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Thauvin-Robinet C, Garde A, Delanne J, Racine C, Rousseau T, Simon E, François M, Moutton S, Sylvie O, Quelin C, Morel G, Goldenberg A, Guerrot AM, Vera G, Gruchy N, Colson C, Boute O, Abel C, Putoux A, Amiel J, Guichet A, Isidor B, Deiller C, Wells C, Rooryck C, Legendre M, Francannet C, Dard R, Sigaudy S, Bruel AL, Safraou H, Denommé-Pichon AS, Nambot S, Asensio MLH, Binquet C, Duffourd Y, Vitobello A, Philippe C, Faivre L, Tran-Mau-Them F, Bourgon N. Prenatal exome sequencing, a powerful tool for improving the description of prenatal features associated with genetic disorders. Prenat Diagn 2024. [PMID: 39138116 DOI: 10.1002/pd.6623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/11/2024] [Accepted: 06/03/2024] [Indexed: 08/15/2024]
Abstract
OBJECTIVE Prenatal exome sequencing (pES) is now commonly used in clinical practice. It can be used to identifiy an additional diagnosis in around 30% of fetuses with structural defects and normal chromosomal microarray analysis (CMA). However, interpretation remains challenging due to the limited prenatal data for genetic disorders. METHOD We conducted an ancillary study including fetuses with pathogenic/likely pathogenic variants identified by trio-pES from the "AnDDI-Prenatome" study. The prenatal phenotype of each patient was categorized as typical, uncommon, or unreported based on the comparison of the prenatal findings with documented findings in the literature and public phenotype-genotype databases (ClinVar, HGMD, OMIM, and Decipher). RESULTS Prenatal phenotypes were typical for 38/56 fetuses (67.9%). For the others, genotype-phenotype associations were challenging due to uncommon prenatal features (absence of recurrent hallmark, rare, or unreported). We report the first prenatal features associated with LINS1 and PGM1 variants. In addition, a double diagnosis was identified in three fetuses. CONCLUSION Standardizing the description of prenatal features, implementing longitudinal prenatal follow-up, and large-scale collection of prenatal features are essential steps to improving pES data interpretation.
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Affiliation(s)
- Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
| | - Thierry Rousseau
- Service de Gynécologie Obstétrique Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Emmanuel Simon
- Service de Gynécologie Obstétrique Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Michel François
- Service de Chirurgie Pédiatrique, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
| | - Odent Sylvie
- Service de Génétique Clinique, Centre de Référence "Anomalies du Développement et Syndromes Malformatifs" de l'Inter-région Ouest, CHU Rennes Hôpital Sud, Rennes, France
| | - Chloe Quelin
- Service de Génétique Clinique, Centre de Référence "Anomalies du Développement et Syndromes Malformatifs" de l'Inter-région Ouest, CHU Rennes Hôpital Sud, Rennes, France
| | - Godelieve Morel
- Service de Génétique Clinique, Centre de Référence "Anomalies du Développement et Syndromes Malformatifs" de l'Inter-région Ouest, CHU Rennes Hôpital Sud, Rennes, France
| | - Alice Goldenberg
- Service de Génétique-Unité de Génétique Clinique, CHU Rouen, Rouen, France
| | - Anne-Marie Guerrot
- Service de Génétique-Unité de Génétique Clinique, CHU Rouen, Rouen, France
| | - Gabriella Vera
- Service de Génétique-Unité de Génétique Clinique, CHU Rouen, Rouen, France
| | - Nicolas Gruchy
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen - Université de Caen, Caen, France
| | - Cindy Colson
- Clinique de Génétique Guy Fontaine et Centre de Référence Maladies Rares "Anomalies Du Développement et Syndromes Malformatifs" Nord-Ouest, CHU Lille, Lille, France
| | - Odile Boute
- Clinique de Génétique Guy Fontaine et Centre de Référence Maladies Rares "Anomalies Du Développement et Syndromes Malformatifs" Nord-Ouest, CHU Lille, Lille, France
| | - Carine Abel
- Service de Génétique, CHU de Lyon HCL - GH Nord-Hôpital de La Croix Rousse, Lyon, France
| | - Audrey Putoux
- Service de Génétique, CHU de Lyon HCL - GH Est-Hôpital Femme Mère Enfant, Bron, France
| | - Jeanne Amiel
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker Enfants Malades, AP-HP, Paris, France
| | - Agnes Guichet
- Plateau de Biochimie et Médecine Moléculaire, CHU d'Angers, Angers, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Caroline Deiller
- Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, Equipe Maladies Génétiques de L'Enfant et de L'Adulte, CHU de Montpellier, Montpellier, France
| | - Constance Wells
- Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, Equipe Maladies Génétiques de L'Enfant et de L'Adulte, CHU de Montpellier, Montpellier, France
| | - Caroline Rooryck
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Marine Legendre
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Christine Francannet
- Service de Génétique Médicale, Pôle Femme et Enfant, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Rodolphe Dard
- Unité Fonctionnelle de Génétique Médicale, Cytogénétique, Génétique Médicale et Biologie de La Reproduction, Centre Hospitalier Intercommunal Poissy-Saint-Germain-en-Laye, Poissy, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, Unité de Génétique Clinique Prénatale, CHU de Marseille-Hôpital de La Timone, Marseille, France
| | - Ange-Line Bruel
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Hana Safraou
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
| | - Marie-Laure Humbert Asensio
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Christine Binquet
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Yannis Duffourd
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Antonio Vitobello
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Christophe Philippe
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Frédéric Tran-Mau-Them
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR 1231, Génétique des Anomalies du Développement, Université́ de Bourgogne Franche-Comté́, Dijon, France
| | - Nicolas Bourgon
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement, CHU Dijon Bourgogne, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- Service d'Obstétrique Maternité́, Chirurgie Médecine et Imagerie Fœtale, Hôpital Necker Enfants Malades, AP-HP, Paris, France
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Taylor-Miller T, Savarirayan R. Progress in managing children with achondroplasia. Expert Rev Endocrinol Metab 2024:1-8. [PMID: 39132812 DOI: 10.1080/17446651.2024.2390416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Achondroplasia is a heritable disorder of the skeleton that affects approximately 300,000 individuals worldwide. Until recently, treatment for this condition has been purely symptomatic. Efficacious treatment options for children are now approved or are in clinical trials. AREAS COVERED This review discusses key advances in the therapeutic management of children with achondroplasia, including vosoritide, the first approved drug, and other emerging precision therapies. These include navepegritide, a long-acting form of C-type natriuretic peptide, and infigratinib, a tyrosine kinase receptor inhibitor, summarizing trial outcomes to date. EXPERT OPINION The advent of the first approved precision therapy for achondroplasia in vosoritide has been a paradigm shifting advance for children affected by this condition. In addition to changing their natural growth history, it is hoped that it will decrease their medical complications and enhance functionality. These new treatment options highlight the importance of prompt prenatal identification and subsequent testing of a suspected fetus with achondroplasia and counseling of families. It is hoped that, in the near future, families will have the option to consider a range of effective targeted therapies that best suit their child with achondroplasia, starting from birth should they choose.
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Affiliation(s)
| | - Ravi Savarirayan
- Victorian Clinical Genetics Service, Melbourne, Parkville, Victoria, Australia
- Molecular Therapies, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
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3
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Wallis M, Bodek SD, Munro J, Rafehi H, Bennett MF, Ye Z, Schneider A, Gardiner F, Valente G, Murdoch E, Uebergang E, Hunter J, Stutterd C, Huq A, Salmon L, Scheffer I, Eratne D, Meyn S, Fong CY, John T, Mullen S, White SM, Brown NJ, McGillivray G, Chen J, Richmond C, Hughes A, Krzesinski E, Fennell A, Chambers B, Santoreneos R, Le Fevre A, Hildebrand MS, Bahlo M, Christodoulou J, Delatycki M, Berkovic SF. Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless. Orphanet J Rare Dis 2024; 19:288. [PMID: 39095811 PMCID: PMC11297648 DOI: 10.1186/s13023-024-03297-5] [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: 08/09/2023] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. METHODS Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. RESULTS In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. CONCLUSION AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.
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Affiliation(s)
- Mathew Wallis
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Simon D Bodek
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia.
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia.
| | - Jacob Munro
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Haloom Rafehi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Mark F Bennett
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Zimeng Ye
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Amy Schneider
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Fiona Gardiner
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Giulia Valente
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Emma Murdoch
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Eloise Uebergang
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
| | - Jacquie Hunter
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Chloe Stutterd
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Aamira Huq
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetic Medicine Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Lucinda Salmon
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Genetics Service, Royal Prince Alfred Hospital, Melbourne, Australia
| | - Ingrid Scheffer
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Department of Paediatrics, Austin Health, Melbourne, Australia
| | - Dhamidhu Eratne
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
- Neuropsychiatry, The Royal Melbourne Hospital, Melbourne, Australia
| | - Stephen Meyn
- Centre for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Chun Y Fong
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
| | - Tom John
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Saul Mullen
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Susan M White
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Melbourne, Australia
- Genetics Service, Mercy Hospital for Women, Melbourne, Australia
| | - Jesse Chen
- Neurology Service, Austin Health, Melbourne, Australia
| | - Chris Richmond
- Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Hughes
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | | | - Andrew Fennell
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Monash Health Genetics Clinic, Melbourne, Australia
| | - Brian Chambers
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, Australia
| | - Renee Santoreneos
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Anna Le Fevre
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Martin Delatycki
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Victorian Clinical Genetics Service, Melbourne, Australia
- Murdoch Children's Research Institute, Melbourne, Parkville, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Samuel F Berkovic
- Austin Health Clinical Genetics Service, Austin Health, Melbourne, Australia
- Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Australia
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4
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Yu QX, Liu N, Zhen L, Lin XM, Wen YJ, Li DZ. Phenotypic and genotypic analysis of 11 fetal cases with Bardet-Biedl syndrome. Prenat Diagn 2024; 44:1105-1110. [PMID: 38840299 DOI: 10.1002/pd.6619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/22/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
OBJECTIVE To present the prenatal sonographic features and genomic spectrum of pregnancies with fetal Bardet-Biedl syndrome (BBS). METHODS This was a retrospective study of 11 cases with BBS diagnosed by prenatal ultrasound and confirmed by genetic testing. Clinical and laboratory data were collected and reviewed for these cases, including maternal demographics, prenatal sonographic findings, molecular testing sequencing results, and pregnancy outcomes. RESULTS All cases had unremarkable first-trimester ultrasound scans without reporting limb malformations. All had second-trimester abnormal ultrasounds: postaxial polydactyly in nine cases (9/11), renal abnormalities in seven (7/11), reduced amniotic fluid volume in two (2/11), central nervous system anomalies in two (2/11), and ascites in three (3/11). Ten fetuses presented with at least two-system anomalies, and one (Case 11) presented with only postaxial polydactyly. Variants were detected in five genes, including BBS2, ARL6/BBS3, BBS7, CEP290/BBS14 and IFT74/BBS22. Ten pregnancies were terminated in the second trimester, while one continued to term. CONCLUSION Enlarged hyperechogenic kidneys and postaxial polydactyly are the two most common sonographic features of fetal BBS. Prenatal diagnosis of BBS can be done with ultrasound and genetic testing although the diagnosis may be made in the second trimester.
