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Kratochwila C, Pomar L, Lebon S, Gengler C, Pavlidou DC, Good JM, Kumps C, Sichitiu J. Prenatal Diagnosis of Warsaw Breakage Syndrome: Fetal Compound Heterozygous Variants in the DDX11 Gene Associated With Growth Restriction, Cerebral, and Extra-Cerebral Malformations. Prenat Diagn 2024; 44:1526-1529. [PMID: 39428552 DOI: 10.1002/pd.6684] [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: 07/23/2024] [Revised: 09/04/2024] [Accepted: 09/27/2024] [Indexed: 10/22/2024]
Abstract
Warsaw Breakage Syndrome (WABS) is a rare autosomal recessive cohesinopathy characterized by growth retardation and congenital anomalies. This report aims to highlight the prenatal diagnosis of WABS through ultrasound findings and genetic testing. We report a case of prenatal diagnosis of WABS in a 24-week gestation fetus exhibiting microcephaly, delayed sulcation, short corpus callosum, cerebellar vermis hypoplasia and intrahepatic portal-systemic shunts. The couple had a history of a prior pregnancy termination due to severe intrauterine growth restriction and cerebral malformations. Whole exome sequencing revealed compound heterozygous pathogenic variants [NM_030653.4:c.1403dupT, p.(Ser469Valfs*32) and c.1672C>T, p.(Arg558*)] in the DDX11 gene, consistent with WABS. The same pathogenic variants were identified in the prior terminated fetus upon subsequent analysis. Postmortem examination of the proband confirmed the prenatal ultrasound findings. This case expands the understanding of the prenatal phenotypic spectrum of WABS by identifying specific cerebral and extracerebral anomalies associated with pathogenic variants in the DDX11 gene. Incorporating advanced genetic diagnostics like whole exome sequencing into prenatal care provides valuable information for genetic counseling and management of rare genetic disorders.
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Affiliation(s)
- C Kratochwila
- Ultrasound and Fetal Medicine Unit, Department Woman-Mother-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - L Pomar
- Ultrasound and Fetal Medicine Unit, Department Woman-Mother-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - S Lebon
- Pediatric Neurology Unit, Department Woman-Mother-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - C Gengler
- Department of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - D C Pavlidou
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - J-M Good
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - C Kumps
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - J Sichitiu
- Ultrasound and Fetal Medicine Unit, Department Woman-Mother-Child, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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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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Reilly K, Sonner S, McCay N, Rolnik DL, Casey F, Seale AN, Watson CJ, Kan A, Lai THT, Chung BHY, Diderich KEM, Srebniak MI, Dempsey E, Drury S, Giordano J, Wapner R, Kilby MD, Chitty LS, Mone F. The incremental yield of prenatal exome sequencing over chromosome microarray for congenital heart abnormalities: A systematic review and meta-analysis. Prenat Diagn 2024; 44:821-831. [PMID: 38708840 DOI: 10.1002/pd.6581] [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: 12/11/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVES To determine the incremental yield of prenatal exome sequencing (PES) over standard testing in fetuses with an isolated congenital heart abnormality (CHA), CHA associated with extra-cardiac malformations (ECMs) and CHA dependent upon anatomical subclassification. METHODS A systematic review of the literature was performed using MEDLINE, EMBASE, Web of Science and grey literature January 2010-February 2023. Studies were selected if they included greater than 20 cases of prenatally diagnosed CHA when standard testing (QF-PCR/chromosome microarray/karyotype) was negative. Pooled incremental yield was determined. PROSPERO CRD 42022364747. RESULTS Overall, 21 studies, incorporating 1957 cases were included. The incremental yield of PES (causative pathogenic and likely pathogenic variants) over standard testing was 17.4% (95% CI, 13.5%-21.6%), 9.3% (95% CI, 6.6%-12.3%) and 35.9% (95% CI, 21.0%-52.3%) for all CHAs, isolated CHAs and CHAs associated with ECMs. The subgroup with the greatest yield was complex lesions/heterotaxy; 35.2% (95% CI 9.7%-65.3%). The most common syndrome was Kabuki syndrome (31/256, 12.1%) and most pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease causing genes (114/224, 50.9%). CONCLUSION The likelihood of a monogenic aetiology in fetuses with multi-system CHAs is high. Clinicians must consider the clinical utility of offering PES in selected isolated cardiac lesions.
