarray) in carefully selected cases. The diagnostic rate increases for certain phenotypes and can range between 6% and 80% where conventional cytogenetics have not detected adiagnosis. Expert oversight is required to ensure that patients receive high-quality, evidence-based care and accurate counseling, supported by amultidisciplinary team familiar with the test and its implications.
Collapse
Affiliation(s)
- James S Castleman
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Wall
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Edgbaston. Birmingham, UK
| | - Denise Williams
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Samantha Doyle
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mark D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
41
|
Dempsey E, Haworth A, Ive L, Dubis R, Savage H, Serra E, Kenny J, Elmslie F, Greco E, Thilaganathan B, Mansour S, Homfray T, Drury S. A report on the impact of rapid prenatal exome sequencing on the clinical management of 52 ongoing pregnancies: a retrospective review. BJOG 2021; 128:1012-1019. [PMID: 32981126 DOI: 10.1111/1471-0528.16546] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Studies have shown that prenatal exome sequencing (PES) improves diagnostic yield in cases of fetal structural malformation. We have retrospectively analysed PES cases from two of the largest fetal medicine centres in the UK to determine the impact of results on management of a pregnancy. DESIGN A retrospective review of clinical case notes. SETTING Two tertiary fetal medicine centres. POPULATION Pregnancies with fetal structural abnormalities referred to clinical genetics via a multidisciplinary team. METHODS We retrospectively reviewed the notes of all patients who had undergone PES. DNA samples were obtained via chorionic villus sampling or amniocentesis. Variants were filtered using patient-specific panels and interpreted using American College of Medical Genetics guidelines. RESULTS A molecular diagnosis was made in 42% (18/43) ongoing pregnancies; of this group, there was a significant management implication in 44% (8/18). A positive result contributed to the decision to terminate a pregnancy in 16% (7/43) of cases. A negative result had a significant impact on management in two cases by affirming the decision to continue pregnancy. CONCLUSIONS We demonstrate that the results of PES can inform pregnancy management. Challenges include variant interpretation with limited phenotype information. These results emphasise the importance of the MDT and collecting phenotype and variant data. As this testing is soon to be widely available, we should look to move beyond diagnostic yield as a measure of the value of PES. TWEETABLE ABSTRACT Prenatal exome sequencing can aid decision-making in pregnancy management; review ahead of routine implementation in NHS.
Collapse
Affiliation(s)
- E Dempsey
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - A Haworth
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - L Ive
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - R Dubis
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - H Savage
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - E Serra
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - J Kenny
- South West Thames Regional Genetics Service, London, UK
| | - F Elmslie
- South West Thames Regional Genetics Service, London, UK
| | - E Greco
- Harris Birthright Centre, King's College London, London, UK.,Barts Health NHS Trust, London, UK
| | - B Thilaganathan
- Fetal Medicine Centre, St George's Hospital, London, UK.,Vascular Biology Unit, St George's University of London, London, UK
| | - S Mansour
- South West Thames Regional Genetics Service, London, UK.,School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - T Homfray
- South West Thames Regional Genetics Service, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| |
Collapse
|
42
|
Beyond diagnostic yield: prenatal exome sequencing results in maternal, neonatal, and familial clinical management changes. Genet Med 2021; 23:909-917. [PMID: 33442022 PMCID: PMC7804210 DOI: 10.1038/s41436-020-01067-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/30/2022] Open
Abstract
Purpose Previous studies have reported that prenatal exome sequencing (pES) can detect monogenic diseases in fetuses with congenital anomalies with diagnostic yields ranging from 6% to 81%, but there are few reports of its clinical utility. Methods We conducted a retrospective chart review of patients who had pES to determine whether results led to clinical management changes. Results Of 20 patients, 8 (40%) received a definitive diagnosis. Seven patients (35%) had medical management changes based on the pES results, including alterations to their delivery plan and neonatal management (such as use of targeted medications, subspecialty referrals, additional imaging and/or procedures). All patients who received a definitive diagnosis and one who received a likely pathogenic variant (n = 9; 45%) received specific counseling about recurrence risk and the medical/developmental prognosis for the baby. In five (25%) cases, the result facilitated a diagnosis in parents and/or siblings. Conclusion pES results can have significant impacts on clinical management, some of which would not be possible if testing is deferred until after birth. To maximize the clinical utility, pES should be prioritized in cases where multiple care options are available and the imaging findings alone are not sufficient to guide parental decision-making, or where postnatal testing will not be feasible.