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Affiliation(s)
- Qiu-Xia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Na Liu
- Obstetrics Unit, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Mei Lin
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun-Jing Wen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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5
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Abulí A, Antolín E, Borrell A, Garcia-Hoyos M, García Santiago F, Gómez Manjón I, Maíz N, González González C, Rodríguez-Revenga L, Valenzuena Palafoll I, Suela J. Guidelines for NGS procedures applied to prenatal diagnosis by the Spanish Society of Gynecology and Obstetrics and the Spanish Association of Prenatal Diagnosis. J Med Genet 2024; 61:727-733. [PMID: 38834294 DOI: 10.1136/jmg-2024-109878] [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: 01/15/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
OBJECTIVE This document addresses the clinical application of next-generation sequencing (NGS) technologies for prenatal genetic diagnosis and aims to establish clinical practice recommendations in Spain to ensure uniformity in implementing these technologies into prenatal care. METHODS A joint committee of expert obstetricians and geneticists was created to review the existing literature on fetal NGS for genetic diagnosis and to make recommendations for Spanish healthcare professionals. RESULTS This guideline summarises technical aspects of NGS technologies, clinical indications in prenatal setting, considerations regarding findings to be reported, genetic counselling considerations as well as data storage and protection policies. CONCLUSIONS This document provides updated recommendations for the use of NGS diagnostic tests in prenatal diagnosis. These recommendations should be periodically reviewed as our knowledge of the clinical utility of NGS technologies, applied during pregnancy, may advance.
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Affiliation(s)
- Anna Abulí
- Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Eugenia Antolín
- Gynecology and Obstetrics, La Paz University Hospital, Madrid, Spain
| | - Antoni Borrell
- Gynecology and Obstetrics, Clinic Hospital of Barcelona, Barcelona, Spain
| | | | | | | | - Nerea Maíz
- Maternal-Fetal Medicine Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Obstetrics, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Laia Rodríguez-Revenga
- Biochemistry and Molecular Genetics, Clinic Hospital of Barcelona, Barcelona, Spain
- August Pi Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | - Javier Suela
- Genetics, Sanitas Central Laboratory, Alcobendas, Spain
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6
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Schubert C, Milverton J, Goodall S, Merlin T. A systematic review to assess the utility of genomic autopsy using exome or genome sequencing in cases of congenital anomalies and perinatal death. Genet Med 2024; 26:101159. [PMID: 38704678 DOI: 10.1016/j.gim.2024.101159] [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: 01/21/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
PURPOSE Exome or genome sequencing (ES or GS) can identify genetic causes of otherwise unexplained congenital anomaly and perinatal death (PND) but is not routine practice. The evidence base for "genomic autopsy" after termination of pregnancy for fetal anomaly (TOPFA) and PND has been synthesized to determine the value of this investigation. METHODS We conducted a systematic review and meta-analysis of studies meeting prespecified inclusion criteria and containing ≥10 cases of TOPFA or PND (with or without major congenital abnormality), in which ES or GS was conducted. We determined test performance, including diagnostic yield, accuracy, and reliability. We also reported outcomes associated with clinical utility and harms, where described. RESULTS From 2245 potentially eligible studies, 32 publications were eligible and had data extracted, representing 2120 cases that could be meta-analyzed. No diagnostic accuracy or comparative studies were identified, although some analysis of concordance between different ES/GS methodologies could be performed. Studies reporting parent-related outcomes or long-term follow-up did not do so in a systematic or quantifiable manner. CONCLUSION Evidence suggests that approximately one-fourth to one-third of fetal losses associated with TOPFA or unexplained PND are associated with a genetic cause identifiable on ES or GS-albeit this estimate varies depending on phenotypic and background risk factors. Despite the large body of evidence on ES and GS, little research has attempted to validate the accuracy of testing, nor measure the clinical or societal outcomes in families that follow the diagnostic investigation in this context.
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Affiliation(s)
- Camille Schubert
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Milverton
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Goodall
- Centre for Health Economics Research and Evaluation, Faculty of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Tracy Merlin
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
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7
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Marchionni E, Guadagnolo D, Mastromoro G, Pizzuti A. Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis. Eur J Hum Genet 2024; 32:759-769. [PMID: 38486024 PMCID: PMC11219734 DOI: 10.1038/s41431-024-01590-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.
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Affiliation(s)
- Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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8
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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.
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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.
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9
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Zemet R, Maktabi MA, Tinfow A, Giordano JL, Heisler TM, Yan Q, Plaschkes R, Stokes J, Walsh JM, Corcoran S, Schindewolf E, Miller K, Talati AN, Miller KA, Blakemore K, Swanson K, Ramm J, Bedei I, Sparks TN, Jelin AC, Vora NL, Gebb JS, Crosby DA, Berkenstadt M, Weisz B, Wapner RJ, Van Den Veyver IB. Amniocentesis in pregnancies at or beyond 24 weeks: an international multicenter study. Am J Obstet Gynecol 2024:S0002-9378(24)00693-8. [PMID: 38914189 DOI: 10.1016/j.ajog.2024.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND Amniocentesis for genetic diagnosis is most commonly done between 15 and 22 weeks of gestation but can be performed at later gestational ages. The safety and genetic diagnostic accuracy of amniocentesis have been well-established through numerous large-scale multicenter studies for procedures before 24 weeks, but comprehensive data on late amniocentesis remain sparse. OBJECTIVE To evaluate the indications, diagnostic yield, safety, and maternal and fetal outcomes associated with amniocentesis performed at or beyond 24 weeks of gestation. STUDY DESIGN We conducted an international multicenter retrospective cohort study examining pregnant individuals who underwent amniocentesis for prenatal diagnostic testing at gestational ages between 24w0d and 36w6d. The study, spanning from 2011 to 2022, involved 9 referral centers. We included singleton or twin pregnancies with documented outcomes, excluding cases where other invasive procedures were performed during pregnancy or if amniocentesis was conducted for obstetric indications. We analyzed indications for late amniocentesis, types of genetic tests performed, their results, and the diagnostic yield, along with pregnancy outcomes and postprocedure complications. RESULTS Of the 752 pregnant individuals included in our study, late amniocentesis was primarily performed for the prenatal diagnosis of structural anomalies (91.6%), followed by suspected fetal infection (2.3%) and high-risk findings from cell-free DNA screening (1.9%). The median gestational age at the time of the procedure was 28w5d, and 98.3% of pregnant individuals received results of genetic testing before birth or pregnancy termination. The diagnostic yield was 22.9%, and a diagnosis was made 2.4 times more often for fetuses with anomalies in multiple organ systems (36.4%) compared to those with anomalies in a single organ system (15.3%). Additionally, the diagnostic yield varied depending on the specific organ system involved, with the highest yield for musculoskeletal anomalies (36.7%) and hydrops fetalis (36.4%) when a single organ system or entity was affected. The most prevalent genetic diagnoses were aneuploidies (46.8%), followed by copy number variants (26.3%) and monogenic disorders (22.2%). The median gestational age at delivery was 38w3d, with an average of 59 days between the procedure and delivery date. The overall complication rate within 2 weeks postprocedure was 1.2%. We found no significant difference in the rate of preterm delivery between pregnant individuals undergoing amniocentesis between 24 and 28 weeks and those between 28 and 32 weeks, reinforcing the procedure's safety across these gestational periods. CONCLUSION Late amniocentesis, at or after 24 weeks of gestation, especially for pregnancies complicated by multiple congenital anomalies, has a high diagnostic yield and a low complication rate, underscoring its clinical utility. It provides pregnant individuals and their providers with a comprehensive diagnostic evaluation and results before delivery, enabling informed counseling and optimized perinatal and neonatal care planning.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.
| | - Mohamad Ali Maktabi
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX
| | - Alexandra Tinfow
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Jessica L Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Thomas M Heisler
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Roni Plaschkes
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Jenny Stokes
- Department of Obstetrics and Gynaecology, National Maternity Hospital, Dublin, Ireland
| | - Jennifer M Walsh
- Department of Obstetrics and Gynaecology, National Maternity Hospital, Dublin, Ireland
| | - Siobhán Corcoran
- Department of Obstetrics and Gynaecology, National Maternity Hospital, Dublin, Ireland
| | - Erica Schindewolf
- The Center for Fetal Diagnosis and Treatment, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kendra Miller
- The Center for Fetal Diagnosis and Treatment, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Asha N Talati
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Kristen A Miller
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Karin Blakemore
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kate Swanson
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA
| | - Jana Ramm
- Department of Prenatal Diagnosis and Fetal Therapy, Justus-Liebig University, Giessen, Germany
| | - Ivonne Bedei
- Department of Prenatal Diagnosis and Fetal Therapy, Justus-Liebig University, Giessen, Germany
| | - Teresa N Sparks
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA
| | - Angie C Jelin
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Neeta L Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Juliana S Gebb
- The Center for Fetal Diagnosis and Treatment, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - David A Crosby
- Department of Obstetrics and Gynaecology, National Maternity Hospital, Dublin, Ireland
| | - Michal Berkenstadt
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel-Hashomer, Israel
| | - Boaz Weisz
- Department of Obstetrics and Gynecology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ignatia B Van Den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Division of Maternal-Fetal Medicine and Reproductive and Prenatal Genetics, Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Fetal Center, Houston, TX.
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10
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Mattar CN, Chew WL, Lai PS. Embryo and fetal gene editing: Technical challenges and progress toward clinical applications. Mol Ther Methods Clin Dev 2024; 32:101229. [PMID: 38533521 PMCID: PMC10963250 DOI: 10.1016/j.omtm.2024.101229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Gene modification therapies (GMTs) are slowly but steadily making progress toward clinical application. As the majority of rare diseases have an identified genetic cause, and as rare diseases collectively affect 5% of the global population, it is increasingly important to devise gene correction strategies to address the root causes of the most devastating of these diseases and to provide access to these novel therapies to the most affected populations. The main barriers to providing greater access to GMTs continue to be the prohibitive cost of developing these novel drugs at clinically relevant doses, subtherapeutic effects, and toxicity related to the specific agents or high doses required. In vivo strategy and treating younger patients at an earlier course of their disease could lower these barriers. Although currently regarded as niche specialties, prenatal and preconception GMTs offer a robust solution to some of these barriers. Indeed, treating either the fetus or embryo benefits from economy of scale, targeting pre-pathological tissues in the fetus prior to full pathogenesis, or increasing the likelihood of complete tissue targeting by correcting pluripotent embryonic cells. Here, we review advances in embryo and fetal GMTs and discuss requirements for clinical application.