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Affiliation(s)
- K Reilly
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - S Sonner
- Centre for Public Health, Queens University Belfast, Belfast, UK
| | - N McCay
- Department of Paediatric Cardiology, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - D L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Victoria, Australia
| | - F Casey
- Department of Paediatric Cardiology, Royal Belfast Hospital for Sick Children, Belfast, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - A N Seale
- Department of Paediatric Cardiology, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Cardiovascular Science, University of Birmingham, Birmingham, UK
| | - C J Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - A Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China
| | - T H T Lai
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China
| | - B H Y Chung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - K E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - E Dempsey
- South West Thames Regional Genetics Service, London, UK
- School of Biological and Molecular Sciences, St George's University of London, London, UK
| | - S Drury
- Congenica Ltd, Biodata Innovation Centre, Wellcome Trust Genome Campus, Hinxton, UK
| | - J Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Columbia University Medical Center, New York, New York, USA
| | - R Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Columbia University Medical Center, New York, New York, USA
| | - M D Kilby
- Fetal Medicine Center, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - L S Chitty
- Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - F Mone
- Centre for Public Health, Queens University Belfast, Belfast, UK
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Naito C, Kosar K, Kishimoto E, Pena L, Huang Y, Hao K, Bernieh A, Kasten J, Villa C, Kishnani P, Deeksha B, Gu M, Asai A. Induced pluripotent stem cell (iPSC) modeling validates reduced GBE1 enzyme activity due to a novel variant, p.Ile694Asn, found in a patient with suspected glycogen storage disease IV. Mol Genet Metab Rep 2024; 39:101069. [PMID: 38516405 PMCID: PMC10955421 DOI: 10.1016/j.ymgmr.2024.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Background Glycogen Storage disease type 4 (GSD4), a rare disease caused by glycogen branching enzyme 1 (GBE1) deficiency, affects multiple organ systems including the muscles, liver, heart, and central nervous system. Here we report a GSD4 patient, who presented with severe hepatosplenomegaly and cardiac ventricular hypertrophy. GBE1 sequencing identified two variants: a known pathogenic missense variant, c.1544G>A (p.Arg515His), and a missense variant of unknown significance (VUS), c.2081T>A (p. Ile694Asn). As a liver transplant alone can exacerbate heart dysfunction in GSD4 patients, a precise diagnosis is essential for liver transplant indication. To characterize the disease-causing variant, we modeled patient-specific GBE1 deficiency using CRISPR/Cas9 genome-edited induced pluripotent stem cells (iPSCs). Methods iPSCs from a healthy donor (iPSC-WT) were genome-edited by CRISPR/Cas9 to induce homozygous p.Ile694Asn in GBE1 (iPSC-GBE1-I694N) and differentiated into hepatocytes (iHep) or cardiomyocytes (iCM). GBE1 enzyme activity was measured, and PAS-D staining was performed to analyze polyglucosan deposition in these cells. Results iPSCGBE1-I694N differentiated into iHep and iCM exhibited reduced GBE1 protein level and enzyme activity in both cell types compared to iPSCwt. Both iHepGBE1-I694N and iCMGBE1-I694N showed polyglucosan deposits correlating to the histologic patterns of the patient's biopsies. Conclusions iPSC-based disease modeling supported a loss of function effect of p.Ile694Asn in GBE1. The modeling of GBE1 enzyme deficiency in iHep and iCM cell lines had multi-organ findings, demonstrating iPSC-based modeling usefulness in elucidating the effects of novel VUS in ultra-rare diseases.