Collapse
|
43
|
Qi Q, Jiang Y, Zhou X, Meng H, Hao N, Chang J, Bai J, Wang C, Wang M, Guo J, Ouyang Y, Xu Z, Xiao M, Zhang VW, Liu J. Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes (Basel) 2020; 11:genes11121397. [PMID: 33255631 PMCID: PMC7759943 DOI: 10.3390/genes11121397] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022] Open
Abstract
The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome sequencing (CES) or whole exome sequencing (WES). Eight-three singleton pregnancies with a normal fetal karyotype were enrolled in this prospective observational study. Pathogenic or likely pathogenic variations were identified in 30 cases (CNVs in 3 cases, SNVs/indels in 27 cases), indicating an overall molecular diagnostic rate of 36.1% (30/83). Two cases had both a CNV of uncertain significance (VOUS) and likely pathogenic SNV, and one case carried both a VOUS CNV and an SNV. We demonstrated that simultaneous analysis of CNVs and SNVs/indels can improve the diagnostic yield of prenatal diagnosis with shortened reporting time, namely, 2–3 weeks. Due to the relatively long TAT for sequential procedure for prenatal genetic diagnosis, as well as recent sequencing technology advancements, it is clinically necessary to consider the simultaneous evaluation of CNVs and SNVs/indels to enhance the diagnostic yield and timely TAT, especially for cases in the late second trimester or third trimester.
Collapse
Affiliation(s)
- Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
- Correspondence: ; Tel.: +86-1851-066-6066
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Hua Meng
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| | - Jiazhen Chang
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China;
| | - Junjie Bai
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Chunli Wang
- AmCare Genomics Lab, Guangzhou 510335, China; (C.W.); (V.W.Z.)
| | - Mingming Wang
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Jiangshan Guo
- Be Creative Lab Co., Ltd. Beijing 101111, China; (J.B.); (M.W.); (J.G.)
| | - Yunshu Ouyang
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Zhonghui Xu
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | - Mengsu Xiao
- Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (H.M.); (Y.O.); (Z.X.); (M.X.)
| | | | - Juntao Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China; (Y.J.); (X.Z.); (N.H.); (J.L.)
| |
Collapse
|
44
|
El-Dessouky SH, Issa MY, Aboulghar MM, Gaafar HM, Elarab AE, Ateya MI, Omar HH, Beetz C, Zaki MS. Prenatal delineation of a distinct lethal fetal syndrome caused by a homozygous truncating KIDINS220 variant. Am J Med Genet A 2020; 182:2867-2876. [PMID: 32909676 DOI: 10.1002/ajmg.a.61858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/19/2020] [Accepted: 08/22/2020] [Indexed: 02/06/2023]
Abstract
Kinase D-interacting substrate of 220 kDa (KIDINS220) is a transmembrane protein playing integral role in growth mediating pathways in the nervous and cardiovascular systems. KIDINS220 heterozygous truncating variants that affect the protein's C-terminus have been associated with a phenotype, so far described only in few unrelated children, including spastic paraplegia, intellectual disability, nystagmus, and obesity. More recently, a homozygous, more N-terminal truncating variant in KIDINS220 gene was suggested to be associated with enlarged cerebral ventricles and limb contractures in three fetuses from a consanguineous family. We confirm the latter finding by presenting the first detailed prenatal identification of a fetal phenotype associated with novel homozygous deleterious frameshift variant in KIDINS220 gene in a consanguineous healthy Egyptian couple. History of unexplained seven miscarriages and a similar stillbirth were recorded. Prenatal ultrasonography revealed limb contractions and ventriculomegaly; in addition to previously unreported cerebellar anomalies, cardiac anomalies and hydrops fetalis. These findings represent an expansion of clinical and molecular spectrum associated with KIDINS220 variants and broaden our understanding of genotype-phenotype relationships in lethal congenital contractures syndromes and associated severe abnormal embryological development. More generally, our study adds KIDINS220 to the rare group of genes which may cause disease by either of two distinct mutational mechanisms.