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Affiliation(s)
- Citra N.Z. Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
- Department of Obstetrics and Gynaecology, National University Health System, Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, 60 Biopolis St, Singapore, Singapore 138672
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
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11
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Gao Z, Zhu X, Ren H, Wang Y, Hua C, Kong X. Prenatal exome sequencing for morphologically normal fetus: Should we be doing it? Prenat Diagn 2024. [PMID: 38862389 DOI: 10.1002/pd.6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
OBJECTIVE We aimed to investigate the yield of prenatal exome sequencing (pES) in morphologically normal fetuses. METHOD This retrospective study analyzed 254 families with morphologically normal fetuses who underwent prenatal trio exome sequencing based on parental request between September 2020 and October 2023. RESULTS Overall, abnormal findings were detected in 8 families (3.1%, 8/254) by pES. Among these, 6 families (2.3%, 6/254) were found to have fetuses affected with monogenic disorders (2 autosomal recessive conditions and 4 autosomal dominant conditions), while 2 families (0.8%, 2/254) were incidentally found to be couples at risk of having a future pregnancy with a recessive condition. Among the six fetuses detected with monogenic disorders, two fetuses carried a de novo variant in OPA1 and NF1, which are known to cause Optic atrophy 1 and Neurofibromatosis, respectively. One fetus was detected with a maternally inherited variant in PKD2 related to polycystic kidney disease 2 (not known to the mother until then). One fetus was detected with a maternally inherited variant in SDHB associated with Pheochromocytoma. Two fetuses carried compound heterozygous variants in NAGLU and GJB2 associated with Mucopolysaccharidosis type IIIB and Deafness, respectively. In the 2 families where parents were found to be carriers but the fetuses were unaffected, heterozygous variants in the GJB2 and SERPINB7 genes were detected in the parents, respectively, which are associated with deafness and palmoplantar keratoderma. CONCLUSION Our research indicated that pES can provide significant critical information for families with morphologically normal fetuses. Prenatal screening with exome sequencing requires careful management and detailed pre-test and post-test genetic counseling.
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Affiliation(s)
- Zhi Gao
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanan Ren
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanfei Wang
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunxiao Hua
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Department of Obstetrics and Gynecology, Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Siranosian J, Lewis C, Hill M, Ormond KE. Exploring prenatal testing preferences among US pregnant individuals: A discrete choice experiment. J Genet Couns 2024; 33:699-708. [PMID: 37646199 DOI: 10.1002/jgc4.1777] [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: 11/04/2022] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Although there are numerous benefits to diagnostic prenatal testing, such as fetal exome sequencing, there are also consequences, including the possibility of receiving variants of uncertain significance or identifying secondary findings. In this study, we utilized a survey-based discrete choice experiment to elicit the preferences of pregnant people in Northern California for hypothetical prenatal genomic tests. Pregnant individuals were invited to complete the survey through advertisements on social media. Five test attributes were studied: likelihood of getting a result, time taken to receive results, who explains results, reporting of uncertain results, and reporting of secondary findings. The survey also gathered information about the participants' demographics, current and past pregnancies, and tolerance of uncertainty using the IUS-12 scale. Participants were eligible if they were female, currently 24 or more weeks pregnant, and able to read/write enough English or Spanish to complete an online survey. Overall, participants (n = 56) preferred the option of having a prenatal test over not having a prenatal test (p < 0.01) and had substantially higher preferences for tests with the highest likelihood of getting a result (p < 0.01). There were also positive preferences for tests that reported secondary findings (p = 0.01) and those where results were returned by a genetic specialist (vs. their prenatal provider) (p = 0.04). These findings can be used to guide conversations between pregnant individuals and genetics specialists, such as genetic counselors, as they weigh the pros and cons of diagnostic prenatal testing options.
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Affiliation(s)
- Jennifer Siranosian
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Celine Lewis
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, London, UK
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Melissa Hill
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kelly E Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, California, USA
- Health Ethics and Policy Lab, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
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13
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Bromley B, Platt LD. First-Trimester Ultrasound Screening in Routine Obstetric Practice. Obstet Gynecol 2024; 143:730-744. [PMID: 38723258 DOI: 10.1097/aog.0000000000005594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 05/18/2024]
Abstract
Technologic advances and ultrasonographer-physician experience in fetal imaging have led to significant improvements in our ability to distinguish between normal and abnormal fetal structural development in the latter part of the first trimester. As a critical component of pregnancy care, assessment of fetal anatomy at the end of the first trimester with a standardized imaging protocol should be offered to all pregnant patients regardless of aneuploidy screening results because it has been demonstrated to identify approximately half of fetal structural malformations. Early identification of abnormalities allows focused genetic counseling, timely diagnostic testing, and subspecialist consultation. In addition, a normal ultrasound examination result offers some degree of reassurance to most patients. Use of cell-free DNA alone for aneuploidy screening while foregoing an accompanying early anatomic evaluation of the fetus will result in many anomalies that are typically detected in the first trimester not being identified until later in pregnancy, thus potentially diminishing the quality of obstetric care for pregnant individuals and possibly limiting their reproductive options, including pregnancy termination.
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Affiliation(s)
- Bryann Bromley
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, and Diagnostic Ultrasound Associates, Brookline, Massachusetts; and the Center for Fetal Medicine and Women's Ultrasound, Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
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14
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Pucel J, Briere LC, Reuter C, Gochyyev P, LeBlanc K. Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med 2024; 26:101115. [PMID: 38436216 PMCID: PMC11161308 DOI: 10.1016/j.gim.2024.101115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases. METHODS In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS. RESULTS Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively). CONCLUSION We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.
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Affiliation(s)
- Jenna Pucel
- MGH Institute of Health Professions, Boston, MA.
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Cardiovascular Medicine, Stanford University, Palo Alto, CA
| | | | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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15
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Gianforcaro K, Pilchman L, Conway L, Moldenhauer JS, Rychik J, Soni S. Is there an increased risk of genetic abnormalities in fetuses with congenital heart disease in the setting of growth restriction? Prenat Diagn 2024; 44:879-887. [PMID: 38804584 DOI: 10.1002/pd.6597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
OBJECTIVE To determine if the presence of fetal growth restriction (FGR) is associated with an increased risk of genetic abnormalities in the setting of congenital heart disease (CHD). METHODS This was a retrospective cohort study involving pregnancies that met the following criteria: (i) prenatal diagnosis of CHD, (ii) singleton live-birth, and (iii) genetic testing was performed either pre- or postnatally. Genetic results were reviewed by a clinical geneticist for updated variant classification. Fetal growth was stratified as appropriate for gestational age (AGA) or FGR. RESULTS Of the total of 445 fetuses that met the study criteria, 325 (73.0%) were AGA and 120 (27.0%) were FGR. Genetic abnormalities were detected in 131 (29.4%) pregnancies. There was a higher rate of genetic abnormalities (36.7% vs. 26.8%, p = 0.04), which was driven by aneuploidies (20.8% vs. 8.9%, p = 0.0006) in the FGR population. Early onset growth restriction was associated with a higher rate of genetic abnormalities (44.5% vs. 25.9%, p = 0.03). The rate of genetic abnormalities was significantly higher in the shunt category as compared to remainder of the cardiac anomalies (62.5% in shunt lesions vs. 24.7%, p < 0.00001). The rates of FGR (40.9% vs. 21.4%, p < 0.0001) and genetic abnormalities (52% vs. 20.4%, p < 0.0001) were significantly higher in the presence of extra-cardiac anomalies (ECA). CONCLUSION The presence of FGR in fetal CHD population was associated with underlying genetic abnormalities, specifically aneuploidies. Patients should be appropriately counseled regarding the higher likelihood of a genetic condition in the presence of FGR, early onset FGR, shunt lesions and ECA.
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Affiliation(s)
- Kathleen Gianforcaro
- Richard D. Wood Jr Center for Fetal Diagnosis & Treatment, Department of General, Thoracic & Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lisa Pilchman
- Richard D. Wood Jr Center for Fetal Diagnosis & Treatment, Department of General, Thoracic & Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura Conway
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie S Moldenhauer
- Richard D. Wood Jr Center for Fetal Diagnosis & Treatment, Department of General, Thoracic & Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jack Rychik
- Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shelly Soni
- Richard D. Wood Jr Center for Fetal Diagnosis & Treatment, Department of General, Thoracic & Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Bucholz EM, Morton SU, Madriago E, Roberts AE, Ronai C. The Evolving Role of Genetic Evaluation in the Prenatal Diagnosis and Management of Congenital Heart Disease. J Cardiovasc Dev Dis 2024; 11:170. [PMID: 38921669 PMCID: PMC11203735 DOI: 10.3390/jcdd11060170] [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: 04/15/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
Congenital heart disease (CHD) is increasingly diagnosed prenatally and the ability to screen and diagnose the genetic factors involved in CHD have greatly improved. The presence of a genetic abnormality in the setting of prenatally diagnosed CHD impacts prenatal counseling and ensures that families and providers have as much information as possible surrounding perinatal management and what to expect in the future. This review will discuss the genetic evaluation that can occur prior to birth, what different genetic testing methods are available, and what to think about in the setting of various CHD diagnoses.