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Affiliation(s)
- Chie Naito
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Karis Kosar
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eriko Kishimoto
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Loren Pena
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yilun Huang
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kaili Hao
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anas Bernieh
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jennifer Kasten
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Chet Villa
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Priya Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke Health, Durham, NC, USA
| | - Bali Deeksha
- Department of Pediatrics, Division of Medical Genetics, Duke Health, Durham, NC, USA
| | - Mingxia Gu
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Akihiro Asai
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Makhamreh MM, Shivashankar K, Araji S, Critchlow E, O'Brien BM, Wodoslawsky S, Berger SI, Al-Kouatly HB. RASopathies are the most common set of monogenic syndromes identified by exome sequencing for nonimmune hydrops fetalis: A systematic review and meta-analysis. Am J Med Genet A 2024; 194:e63494. [PMID: 38156365 DOI: 10.1002/ajmg.a.63494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
RASopathies are a group of malformation syndromes known to lead to nonimmune hydrops fetalis (NIHF) in severe presentations. Pathogenic variants can be de novo or parentally inherited. Despite being a known frequent presentation, the fraction of monogenic NIHF cases due to RASopathies is limited in the literature. Also, the specific parental contribution of RASopathies to NIHF is not well described. Our objective was to review pooled exome sequencing (ES) diagnostic yield of RASopathies for NIHF and to determine the parental contribution of RASopathy to NIHF. We performed a systematic review of prenatal ES studies from January 1, 2000 to August 1, 2022. Thirty-six studies met inclusion criteria. Cases with RASopathy gene variants were reviewed. NIHF cases were further classified as isolated or non-isolated. Thirty-six ES studies including 46 pregnancies with NIHF and a diagnosed RASopathy were reviewed. Forty-four diagnostic variants and 2 variants of uncertain significance in 12 RASopathy genes were identified. Expanding on what was previously published, a total of 506 NIHF cases were extracted with 191 cases yielding a positive diagnosis by ES. The overall rate of RASopathy diagnosis in clinically diagnosed NIHF cases was 9% (44/506). The rate of RASopathy diagnosis among NIHF cases with positive genetic diagnosis by ES was 23% (44/191). Of the 46 cases identified, 13 (28%) variants were parentally inherited; specifically, 5/13 (38%) maternal, 3/13 (23%) paternal, 2/13 (15%) biparental, and 3/13 (23%) unspecified. Majority of NIHF cases 29/46 (63%) were isolated. Among NIHF cases with positive ES diagnoses, RASopathy diagnostic yield by ES was 23%. NIHF secondary to RASopathies was parentally inherited in 28% of cases. Most cases of NIHF due to RASopathy were isolated, with no prenatal detection of associated anomalies.
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Affiliation(s)
- Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Sarah Araji
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Mississippi, Jackson, Mississippi, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Barbara M O'Brien
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research and Rare Disease Institute, Children's National Medical Center, Washington, DC, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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Zhao E, Bomback M, Khan A, Murthy SK, Solowiejczyk D, Vora NL, Gilmore KL, Giordano JL, Wapner RJ, Sanna-Cherchi S, Lyford A, Jelin AC, Gharavi AG, Hays T. The expanded spectrum of human disease associated with GREB1L likely includes complex congenital heart disease. Prenat Diagn 2024; 44:343-351. [PMID: 38285371 PMCID: PMC11040453 DOI: 10.1002/pd.6527] [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: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE GREB1L has been linked prenatally to Potter's sequence, as well as less severe anomalies of the kidney, uterus, inner ear, and heart. The full phenotypic spectrum is unknown. The purpose of this study was to characterize known and novel pre- and postnatal phenotypes associated with GREB1L. METHODS We solicited cases from the Fetal Sequencing Consortium, screened a population-based genomic database, and conducted a comprehensive literature search to identify disease cases associated with GREB1L. We present a detailed phenotypic spectrum and molecular changes. RESULTS One hundred twenty-seven individuals with 51 unique pathogenic or likely pathogenic GREB1L variants were identified. 24 (47%) variants were associated with isolated kidney anomalies, 19 (37%) with anomalies of multiple systems, including one case of hypoplastic left heart syndrome, five (10%) with isolated sensorineural hearing loss, two (4%) with isolated uterine agenesis; and one (2%) with isolated tetralogy of Fallot. CONCLUSION GREB1L may cause complex congenital heart disease (CHD) in humans. Clinicians should consider GREB1L testing in the setting of CHD, and cardiac screening in the setting of GREB1L variants.
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Affiliation(s)
- Emily Zhao
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miles Bomback
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarath Krishna Murthy
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David Solowiejczyk
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly L. Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Jessica L. Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alex Lyford
- Department of Mathematics and Statistics, Middlebury College, Middlebury, Vermont, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas Hays
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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Sonner S, Reilly K, Woolf AS, Chandler N, Kilby MD, Maher ER, Flanagan C, McKnight AJ, Mone F. When should we offer antenatal sequencing for urinary tract malformations? A systematic review, cohort study and meta-analysis. Prenat Diagn 2024; 44:187-195. [PMID: 38056891 DOI: 10.1002/pd.6479] [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: 09/11/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
OBJECTIVE Determine the incremental yield of prenatal exome sequencing (PES) over chromosome microarray (CMA) and/or karyotype for urinary tract malformations (UTMs). METHOD A prospective cohort study encompassing data from the English Genomic Medicine Service North Thames Laboratory Hub for fetuses with bilateral echogenic kidneys (BEKs) was combined with data from a systematic review. MEDLINE, EMBASE, Web of Science, MedRxiv and GreyLit were searched from 01/2010-02/2023 for studies reporting on the yield of PES over CMA or karyotype in fetuses with UTMs. Pooled incremental yield was determined using a random effects model. PROSPERO CRD42023364544. RESULTS Fourteen studies (410 cases) were included. The incremental yield for multisystem UTMs, any isolated UTMs, and BEKs was 31% [95% CI, 18%-46%; I2 = 78%], 16% [95% CI, 6%-26%; I2 = 80%] and 51% [95% CI, 27%-75%; I2 = 34%]. The most common clinical diseases and syndromes identified, based on the variant genes detected, were Bardet-Biedl syndrome (BBS genes), dominant and recessive polycystic kidney diseases (PKD1, PKD2 and PKHD1) and renal cysts and diabetes syndrome (HNF1B). CONCLUSION There was a notable incremental genetic diagnostic yield when PES was applied to multisystem UTMs and BEKs. There was a modest incremental yield when this technique was used for UTMs other than BEKs.