Collapse
Affiliation(s)
- Sara H El-Dessouky
- Prenatal Diagnosis and Fetal Medicine Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mona M Aboulghar
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Hassan M Gaafar
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Ahmed Ezz Elarab
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Mohamed I Ateya
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Cairo University, Cairo, Egypt
| | - Heba H Omar
- Diagnostic and Research Department, Centogene AG, Rostock, Germany
| | - Christian Beetz
- Diagnostic and Research Department, Centogene AG, Rostock, Germany
| | - Maha Saad Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| |
Collapse
|
45
|
van der Made CI, Simons A, Schuurs-Hoeijmakers J, van den Heuvel G, Mantere T, Kersten S, van Deuren RC, Steehouwer M, van Reijmersdal SV, Jaeger M, Hofste T, Astuti G, Corominas Galbany J, van der Schoot V, van der Hoeven H, Hagmolen of ten Have W, Klijn E, van den Meer C, Fiddelaers J, de Mast Q, Bleeker-Rovers CP, Joosten LAB, Yntema HG, Gilissen C, Nelen M, van der Meer JWM, Brunner HG, Netea MG, van de Veerdonk FL, Hoischen A. Presence of Genetic Variants Among Young Men With Severe COVID-19. JAMA 2020; 324:663-673. [PMID: 32706371 PMCID: PMC7382021 DOI: 10.1001/jama.2020.13719] [Citation(s) in RCA: 502] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
IMPORTANCE Severe coronavirus disease 2019 (COVID-19) can occur in younger, predominantly male, patients without preexisting medical conditions. Some individuals may have primary immunodeficiencies that predispose to severe infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). OBJECTIVE To explore the presence of genetic variants associated with primary immunodeficiencies among young patients with COVID-19. DESIGN, SETTING, AND PARTICIPANTS Case series of pairs of brothers without medical history meeting the selection criteria of young (age <35 years) brother pairs admitted to the intensive care unit (ICU) due to severe COVID-19. Four men from 2 unrelated families were admitted to the ICUs of 4 hospitals in the Netherlands between March 23 and April 12, 2020. The final date of follow-up was May 16, 2020. Available family members were included for genetic variant segregation analysis and as controls for functional experiments. EXPOSURE Severe COVID-19. MAIN OUTCOME AND MEASURES Results of rapid clinical whole-exome sequencing, performed to identify a potential monogenic cause. Subsequently, basic genetic and immunological tests were performed in primary immune cells isolated from the patients and family members to characterize any immune defects. RESULTS The 4 male patients had a mean age of 26 years (range, 21-32), with no history of major chronic disease. They were previously well before developing respiratory insufficiency due to severe COVID-19, requiring mechanical ventilation in the ICU. The mean duration of ventilatory support was 10 days (range, 9-11); the mean duration of ICU stay was 13 days (range, 10-16). One patient died. Rapid clinical whole-exome sequencing of the patients and segregation in available family members identified loss-of-function variants of the X-chromosomal TLR7. In members of family 1, a maternally inherited 4-nucleotide deletion was identified (c.2129_2132del; p.[Gln710Argfs*18]); the affected members of family 2 carried a missense variant (c.2383G>T; p.[Val795Phe]). In primary peripheral blood mononuclear cells from the patients, downstream type I interferon (IFN) signaling was transcriptionally downregulated, as measured by significantly decreased mRNA expression of IRF7, IFNB1, and ISG15 on stimulation with the TLR7 agonist imiquimod as compared with family members and controls. The production of IFN-γ, a type II IFN, was decreased in patients in response to stimulation with imiquimod. CONCLUSIONS AND RELEVANCE In this case series of 4 young male patients with severe COVID-19, rare putative loss-of-function variants of X-chromosomal TLR7 were identified that were associated with impaired type I and II IFN responses. These preliminary findings provide insights into the pathogenesis of COVID-19.
Collapse
Affiliation(s)
- Caspar I. van der Made
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Guus van den Heuvel
- Pulmonology Department, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Simone Kersten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rosanne C. van Deuren
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Martin Jaeger
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Vyne van der Schoot
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Hans van der Hoeven
- Department of Intensive Care, Radboud University Medical Center Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Eva Klijn
- Department of Intensive Care, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Jeroen Fiddelaers
- Department of Pulmonology, Admiraal de Ruyter Ziekenhuis, Goes, the Netherlands
| | - Quirijn de Mast
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Chantal P. Bleeker-Rovers
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A. B. Joosten
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jos W. M. van der Meer
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
- GROW School of Oncology and developmental biology, and MHeNs School of Mental Health and Neuroscience, Maastricht University, the Netherlands
| | - Mihai G. Netea
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
- Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Frank L. van de Veerdonk
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud University Medical Center Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
46
|
Deden C, Neveling K, Zafeiropopoulou D, Gilissen C, Pfundt R, Rinne T, de Leeuw N, Faas B, Gardeitchik T, Sallevelt SCEH, Paulussen A, Stevens SJC, Sikkel E, Elting MW, van Maarle MC, Diderich KEM, Corsten-Janssen N, Lichtenbelt KD, Lachmeijer G, Vissers LELM, Yntema HG, Nelen M, Feenstra I, van Zelst-Stams WAG. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging. Prenat Diagn 2020; 40:972-983. [PMID: 32333414 PMCID: PMC7497059 DOI: 10.1002/pd.5717] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/01/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Objective The purpose of this study was to explore the diagnostic yield and clinical utility of trio‐based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging. Methods In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7). Results A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases. Conclusions These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.
Collapse
Affiliation(s)
- Chantal Deden
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Dimitra Zafeiropopoulou
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Brigitte Faas
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Aimee Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Esther Sikkel
- Department of Obstetrics and Gynecology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Mariet W Elting
- Department of Clinical Genetics, AMsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Merel C van Maarle
- Department of Clinical Genetics, AMsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicole Corsten-Janssen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Klaske D Lichtenbelt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Guus Lachmeijer
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Wendy A G van Zelst-Stams
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| |
Collapse
|