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Affiliation(s)
- Emily M. Bucholz
- Section of Cardiology, Department of Pediatrics, University of Colorado Denver, Denver, CO 80204, USA
| | - Sarah U. Morton
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Erin Madriago
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Amy E. Roberts
- Department of Cardiology, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Christina Ronai
- Department of Cardiology, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Yue F, Yang X, Liu N, Liu R, Zhang H. Prenatal diagnosis and pregnancy outcomes in fetuses with ventriculomegaly. Front Med (Lausanne) 2024; 11:1349171. [PMID: 38784233 PMCID: PMC11111914 DOI: 10.3389/fmed.2024.1349171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Objective Genetic etiology plays a critical role in fetal ventriculomegaly (VM). However, the studies on chromosomal copy number variants (CNVs) in fetal VM are limited. This study aimed to investigate the chromosomal CNVs in fetuses with mild to moderate VM, and explore its genotype-phenotype correlation. Methods A total of 242 fetuses with mild to moderate VM detected by prenatal ultrasound were enrolled in our study from October 2018 to October 2022. All cases underwent chromosomal microarray analysis (CMA) and G-banding simultaneously. All VM cases were classified different subgroups according to the maternal age, severity, VM distribution and presence/absence of other ultrasound abnormalities. The pregnancy outcomes and health conditions after birth were followed up. We also performed a pooled analysis regarding likely pathogenic and pathogenic CNVs (LP/P CNVs) for VM. Results The detection rate of chromosomal abnormalities by karyotyping was 9.1% (22/242), whereas it was 16.5% (40/242) when CMA was conducted (P < 0.05). The total detection rate of chromosomal abnormalities by karyotyping and CMA was 21.1% (51/242). A 12.0% incremental yield of CMA over karyotyping was observed. The detection rate of total genetic variants in fetuses with bilateral VM was significantly higher than in fetuses with unilateral VM (30.0% vs. 16.7%, P = 0.017). No significant differences were discovered between isolated VM and non-isolated VM, or between mild and moderate VM, or between advanced maternal age (AMA) and non-AMA (all P > 0.05). 28 fetuses with VM were terminated and 214 fetuses were delivered: one presented developmental delay and one presented congenital heart disease. The VM cases with both positive CMA and karyotypic results had a higher rate of termination of pregnancy than those with either a positive CMA or karyotypic result, or both negative testing results (P < 0.001). Conclusion The combination of CMA and karyotyping should be adopted to improve the positive detection rate of chromosomal abnormalities for VM. The total genetic abnormalities detected using both techniques would affect the final pregnancy outcomes. LP/P CNVs at 16p11.2, 17p13, and 22q11.21 were identified as the top three chromosomal hotspots associated with VM, which would enable genetic counselors to provide more precise genetic counseling for VM pregnancies.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Xiao Yang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ning Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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18
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Qi Q, Jiang Y, Zhou X, Lü Y, Xiao R, Bai J, Lou H, Sun W, Lian Y, Hao N, Li M, Chang J. Whole-genome sequencing analysis in fetal structural anomalies: novel phenotype-genotype discoveries. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:664-671. [PMID: 37842862 DOI: 10.1002/uog.27517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
OBJECTIVES The identification of structural variants and single-nucleotide variants is essential in finding molecular etiologies of monogenic genetic disorders. Whole-genome sequencing (WGS) is becoming more widespread in genetic disease diagnosis. However, data on its clinical utility remain limited in prenatal practice. We aimed to expand our understanding of implementing WGS in the genetic diagnosis of fetal structural anomalies. METHODS We employed trio WGS with a minimum coverage of 40× on the MGI DNBSEQ-T7 platform in a cohort of 17 fetuses presenting with aberrations detected by ultrasound, but uninformative findings of standard chromosomal microarray analysis (CMA) and exome sequencing (ES). RESULTS Causative genetic variants were identified in two families, with an increased diagnostic yield of 11.8% (2/17). Both were exon-level copy-number variants of small size (3.03 kb and 5.16 kb) and beyond the detection thresholds of CMA and ES. Moreover, to the best of our knowledge, we have described the first prenatal instance of the association of FGF8 with holoprosencephaly and facial deformities. CONCLUSIONS Our analysis demonstrates the clinical value of WGS in the diagnosis of the underlying etiology of fetuses with structural abnormalities, when routine genetic tests have failed to provide a diagnosis. Additionally, the novel variants and new fetal manifestations have expanded the mutational and phenotypic spectrums of BBS9 and FGF8. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- Q Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Y Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - X Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Y Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - R Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R&D Center, Zhejiang, China
| | - J Bai
- Becreative Lab Co. Ltd, Beijing, China
| | - H Lou
- Becreative Lab Co. Ltd, Beijing, China
| | - W Sun
- Biosan Biochemical Technologies Co. Ltd., Zhejiang, China
| | - Y Lian
- Biosan Biochemical Technologies Co. Ltd., Zhejiang, China
| | - N Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - M Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - J Chang
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
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19
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Bulas DI, Fraser JL, Cilli K. Using MRI derived observed to expected total lung volume to predict lethality in fetal skeletal dysplasia. Pediatr Radiol 2024; 54:854-856. [PMID: 38438708 DOI: 10.1007/s00247-024-05893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/06/2024]
Affiliation(s)
- Dorothy I Bulas
- Department of Diagnostic Imaging and Radiology, Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, 111 Michigan Ave, Washington, DC, 20010, USA.
| | - Jamie L Fraser
- Division of Genetics and Metabolism, Department of Pediatrics, Rare Disease Institute, Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, 7125 Michigan Ave, Washington, DC, 20012, USA
| | - Kate Cilli
- Department of Diagnostic Imaging and Radiology, Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, 111 Michigan Ave, Washington, DC, 20010, USA
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, 111 Michigan Ave, Washington, DC, 20010, USA
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20
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Westenius E, Conner P, Pettersson M, Sahlin E, Papadogiannakis N, Lindstrand A, Iwarsson E. Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:658-663. [PMID: 38268232 DOI: 10.1002/uog.27592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE To investigate the diagnostic yield of trio whole-genome sequencing (WGS) in fetuses with various congenital malformations referred to a tertiary center for prenatal diagnosis. METHODS In this prospective study, 50 pregnancies with different congenital malformations, negative for trisomies and causative copy-number variants, were analyzed further with fetal-parental trio WGS analysis. Parents were eligible for inclusion if they accepted further investigation following the detection of isolated or multiple malformations on prenatal ultrasound. Cases with isolated increased nuchal translucency, gamete donation or multiple pregnancy were excluded. WGS with the Illumina Inc. 30× polymerase-chain-reaction-free short-read sequencing included analysis of single-nucleotide variants, insertions and deletions, structural variants, short tandem repeats and copy-number identification of SMN1 and SMN2 genes. RESULTS A molecular diagnosis was achieved in 13/50 (26%) cases. Causative sequence variants were identified in 12 genes: FGFR3 (n = 2), ACTA1 (n = 1), CDH2 (n = 1), COL1A2 (n = 1), DHCR7 (n = 1), EYA1 (n = 1), FBXO11 (n = 1), FRAS1 (n = 1), L1CAM (n = 1), OFD1 (n = 1), PDHA1 (n = 1) and SOX9 (n = 1). The phenotypes of the cases were divided into different groups, with the following diagnostic yields: skeletal malformation (4/9 (44%)), multisystem malformation (3/7 (43%)), central nervous system malformation (5/15 (33%)) and thoracic malformation (1/10 (10%)). Additionally, two cases carried variants that were considered potentially clinically relevant, even though they were assessed as variants of uncertain significance, according to the guidelines provided by the American College of Medical Genetics and Genomics. Overall, we identified a causative or potentially clinically relevant variant in 15/50 (30%) cases. CONCLUSIONS We demonstrate a diagnostic yield of 26% with clinical WGS in prenatally detected congenital malformations. This study emphasizes the benefits that WGS can bring to the diagnosis of fetal structural anomalies. It is important to note that causative chromosomal aberrations were excluded from our cohort before WGS. As chromosomal aberrations are a well-known cause of prenatally detected congenital malformations, future studies using WGS as a primary diagnostic test, including assessment of chromosomal aberrations, may show that the detection rate exceeds the diagnostic yield of this study. WGS can add clinically relevant information, explaining the underlying cause of the fetal anomaly, which will provide information concerning the specific prognosis of the condition, as well as estimate the risk of recurrence. A genetic diagnosis can also provide more reproductive choice for future pregnancies. © 2024 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E Westenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - P Conner
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - M Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - N Papadogiannakis
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - A Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
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21
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Grausz N, Senat MV, Colmant C, Boizard A, Benachi A, Bouchghoul H. Idiopathic polyhydramnios and postnatal outcomes of children: The role of exome sequencing. Prenat Diagn 2024. [PMID: 38682787 DOI: 10.1002/pd.6573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVES The objective of our study was to evaluate the long-term outcome of children born from a pregnancy complicated by idiopathic polyhydramnios. The secondary objective was to investigate factors associated with adverse outcomes. METHODS We conducted a retrospective study in two prenatal diagnosis centers between January 1, 2009 and December 31, 2020. Inclusion criteria were pregnancies with a diagnosis of idiopathic polyhydramnios, defined by a deepest pocket greater than 8 cm, no detectable abnormality at ultrasound and a negative amniotic fluid assessment including karyotype, chromosomal microarray, biochemical assays (electrolytes and digestive enzymes), and viruses (parvovirus B19 and cytomegalovirus). One-year outcomes of these children were collected. The primary endpoint was adverse postnatal outcome, defined by at least one of the following criteria: stillbirth, neonatal death, or serious and incurable condition diagnosed in the first year of life. RESULTS Of the 245 women referred for isolated polyhydramnios, 73 were diagnosed with idiopathic polyhydramnios after prenatal investigations. The mean age at follow-up of children was 28 months (95% CI 20-36). An adverse outcome occurred in 25% of cases (18/73), with one stillbirth, two neonatal deaths, and 15 severe conditions diagnosed postnatally, including a rate of monogenic disorders of 8.2% (6/73). Pediatric follow-up was normal for 75% of the children (55/73), including a rate of 9% (5/55) of curable conditions. Repeated amnioreduction was independently associated with an adverse outcome. CONCLUSION Pregnant women with polyhydramnios should be informed of the increased risk of 25% of perinatal mortality and serious conditions diagnosed after birth.
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Affiliation(s)
- Noémie Grausz
- Department of Obstetrics, Bicêtre University Hospital, Le Kremlin-Bicêtre, France
- Department of Obstetrics, Antoine Béclère University Hospital, Clamart, France
| | - Marie-Victoire Senat
- Department of Obstetrics, Bicêtre University Hospital, Le Kremlin-Bicêtre, France
| | - Claire Colmant
- Department of Obstetrics, Necker University Hospital, Paris, France
| | - Anne Boizard
- Department of Obstetrics, Bicêtre University Hospital, Le Kremlin-Bicêtre, France
| | - Alexandra Benachi
- Department of Obstetrics, Antoine Béclère University Hospital, Clamart, France
| | - Hanane Bouchghoul
- Department of Obstetrics, Bordeaux University Hospital, Bordeaux, France
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22
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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.
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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
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23
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Allen SK, Chandler NJ, Kinning E, Harrison V, Brothwell SLC, Vijay S, Castleman J, Cilliers D. Diagnosis of inborn errors of metabolism through prenatal exome sequencing with targeted analysis for fetal structural anomalies. Prenat Diagn 2024; 44:432-442. [PMID: 38063435 DOI: 10.1002/pd.6476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 04/11/2024]
Abstract
OBJECTIVES The value of prenatal exome sequencing (pES) for fetuses with structural anomalies is widely reported. In England, testing is conducted through trio exome sequencing and analysis of a gene panel. Over a 30-month period testing of 921 pregnancies resulted in a genetic diagnosis in 32.8% of cases (302/921). Here we review cases diagnosed with an inborn error of metabolism. METHODS Diagnoses of inborn errors of metabolism (IEM) were classified according to the ICIMD classification system. Genetic diagnoses were assessed against Human Phenotype Ontology terms, gestation of scan findings and literature evidence. RESULTS 35/302 diagnoses (11.6%) represented IEM. Almost half affected metabolism of complex macromolecules and organelles (n = 16), including congenital disorders of glycosylation (n = 8), peroxisome biogenesis disorders (n = 4), and lysosomal storage disorders (n = 4). There were eight disorders of lipid metabolism and transport, the majority being genes in the cholesterol biosynthesis pathway, eight disorders of intermediary metabolism, of which seven were defects in "energy" processes, and two diagnoses of alkaline phosphatase deficiency. CONCLUSIONS Review of pES diagnoses and ultrasound scan findings is key to understanding genotype-phenotype correlations. IEM are genetically heterogeneous and may present with variable scan findings, which makes an individual diagnosis difficult to suspect. Diagnosis during pregnancy is particularly important for many IEM with respect to prognosis and early neonatal management.
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Affiliation(s)
- Stephanie K Allen
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Natalie J Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Esther Kinning
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Shona L C Brothwell
- Department of Inherited Metabolic Diseases, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Suresh Vijay
- Department of Inherited Metabolic Diseases, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - James Castleman
- Fetal Medicine Department, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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24
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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.
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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
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25
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Vora NL, Langlois S, Chitty LS. Current controversy in prenatal diagnosis: The use of cfDNA to screen for monogenic conditions in low risk populations is ready for clinical use. Prenat Diagn 2024; 44:389-397. [PMID: 37991340 DOI: 10.1002/pd.6469] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
Noninvasive cfDNA testing for monogenic disorders (sgNIPT) has become integrated into the care of pregnant women at increased risk based on carrier status, known family history, or ultrasound anomalies. The availability of commercial tests for common autosomal recessive and de novo autosomal dominant conditions has led to the use of these tests in low-risk pregnancies. However, is the technology ready for use in this low-risk population? This report is a summary of the debate on this topic at the 27th International Conference on Prenatal Diagnosis and Therapy. Both expert debaters provided strong arguments in favor and against the use of sgNIPT in low-risk pregnancies. The argument in favor of sgNIPT for autosomal recessive conditions is that it allows the identification of affected pregnancies without the need for involving the partner in testing. Arguments for sgNIPT for autosomal dominant conditions include identification of affected fetuses that would have either presented later in pregnancy with fetal anomalies or not been detected prenatally given normal ultrasounds, respect for patient autonomy and patient desire for information. Strong arguments were made against offering sgNIPT screening. Given that traditional carrier screening for recessive conditions can be carried out in many jurisdictions, the added value of sgNIPT has not been clearly demonstrated. Arguments against sgNIPT for autosomal dominant conditions included the total lack of clinical validation studies and the risk of false reassurance in cases of negative results and unnecessary invasive procedures in cases of false positive results. Although there is a desire to take advantage of new technologies to improve the detection of monogenic disorders in low-risk populations, based on the discussion and the audience vote, it appears premature to offer sgNIPT to all low risk pregnant women. Further clinical validation studies are needed prior to broad implementation.
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Affiliation(s)
- Neeta L Vora
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lyn S Chitty
- Genetics and Genomic Medicine, UCL Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, England
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26
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Mordaunt DA, Gonzalez FS, Lunke S, Eggers S, Sadedin S, Chong B, Dalziel K, Stark Z, Goranitis I. The cost of proband and trio exome and genome analysis in rare disease: A micro-costing study. Genet Med 2024; 26:101058. [PMID: 38164890 DOI: 10.1016/j.gim.2023.101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
PURPOSE Rare disease genomic testing is a complex process involving various resources. Accurate resource estimation is required for informed prioritization and reimbursement decisions. This study aims to analyze the costs and cost drivers of clinical genomic testing. METHODS Based on genomic sequencing workflows we microcosted limited virtual panel analysis on exome sequencing backbone, proband and trio exome, and genome testing for proband and trio analysis in 2023 Australian Dollars ($). Deterministic and probabilistic sensitivity analyses were undertaken. RESULTS Panel testing costs AUD $2373 ($733-$6166), and exome sequencing costs $2823 ($802-$7206) and $5670 ($2006-$11,539) for proband and trio analysis, respectively. Genome sequencing costs $4840 ($2153-$9890) and $11,589 ($5842-$16,562) for proband and trio analysis. The most expensive cost component of genomic testing was sequencing (36.9%-69.4% of total cost), with labor accounting for 27.1%-63.2% of total cost. CONCLUSION We provide a comprehensive analysis of rare disease genomic testing costs, for a range of clinical testing types and contexts. This information will accurately inform economic evaluations of rare disease genomic testing and decision making on policy settings that assist with implementation, such as genomic testing reimbursement.
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Affiliation(s)
- Dylan A Mordaunt
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Australia; Department of Paediatrics, University of Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia
| | - Francisco Santos Gonzalez
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Australia; Department of Paediatrics, University of Melbourne, Australia
| | - Sebastian Lunke
- Murdoch Children's Research Institute, Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia; Australian Genomics Health Alliance, Melbourne, Australia; Department of Pathology. University of Melbourne, Australia
| | - Stefanie Eggers
- Murdoch Children's Research Institute, Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia
| | - Simon Sadedin
- Murdoch Children's Research Institute, Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia
| | - Belinda Chong
- Murdoch Children's Research Institute, Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia
| | - Kim Dalziel
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Zornitza Stark
- Department of Paediatrics, University of Melbourne, Australia; Women's and Children's Division, Southern Adelaide Local Health Network, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Australian Genomics Health Alliance, Melbourne, Australia.
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27
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Duyzend MH, Cacheiro P, Jacobsen JO, Giordano J, Brand H, Wapner RJ, Talkowski ME, Robinson PN, Smedley D. Improving prenatal diagnosis through standards and aggregation. Prenat Diagn 2024; 44:454-464. [PMID: 38242839 PMCID: PMC11006584 DOI: 10.1002/pd.6522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/21/2024]
Abstract
Advances in sequencing and imaging technologies enable enhanced assessment in the prenatal space, with a goal to diagnose and predict the natural history of disease, to direct targeted therapies, and to implement clinical management, including transfer of care, election of supportive care, and selection of surgical interventions. The current lack of standardization and aggregation stymies variant interpretation and gene discovery, which hinders the provision of prenatal precision medicine, leaving clinicians and patients without an accurate diagnosis. With large amounts of data generated, it is imperative to establish standards for data collection, processing, and aggregation. Aggregated and homogeneously processed genetic and phenotypic data permits dissection of the genomic architecture of prenatal presentations of disease and provides a dataset on which data analysis algorithms can be tuned to the prenatal space. Here we discuss the importance of generating aggregate data sets and how the prenatal space is driving the development of interoperable standards and phenotype-driven tools.
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Affiliation(s)
- Michael H. Duyzend
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Pilar Cacheiro
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Julius O.B. Jacobsen
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jessica Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J. Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
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28
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Mighton C, Noor A, Watkins N, Di Gioacchino V, Lerner-Ellis J, Wong A, Mukharryamova E, Anggala N, Chitayat D, Greenfeld E. Validation of low-pass genome sequencing for prenatal diagnosis. Prenat Diagn 2024; 44:443-453. [PMID: 38279846 DOI: 10.1002/pd.6525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/11/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024]
Abstract
OBJECTIVE Chromosomal microarray (CMA), while considered the gold standard for detecting copy number variants (CNVs) in prenatal diagnostics, has its limitations, including the necessity to replace aging microarray equipment, low throughput, a static design, and an inefficient multi-day workflow. This study evaluates the feasibility of low-pass genome sequencing (LP-GS) as a potential replacement for CMA in prenatal diagnostics. METHODS We comprehensively compared LP-GS at 10x and 5x average depths with CMA in a prenatal laboratory. We examined parameters, including concordance, sensitivity, specificity, workflow efficiency, and cost-effectiveness. RESULTS We found a high degree of agreement between LP-GS and CMA for detecting CNVs and absence of heterozygosity. Furthermore, compared to CMA, LP-GS increased workflow efficiency and proved to be cost-neutral at 10x and cost-effective at 5x. CONCLUSION Our study suggests that LP-GS is a promising alternative to CMA in prenatal diagnostics, offering advantages, including a more efficient workflow and scalability for larger testing volumes. Importantly, for clinical laboratories that have adopted next-generation sequencing in a separate capacity, LP-GS facilitates a unified NGS-centric approach, enabling workflow consolidation. By offering a single, streamlined platform for detecting a broad range of genetic variants, LP-GS may represent a critical step toward enhancing the diagnostic capabilities of prenatal laboratories.
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Affiliation(s)
- Chloe Mighton
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Institute of Health Policy Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Abdul Noor
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Watkins
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Vanessa Di Gioacchino
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Wong
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elvira Mukharryamova
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Nina Anggala
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Elena Greenfeld
- Division of Diagnostic Medical Genetics, Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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29
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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.
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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
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30
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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.
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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
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31
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Libman V, Macarov M, Friedlander Y, Hochner-Celnikier D, Sompolinsky Y, Dior UP, Osovsky M, Basel-Salmon L, Wiznitzer A, Neumark Y, Meiner V, Frumkin A, Hochner H, Shkedi-Rafid S. Women's attitudes towards disclosure of genetic information in pregnancy with varying levels of penetrance. Prenat Diagn 2024; 44:270-279. [PMID: 38221678 DOI: 10.1002/pd.6518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Chromosomal-microarray-analysis (CMA) may reveal susceptibility-loci (SL) of varied penetrance for autism-spectrum-disorder (ASD) and other neurodevelopmental conditions. Attitudes of women/parents to disclosure of SL during pregnancy are understudied. METHODS A multiple-choice questionnaire was distributed to postpartum women. Data were collected on women's interest to receive prenatal genetic information with various levels of penetrance. RESULTS Women's (n = 941) disclosure choices were dependent on the magnitude of risk: approximately 70% supported disclosure of either full or 40% penetrance, 53% supported disclosure at a 20% risk threshold, and 40% supported disclosure at 10% or less. Although most women supported, rejected or were indecisive about disclosure consistently across all risk levels, nearly one-quarter (24%) varied their responses based on penetrance, and this was associated with religiosity, education, parity and concern about fetal health (p-values <0.04). Among those who varied their choices, the risk threshold was lower among secular women (20%) than among ultraorthodox women (40%). In a multivariable analysis, ultraorthodox women were much less likely to vary their choices on ASD disclosure compared with secular women (aOR = 0.37, p < 0.001). CONCLUSION Women's attitudes toward disclosure are influenced by the level of risk and their individual characteristics. We therefore encourage engaging women/couples in disclosure decisions regarding uncertain and probabilistic results from prenatal genomic tests.
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Affiliation(s)
- Vitalia Libman
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Macarov
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Drorith Hochner-Celnikier
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yishai Sompolinsky
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri P Dior
- Department of Obstetrics and Gynecology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Osovsky
- Department of Neonatology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children Medical Center, Petah Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arnon Wiznitzer
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Helen Schneider Hospital for Women, Rabin Medical Center, Petah Tikva, Israel
| | - Yehuda Neumark
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Frumkin
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, Jerusalem, Israel
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Rothschild HT, Lianoglou BR, Sahin Hodoglugil NN, Tick K, Brown JEH, Sparks TN. Trust in prenatal exome sequencing for expectant families facing unexplained fetal anomalies. Prenat Diagn 2024; 44:263-269. [PMID: 38158591 PMCID: PMC10947859 DOI: 10.1002/pd.6507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/10/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE Despite exome sequencing (ES) becoming increasingly incorporated into the prenatal setting, few studies have elucidated motivations for and trust in ES and genomic research among a diverse cohort of patients and their partners. METHODS This is a qualitative study that involved semi-structured interviews with pregnant or recently pregnant individuals and their partners, interviewed separately, in the setting of ES performed through research for a fetal structural anomaly. All interview transcripts were coded thematically and developed by a multidisciplinary team. RESULTS Thirty-five individuals participated, the majority of whom (66%) self-identified as a racial or ethnic group underrepresented in genomic research. Many patients and their partners expressed trust in the healthcare system and research process and appreciated the extensive testing for information and closure. There were nonetheless concerns about data privacy and protection for individuals, including those underrepresented, who participated in genomic testing and studies. CONCLUSION Our findings illustrate important elements of motivation, trust and concern related to prenatal ES performed in the research setting, taking into account the perspectives not only of diverse and underrepresented study participants but also partners of pregnant individuals.
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Affiliation(s)
- Harriet T Rothschild
- School of Medicine, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Billie R Lianoglou
- Center for Maternal Fetal Precision Medicine, UCSF, San Francisco, California, USA
- Department of Surgery, UCSF, San Francisco, California, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | | | - Katie Tick
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, California, USA
| | - Julia E H Brown
- Program in Bioethics, UCSF, San Francisco, California, USA
- Institute for Health & Aging, School of Nursing, UCSF, San Francisco, California, USA
| | - Teresa N Sparks
- Center for Maternal Fetal Precision Medicine, UCSF, San Francisco, California, USA
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, UCSF, San Francisco, California, USA
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Olayiwola JO, Marhabaie M, Koboldt D, Matthews T, Siemon A, Mouhlas D, Porter T, Kyle G, Myers C, Mei H, Hou YC, Babcock M, Hunter J, Schieffer KM, Akkari Y, Reshmi S, Cottrell C, Mathew MT, Leung ML. Clinically significant findings in a decade-long retrospective study of prenatal chromosomal microarray testing. Mol Genet Genomic Med 2024; 12:e2349. [PMID: 38263869 PMCID: PMC10958178 DOI: 10.1002/mgg3.2349] [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: 07/04/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) is commonly utilized in the obstetrics setting. CMA is recommended when one or more fetal structural abnormalities is identified. CMA is also commonly used to determine genetic etiologies for miscarriages, fetal demise, and confirming positive prenatal cell-free DNA screening results. METHODS In this study, we retrospectively examined 523 prenatal and 319 products-of-conception (POC) CMA cases tested at Nationwide Children's Hospital from 2011 to 2020. We reviewed the referral indications, the diagnostic yield, and the reported copy number variants (CNV) findings. RESULTS In our cohort, the diagnostic yield of clinically significant CNV findings for prenatal testing was 7.8% (n = 41/523) compared to POC testing (16.3%, n = 52/319). Abnormal ultrasound findings were the most common indication present in 81% of prenatal samples. Intrauterine fetal demise was the common indication identified in POC samples. The most common pathogenic finding observed in all samples was isolated trisomy 21, detected in seven samples. CONCLUSION Our CMA study supports the clinical utility of prenatal CMA for clinical management and identifying genetic etiology in POC arrays. In addition, it provides insight to the spectrum of prenatal and POC CMA results as detected in an academic hospital clinical laboratory setting that serves as a reference laboratory.
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Lin XM, Zhen L, Wen YJ, Yu QX, Li DZ. Isolated polyhydramnios: Is a genetic evaluation of value? Eur J Obstet Gynecol Reprod Biol 2024; 293:115-118. [PMID: 38141485 DOI: 10.1016/j.ejogrb.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
OBJECTIVE To analyze the risk for genetic aberrations and pregnancy outcomes in pregnancies with isolated polyhydramnios. STUDY DESIGN This was a retrospective study of singleton pregnancies complicated by isolated polyhydramnios that underwent genetic amniocentesis between 2016 and 2021. Clinical and laboratory data were collected and reviewed for these cases, including maternal demographics, prenatal sonographic findings, chromosomal microarray results, and pregnancy outcomes. RESULTS A total of 94 singleton pregnancies were included. Three (3.2%) cases with chromosomal abnormalities were detected, including 2 case of trisomy 21 and 1 of 22q21.1 microdeletion. One case was diagnosed as Prader-Willi syndrome caused by maternal uniparental disomy of chromosome 15. Perinatal death occurred in 1 case with severe polyhydramnios, and was retrospectively diagnosed as Bartter syndrome. Of the 90 infants survived, two were identified to have single gene disorders after birth by whole exome sequencing. CONCLUSION We first attempted to determine the value of exome sequencing in pregnancies with isolated polyhydramnios. Our results warrant more studies to evaluate advanced genetic testing technologies used in such pregnancies.
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Affiliation(s)
- Xiao-Mei Lin
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yun-Jing Wen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiu-Xia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, China.
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Hadjipanteli A, Theodosiou A, Papaevripidou I, Evangelidou P, Alexandrou A, Salameh N, Kallikas I, Kakoullis K, Frakala S, Oxinou C, Marnerides A, Kousoulidou L, Anastasiadou VC, Sismani C. Sodium Channel Gene Variants in Fetuses with Abnormal Sonographic Findings: Expanding the Prenatal Phenotypic Spectrum of Sodium Channelopathies. Genes (Basel) 2024; 15:119. [PMID: 38255008 PMCID: PMC10815715 DOI: 10.3390/genes15010119] [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: 12/21/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Voltage-gated sodium channels (VGSCs) are responsible for the initiation and propagation of action potentials in the brain and muscle. Pathogenic variants in genes encoding VGSCs have been associated with severe disorders including epileptic encephalopathies and congenital myopathies. In this study, we identified pathogenic variants in genes encoding the α subunit of VGSCs in the fetuses of two unrelated families with the use of trio-based whole exome sequencing, as part of a larger cohort study. Sanger sequencing was performed for variant confirmation as well as parental phasing. The fetus of the first family carried a known de novo heterozygous missense variant in the SCN2A gene (NM_001040143.2:c.751G>A p.(Val251Ile)) and presented intrauterine growth retardation, hand clenching and ventriculomegaly. Neonatally, the proband also exhibited refractory epilepsy, spasms and MRI abnormalities. The fetus of the second family was a compound heterozygote for two parentally inherited novel missense variants in the SCN4A gene (NM_000334.4:c.4340T>C, p.(Phe1447Ser), NM_000334.4:c.3798G>C, p.(Glu1266Asp)) and presented a severe prenatal phenotype including talipes, fetal hypokinesia, hypoplastic lungs, polyhydramnios, ear abnormalities and others. Both probands died soon after birth. In a subsequent pregnancy of the latter family, the fetus was also a compound heterozygote for the same parentally inherited variants. This pregnancy was terminated due to multiple ultrasound abnormalities similar to the first pregnancy. Our results suggest a potentially crucial role of the VGSC gene family in fetal development and early lethality.
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Affiliation(s)
- Andrea Hadjipanteli
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Athina Theodosiou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Ioannis Papaevripidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Paola Evangelidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Angelos Alexandrou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Nicole Salameh
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | | | | | | | - Christina Oxinou
- Christina Oxinou Histopathology/Cytology Laboratory, 1065 Nicosia, Cyprus
| | | | - Ludmila Kousoulidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | | | - Carolina Sismani
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
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Li M, Hao N, Jiang Y, Xue H, Dai Y, Wang M, Bai J, Lv Y, Qi Q, Zhou X. Contribution of uniparental disomy to fetal growth restriction: a whole-exome sequencing series in a prenatal setting. Sci Rep 2024; 14:238. [PMID: 38168635 PMCID: PMC10762123 DOI: 10.1038/s41598-023-50584-5] [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: 09/12/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Fetal growth restriction (FGR), a leading cause of perinatal morbidity and mortality, is caused by fetal, maternal, and placental factors. Uniparental disomy (UPD) is a rare condition that leads to imprinting effects, low-level mosaic aneuploidies and homozygosity for pathogenic variants. In the present study, UPD events were detected in 5 women with FGR by trio exome sequencing (trio-WES) of a cohort of 150 FGR cases. Furthermore, noninvasive prenatal testing results of the 5 patients revealed a high risk of rare autosomal trisomy. Trio-WES showed no copy-number variations (CNVs) or nondisease-causing mutations associated with FGR. Among the 5 women with FGR, two showed gene imprinting, and two exhibited confined placental mosaicism (CPM) by copy number variant sequencing (CNV-seq). The present study showed that in FGR patients with UPD, the detection of imprinted genes and CPM could enhance the genetic diagnosis of FGR.
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Affiliation(s)
- Mengmeng Li
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Na Hao
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yulin Jiang
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Yifang Dai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Mingming Wang
- GenoDecode (Beijing) Co. Ltd., Beijing, 101160, China
| | - Junjie Bai
- Be Creative Lab (Beijing) Co. Ltd., Beijing, 100176, China
| | - Yan Lv
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qingwei Qi
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiya Zhou
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F. Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:15-23. [PMID: 37725747 DOI: 10.1002/uog.27491] [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: 06/30/2023] [Revised: 08/08/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- N Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, Cambridge, UK
| | - C Sproule
- Department of Obstetrics & Gynaecology, South Eastern Health and Social Care Trust, Belfast, UK
| | - K W Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Z Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - K Gajewska-Knapik
- Department of Obstetrics & Gynaecology, Cambridge University Hospitals, Cambridge, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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Gold NB, Nadel A, Green RC. Ready or not, genomic screening of fetuses is already here. Genet Med 2024; 26:101008. [PMID: 37860970 PMCID: PMC10842943 DOI: 10.1016/j.gim.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Affiliation(s)
- Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA; Harvard Medical School, Boston, MA.
| | - Allan Nadel
- Harvard Medical School, Boston, MA; Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA; Broad Institute, Boston, MA
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Borrell A, Ordoñez E, Pauta M, Otaño J, Paz-y-Miño F, de Almeida M, León M, Cirigliano V. Prenatal Exome Sequencing Analysis in Fetuses with Various Ultrasound Findings. J Clin Med 2023; 13:181. [PMID: 38202188 PMCID: PMC10780147 DOI: 10.3390/jcm13010181] [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: 10/20/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
OBJECTIVES To evaluate the use of Exome Sequencing (ES) for the detection of genome-wide Copy Number Variants (CNVs) and the frequency of SNVs-InDels in selected genes related to developmental disorders in a cohort of consecutive pregnancies undergoing invasive diagnostic procedures for minor or simple ultrasound findings with no indication of ES. METHODS Women undergoing invasive diagnostic testing (chorionic villus sampling or amniocentesis) for QF-PCR and chromosomal microarray analysis (CMA) due to prenatal ultrasound findings without an indication for ES were selected over a five-month period (May-September 2021). ES was performed to compare the efficiency of genome-wide CNV detection against CMA analysis and to detect monogenic disorders. Virtual gene panels were selected to target genes related to ultrasound findings and bioinformatic analysis was performed, prioritizing variants based on the corresponding HPO terms. The broad Fetal Gene panel for developmental disorders developed by the PAGE group was also included in the analysis. RESULTS A total of 59 out of 61 women consented to participate in this study. There were 36 isolated major fetal anomalies, 11 aneuploidy markers, 6 minor fetal anomalies, 4 multiple anomalies, and 2 other ultrasound signs. Following QF-PCR analysis, two uncultured samples were excluded from this study, and six (10%) common chromosome aneuploidies were detected. In the remaining 51 cases, no pathogenic CNVs were detected at CMA, nor were any pathogenic variants observed in gene panels only targeting the ultrasound indications. Two (3.9%) monogenic diseases, apparently unrelated to the fetal phenotype, were detected: blepharo-cheilo-odontic syndrome (spina bifida) and Duchenne muscular dystrophy (pyelocaliceal dilation). CONCLUSIONS In our series of pregnancies with ultrasound findings, common aneuploidies were the only chromosomal abnormalities present, which were detected in 10% of cases. ES CNV analysis was concordant with CMA results in all cases. No additional findings were provided by only targeting selected genes based on ultrasound findings. Broadening the analysis to a larger number of genes involved in fetal developmental disorders revealed monogenic diseases in 3.9% of cases, which, although apparently not directly related to the indications, were clinically relevant.
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Affiliation(s)
- Antoni Borrell
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Elena Ordoñez
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Montse Pauta
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Juan Otaño
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Fernanda Paz-y-Miño
- Barcelona Centre for Maternal-Fetal and Neonatal Medicine (BCNatal), Hospital Clínic Barcelona, Universitat de Barcelona, 08007 Barcelona, Spain; (J.O.); (F.P.-y.-M.)
| | - Mafalda de Almeida
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Miriam León
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
| | - Vincenzo Cirigliano
- Veritas Genetics, c/Zamora 46-48, 08005 Barcelona, Spain; (E.O.); (M.d.A.); (M.L.); (V.C.)
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Peralta CFA, Medrado AP, Botelho RD, Jorge Rodrigues da Costa K, Imada V, Lamis F. Percutaneous fetal endoscopic third ventriculostomy for severe isolated cerebral ventriculomegaly. Prenat Diagn 2023; 43:1614-1621. [PMID: 37940634 DOI: 10.1002/pd.6465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/25/2023] [Accepted: 10/28/2023] [Indexed: 11/10/2023]
Abstract
OBJECTIVE To demonstrate the feasibility and preliminary results of percutaneous fetal endoscopic third ventriculostomy (ETV) in human fetuses (pfETV) with isolated progressive and/or severe bilateral cerebral ventriculomegaly (IPSBV). METHODS The initial results of pfETV for IPSBV were described. Perioperative, perinatal and postnatal variables were described. The Ages and Stages Questionnaire (ASQ-3), 3rd edition (ASQ-3) was used for follow-up of all infants. RESULTS Successful pfETV was performed in 10/11 (91%) fetuses, at a median gestational age (GA) of 28.7 weeks (25.3-30.7). There were no perioperative complications. After pfETV, 70% (7/10) of the fetuses had a decreased or stabilized lateral ventricle atria|lateral ventricle's atria. The median GA at delivery was 38.2 weeks (35.9-39.3). There were no perinatal complications. The postnatal ventriculoperitoneal shunt rate was 80% (8/10). Among neonates/infants who had prenatal stabilization or a decrease in the LVAs, 4 (4/7: 57.1%) had abnormal scores on the ASQ-3. Among neonates/infants that experienced prenatal increases in the LVAs, all of them (3/3: 100%) had abnormal scores on the ASQ-3. CONCLUSION Percutaneous ETV is feasible in human fetuses with progressive and/or severe cerebral ventriculomegaly and seems to be a safe procedure for both the mother and the fetus.
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Affiliation(s)
- Cleisson Fábio Andrioli Peralta
- Fetal Medicine Unit, HCor Hospital do Coração, São Paulo, Brazil
- Fetal Medicine and Surgery Center (Gestar), São Paulo, Brazil
- Fetal Medicine Unit, CETRUS - São Paulo Ultrasound Training Center, São Paulo, Brazil
| | - Aletea Patrícia Medrado
- Fetal Medicine Unit, HCor Hospital do Coração, São Paulo, Brazil
- Fetal Medicine and Surgery Center (Gestar), São Paulo, Brazil
- Fetal Medicine Unit, CETRUS - São Paulo Ultrasound Training Center, São Paulo, Brazil
| | - Rafael Davi Botelho
- Fetal Medicine Unit, HCor Hospital do Coração, São Paulo, Brazil
- Fetal Medicine and Surgery Center (Gestar), São Paulo, Brazil
| | - Karina Jorge Rodrigues da Costa
- Fetal Medicine Unit, HCor Hospital do Coração, São Paulo, Brazil
- Fetal Medicine and Surgery Center (Gestar), São Paulo, Brazil
| | - Vanessa Imada
- Department of Neurosurgery, HCor Hospital do Coração, São Paulo, Brazil
| | - Fabricio Lamis
- Department of Neurosurgery, HCor Hospital do Coração, São Paulo, Brazil
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Mordaunt DA, Stark Z, Santos Gonzalez F, Dalziel K, Goranitis I. Development of a microcosting protocol to determine the economic cost of diagnostic genomic testing for rare diseases in Australia. BMJ Open 2023; 13:e069441. [PMID: 38030253 PMCID: PMC10689401 DOI: 10.1136/bmjopen-2022-069441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION Genomic testing is a relatively new, disruptive and complex health technology with multiple clinical applications in rare diseases, cancer and infection control. Genomic testing is increasingly being implemented into clinical practice, following regulatory approval, funding and adoption in models of care, particularly in the area of rare disease diagnosis. A significant barrier to the adoption and implementation of genomic testing is funding. What remains unclear is what the cost of genomic testing is, what the underlying drivers of cost are and whether policy differences contribute to cost variance in different jurisdictions, such as the requirement to have staff with a medical license involved in testing. This costing study will be useful in future economic evaluations and health technology assessments to inform optimal levels of reimbursement and to support comprehensive and comparable assessment of healthcare resource utilisation in the delivery of genomic testing globally. METHODS A framework is presented that focuses on uncovering the process of genomic testing for any given laboratory, evaluating its utilisation and unit costs, and modelling the cost drivers and overall expenses associated with delivering genomic testing. The goal is to aid in refining and implementing policies regarding both the regulation and funding of genomic testing. A process-focused (activity-based) methodology is outlined, which encompasses resources, assesses individual cost components through a combination of bottom-up and top-down microcosting techniques and allows disaggregation of resource type and process step. ETHICS AND DISSEMINATION The outputs of the study will be reported at relevant regional genetics and health economics conferences, as well as submitted to a peer-reviewed journal focusing on genomics. Human research ethics committee approval is not required for this microcosting study. This study does not involve research on human subjects, and all data used in the analysis are either publicly available.
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Affiliation(s)
- Dylan A Mordaunt
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Women's and Children's Division, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Australian Genomics Health Alliance, Australia, UK
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Francisco Santos Gonzalez
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kim Dalziel
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
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Miceikaitė I, Hao Q, Brasch-Andersen C, Fagerberg CR, Torring PM, Kristiansen BS, Ousager LB, Sperling L, Ibsen MH, Löser K, Larsen MJ. Comprehensive Noninvasive Fetal Screening by Deep Trio-Exome Sequencing. N Engl J Med 2023; 389:2017-2019. [PMID: 37991863 DOI: 10.1056/nejmc2307918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Affiliation(s)
| | - Qin Hao
- Odense University Hospital, Odense, Denmark
| | | | | | | | | | | | | | - Mette H Ibsen
- University Hospital of Southwestern Jutland, Esbjerg, Denmark
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Moradi B, Ariaei A, Heidari-Foroozan M, Banihashemian M, Ghorani H, Rashidi-Nezhad A, Kazemi MA, Taheri MS. Diagnostic yield of prenatal exome sequencing in the genetic screening of fetuses with brain anomalies detected by MRI and ultrasonography: A systematic review and meta-analysis. BJOG 2023. [PMID: 37932235 DOI: 10.1111/1471-0528.17710] [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: 04/22/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Brain anomalies (BAs) have been the focus of research, as they have a high impact on fetal health but therapeutic and diagnostic approaches are limited. OBJECTIVES In this study, the application and efficiency of exome sequencing (ES) in detecting different cases of BAs in fetuses were evaluated and compared with chromosomal microarray analysis (CMA). SEARCH STRATEGY To conduct this study, three databases including PubMed, Web of Science and Embase were utilised with the keywords 'prenatal', 'diagnoses', 'brain anomalies' and 'exome sequencing'. SELECTION CRITERIA Studies were included based on the STARD checklist, for which the ES and CMA diagnostic yields were calculated. DATA COLLECTION AND ANALYSIS Meta-analysis was performed on the included studies using a random-effects model and subgroup analysis to define the risk difference between them. MAIN RESULTS We included 11 studies representing 779 fetuses that implemented ES along with imaging techniques. The pooled ES diagnostic yield in fetuses with BAs detected through magnetic resonance imaging (MRI) and ultrasonography was 26.53%, compared with 3.46% for CMA. The risk difference between ES and CMA for complex BAs was 0.36 [95% confidence interval (CI) 0.24-0.47], which was higher than for single BAs (0.22; 95% CI 0.18-0.25]. CONCLUSIONS ES is a useful method with a significantly higher diagnostic yield than CMA for genetic assessment of fetuses with complex BAs detected by imaging techniques. Moreover, ES could be applied to suspected fetuses with related family histories to predict congenital diseases with high efficiency.
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Affiliation(s)
- Behnaz Moradi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Yas Complex Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Armin Ariaei
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Heidari-Foroozan
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Banihashemian
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Ghorani
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Centre, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Kazemi
- Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiology, Amiralam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Sanei Taheri
- Department of Radiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Qin Y, Yao Y, Liu N, Wang B, Liu L, Li H, Gao T, Xu R, Wang X, Zhang F, Song J. Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases. BMC Med Genomics 2023; 16:262. [PMID: 37880672 PMCID: PMC10601195 DOI: 10.1186/s12920-023-01697-3] [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: 03/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) significantly improves the diagnosis of the etiology of fetal structural anomalies. This study aims to evaluate the diagnostic value of prenatal WES and to investigate the pathogenic variants in structurally abnormal fetuses. METHODS We recruited 144 fetuses with structural anomalies between 14 and 2020 and 15 December 2021 in the study. Genetic screening was performed by WES combined with karyotyping and chromosomal microarray analysis. The molecular diagnostic yield of prenatal WES for each type of fetal structural anomaly and the identified pathogenic genes and mutations were reported. RESULTS In this study, we retrospectively analyzed the clinical and genetic data of 145 structurally anomalous fetuses. These cases were classified into 9 phenotypic classes based on antenatal ultrasound findings. Thirty-eight pathogenic variants in 24 genes were identified in 35 of the 145 cases, including 14 novel variants in 13 genes (EP300, MYH3, TSC2, MMP9, CPLANE1, INVS, COL1A1, EYA1, TTC21B, MKS1, COL11A2, PDHA1 and L1CAM). Five additional pathogenic variants were classified as incidental findings. Our study showed that the overall diagnosis rate of WES was 28.1% (27/96) in the parent-fetus trio cases and 16.3% (8/49) in the proband-only cases. Fetuses with musculoskeletal anomalies had the highest diagnostic yield (51.4%, 19/37). In addition, FGFR3 and COL1A1 were the most common pathogenic genes. CONCLUSIONS Our work expands the mutation spectrum of the genes associated with fetal structural anomalies and provides valuable information for future parental genetic counselling and pregnancy management of the structurally anomalous fetuses.
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Affiliation(s)
- Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Yanyi Yao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Hui Li
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Tangxinzi Gao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Runhong Xu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Fanglian Zhang
- Honghu Hospital of Traditional Chinese Medicine, Jingzhou, 433200, Hubei Province, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China.
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Sahin-Hodoglugil NN, Lianoglou BR, Ackerman S, Sparks TN, Norton ME. Access to prenatal exome sequencing for fetal malformations: A qualitative landscape analysis in the US. Prenat Diagn 2023; 43:1394-1405. [PMID: 37752660 PMCID: PMC10846391 DOI: 10.1002/pd.6444] [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: 07/07/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023]
Abstract
OBJECTIVE There is increasing evidence supporting the clinical utility of next generation sequencing for identifying fetal genetic disorders. However, there are limited data on the demand for and accessibility of these tests, as well as payer coverage in the prenatal context. We sought to identify clinician perspectives on the utility of prenatal exome sequencing (ES) and on equitable access to genomic technologies for the care of pregnancies complicated by fetal structural anomalies. METHOD We conducted two focus group discussions and six interviews with a total of 13 clinicians (11 genetic counselors; 2 Maternal Fetal Medicine/Geneticists) from U.S. academic centers and community clinics. RESULTS Participants strongly supported ES for prenatal diagnostic testing in pregnancies with fetal structural anomalies. Participants emphasized the value of prenatal ES as an opportunity for a continuum of care before, during, and after a pregnancy, not solely as informing decisions about abortions. Cost and coverage of the test was the main access barrier, and research was the main pathway to access ES in academic centers. CONCLUSION Further integrating the perspectives of additional key stakeholders are important for understanding clinical utility, developing policies and practices to address access barriers, and assuring equitable provision of prenatal diagnostic testing.
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Affiliation(s)
- Nuriye N. Sahin-Hodoglugil
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
- Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
| | - Billie R. Lianoglou
- Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- Division of Surgery, University of California San Francisco, San Francisco, California, USA
| | - Sara Ackerman
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, California, USA
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, California, USA
| | - Teresa N. Sparks
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
- Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
| | - Mary E. Norton
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
- Center for Maternal-Fetal Precision Medicine, University of California San Francisco, San Francisco, California, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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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.
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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)
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Hu P, Zhang Q, Cheng Q, Luo C, Zhang C, Zhou R, Meng L, Huang M, Wang Y, Wang Y, Qiao F, Xu Z. Whole genome sequencing vs chromosomal microarray analysis in prenatal diagnosis. Am J Obstet Gynecol 2023; 229:302.e1-302.e18. [PMID: 36907537 DOI: 10.1016/j.ajog.2023.03.005] [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: 11/03/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND Emerging studies suggest that whole genome sequencing provides additional diagnostic yield of genomic variants when compared with chromosomal microarray analysis in the etiologic diagnosis of infants and children with suspected genetic diseases. However, the application and evaluation of whole genome sequencing in prenatal diagnosis remain limited. OBJECTIVE This study aimed to evaluate the accuracy, efficacy, and incremental yield of whole genome sequencing in comparison with chromosomal microarray analysis for routine prenatal diagnosis. STUDY DESIGN In this prospective study, a total of 185 unselected singleton fetuses with ultrasound-detected structural anomalies were enrolled. In parallel, each sample was subjected to whole genome sequencing and chromosomal microarray analysis. Aneuploidies and copy number variations were detected and analyzed in a blinded fashion. Single nucleotide variations and insertions and deletions were confirmed by Sanger sequencing, and trinucleotide repeats expansion variants were verified using polymerase chain reaction plus fragment-length analysis. RESULTS Overall, genetic diagnoses using whole genome sequencing were obtained for 28 (15.1%) cases. Whole genome sequencing not only detected all these aneuploidies and copy number variations in the 20 (10.8%) diagnosed cases identified by chromosomal microarray analysis, but also detected 1 case with an exonic deletion of COL4A2 and 7 (3.8%) cases with single nucleotide variations or insertions and deletions. In addition, 3 incidental findings were detected including an expansion of the trinucleotide repeat in ATXN3, a splice-sites variant in ATRX, and an ANXA11 missense mutation in a case of trisomy 21. CONCLUSION Compared with chromosomal microarray analysis, whole genome sequencing increased the additional detection rate by 5.9% (11/185). Using whole genome sequencing, we detected not only aneuploidies and copy number variations, but also single nucleotide variations and insertions and deletions, trinucleotide repeat expansions, and exonic copy number variations with high accuracy in an acceptable turnaround time (3-4 weeks). Our results suggest that whole genome sequencing has the potential to be a new promising prenatal diagnostic test for fetal structural anomalies.
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Affiliation(s)
- Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qing Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
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Wilkes C, Graetz M, Downie L, Bethune M, Chong D. Prenatal diagnosis of cleft lip and/or palate: What do we tell prospective parents? Prenat Diagn 2023; 43:1310-1319. [PMID: 37552068 DOI: 10.1002/pd.6418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023]
Abstract
Cleft lip and/or palate (CL/CP) is the most common congenital craniofacial anomaly and parents often ask, "how did this happen?" Patients and families may benefit from access to a multidisciplinary team (MDT) from prenatal diagnosis into early adulthood. Multiple factors can contribute to the development of a cleft. We discuss the epidemiology and risk factors that increase the likelihood of having a newborn with a cleft. The purpose of this article is to review the prenatal investigations involved in the diagnosis and workup of these patients in addition to postpartum treatment, prognostic factors, and counseling families regarding future recurrence risk.
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Affiliation(s)
- Courtney Wilkes
- Department of Plastic and Maxillofacial Surgery, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Melissa Graetz
- Department of Genetics, Mercy Hospital for Women, Melbourne, Victoria, Australia
| | - Lilian Downie
- Department of Genetics, Mercy Hospital for Women, Melbourne, Victoria, Australia
| | - Michael Bethune
- Department of Medical Imaging and Perinatal Medicine, The Mercy Hospital for Women, Melbourne, Victoria, Australia
- Specialist Women's Ultrasound, Melbourne, Victoria, Australia
| | - David Chong
- Department of Plastic and Maxillofacial Surgery, The Royal Children's Hospital, Melbourne, Victoria, Australia
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Kanneganti A, Gosavi AT, Lim MXK, Li WLS, Chia DA, Choolani MA, Chen CK, Biswas A. Fetal congenital heart diseases: Diagnosis by anatomical scans, echocardiography and genetic tests. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2023; 52:420-431. [PMID: 38920167 DOI: 10.47102/annals-acadmedsg.2022472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Objective To determine the distribution of major fetal congenital heart diseases (CHDs) diagnosed antenatally during routine second-trimester obstetric anatomical scans in an unselected population at a single tertiary centre and to characterise and stratify risk factors, genetic diagnosis and long-term health at 4 years old. Method A single-centre cohort study of all major fetal CHDs detected on routine obstetric fetal anatomical ultrasound scans between January 2014 and December 2017 was performed in an unselected population. Demographic details, fetal echocardiogram reports, genetic test results, delivery outcomes and postnatal progress were stratified by CHD subtype. Results Of 20,031 screened pregnancies, 109 pregnancies (0.53%) had major fetal CHDs. The most common subtypes were coarctation of aorta (17.4%), transposition of great arteries (16.5%), and tetralogy of Fallot and univentricular hearts (13.8% each). Of the 60.5% that underwent confirmatory genetic testing-mostly conventional karyotyping and testing for 22q11 microdeletion-about a quarter had abnormalities, of which 22q microdeletion was the most common. We had complete obstetric data in 85 pregnancies (78%), of which 76.5% progressed to live birth. Among these, 92.1% of postnatal echocardiograms concurred with antenatal ones. At 4 years old, 43.2% of offspring had no medical or developmental issues, 20.0% had mild medical or developmental issues, 21.5% had major medical or developmental issues, and 12.3% had deceased. Conclusion Fetal echocardiograms accurately diagnose CHDs. Future studies should evaluate the roles of chromosomal microarray and next-generation sequencing in diagnosing CHD.
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Affiliation(s)
- Abhiram Kanneganti
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Arundhati Tushar Gosavi
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mei Xian Karen Lim
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Wei Ling Sarah Li
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Dawn Ak Chia
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Mahesh Arjandas Choolani
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ching Kit Chen
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Cardiology, Department of Paediatrics, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Arijit Biswas
- Department of Obstetrics and Gynaecology, National University Hospital, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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50
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Miceikaite I, Fagerberg C, Brasch-Andersen C, Torring PM, Kristiansen BS, Hao Q, Sperling L, Ibsen MH, Löser K, Bendsen EA, Ousager LB, Larsen MJ. Comprehensive prenatal diagnostics: Exome versus genome sequencing. Prenat Diagn 2023; 43:1132-1141. [PMID: 37355983 DOI: 10.1002/pd.6402] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
OBJECTIVE This study aimed to assess the diagnostic yield of prenatal genetic testing using trio whole exome sequencing (WES) and trio whole genome sequencing (WGS) in pregnancies with fetal anomalies by comparing the results with conventional chromosomal microarray (CMA) analysis. METHODS A total of 40 pregnancies with fetal anomalies or increased nuchal translucency (NT ≥ 5 mm) were included between the 12th and 21st week of gestation. Trio WES/WGS and CMA were performed in all cases. RESULTS The trio WES/WGS analysis increased the diagnostic yield by 25% in cases with negative CMA results. Furthermore, all six chromosomal aberrations identified by CMA were independently detected by WES/WGS analysis. In total, 16 out of 40 cases obtained a genetic sequence variant, copy number variant, or aneuploidy explaining the phenotype, resulting in an overall WES/WGS diagnostic yield of 40%. WES analysis provided a more reliable identification of mosaic sequence variants than WGS because of its higher sequencing depth. CONCLUSIONS Prenatal WES/WGS proved to be powerful diagnostic tools for fetal anomalies, surpassing the diagnostic yield of CMA. They have the potential to serve as standalone methods for prenatal diagnosis. The study highlighted the limitations of WGS in accurately detecting mosaic variants, which is particularly relevant when analyzing chorionic villus samples.
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Affiliation(s)
- Ieva Miceikaite
- Department of Clinical Research, Clinical Genome Center & Human Genetics Unit, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Charlotte Brasch-Andersen
- Department of Clinical Research, Clinical Genome Center & Human Genetics Unit, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Qin Hao
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Lene Sperling
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Odense University Hospital, Odense, Denmark
| | - Mette Holm Ibsen
- Department of Gynecology and Obstetrics, University Hospital of Southwestern Jutland, Esbjerg, Denmark
| | - Katrin Löser
- Department of Women's Diseases and Births, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Eske Alf Bendsen
- Department of Gynecology and Obstetrics, Kolding University Hospital, Kolding, Denmark
| | - Lilian Bomme Ousager
- Department of Clinical Research, Clinical Genome Center & Human Genetics Unit, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Martin Jakob Larsen
- Department of Clinical Research, Clinical Genome Center & Human Genetics Unit, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
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