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Affiliation(s)
- Sarah Sonner
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Kelly Reilly
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Cheryl Flanagan
- Institute of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Fionnuala Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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Brewer CJ, Makhamreh MM, Shivashankar K, McLaren R, Toro M, Berger SI, Al-Kouatly HB. PIEZO1 is the most common monogenic etiology of non-immune hydrops fetalis detected by prenatal exome sequencing. Prenat Diagn 2023; 43:1556-1566. [PMID: 37902181 DOI: 10.1002/pd.6451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023]
Abstract
OBJECTIVE To clarify the relevance of PIEZO1 variants detected by prenatal exome in the context of non-immune hydrops fetalis (NIHF). METHODS A systematic review of prenatal exome studies from 1/1/2000-8/1/2022 was performed. Thirty-six studies met the inclusion criteria. PIEZO1 variants were categorized by disease mode (dominant (AD) versus recessive (AR)) and classified by the American College of Medical Genetics and Genomics (ACMG) guidelines. RESULTS Twenty-two pregnancies with 35 distinct PIEZO1 variants were included. We deemed PIEZO1 variants to be "likely diagnostic" in 12/22 pregnancies, "possibly diagnostic" in 7/22, and "unlikely diagnostic" in 3/22. In total, 19 of 191 NIHF cases diagnosed by prenatal exome were attributed to PIEZO1. Among likely diagnosed cases, the disease mode was AR in eight and AD in four. PIEZO1 variants causing AR NIHF were characterized by loss of function and isolated NIHF phenotype. PIEZO1 variants causing AD NIHF were characterized by gain of function in red blood cells, scarcity in databases, and sporadic inheritance. Missense variants associated with NIHF were clustered in three domains: transmembrane helical unit 4 (THU4), THU5, and the Cap. CONCLUSION PIEZO1 variants were reported in 10% of NIHF cases diagnosed by prenatal exome, making PIEZO1 the most common single gene reported in NIHF.
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Affiliation(s)
- Casey J Brewer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mona M Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Rodney McLaren
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mariella Toro
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Seth I Berger
- Center for Genetic Medicine Research/Rare Disease Institute, Children's National Medical Center, Washington, District of Columbia, USA
| | - Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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9
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Goumy C, Guy Ouedraogo Z, Soler G, Eymard-Pierre E, Laurichesse H, Delabaere A, Gallot D, Bouchet P, Perthus I, Pebrel-Richard C, Gouas L, Salaun G, Salse J, Véronèse L, Tchirkov A. Optical genome mapping for prenatal diagnosis: A prospective study. Clin Chim Acta 2023; 551:117594. [PMID: 37832906 DOI: 10.1016/j.cca.2023.117594] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
PURPOSE Cytogenetic analysis provides important information for prenatal decision-making and genetic counseling. Optical genome mapping (OGM) has demonstrated its performances in retrospective studies. In our prospective study, we assessed the quality of DNA obtained from cultures of amniotic fluid (AF) and chorionic villi (CV) and evaluated the ability of OGM to detect all clinically relevant aberrations identified by standard methods. METHODS A total of 37 prenatal samples from pregnancies with a fetal anomaly on ultrasound were analyzed prospectively by OGM between January 1, 2021 and June 31, 2022. OGM results were interpreted blindly and compared to the results obtained by standard techniques. RESULTS OGM results were interpretable in 92% of samples. We observed 100% concordance between OGM and karyotype and/or chromosomal microarray results. In addition, OGM identified a median of 30 small (<100 kb) structural variations per case with the involvement of 12 OMIM genes, of which 3 were OMIM morbid genes. CONCLUSION This prospective study showed OGM performed well in detecting genomic alterations in cell cultures from prenatal samples. The place of OGM in relation to CMA or exome sequencing remains to be defined in order to optimize the prenatal diagnostic procedure.
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Affiliation(s)
- Carole Goumy
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France.
| | - Zangbéwendé Guy Ouedraogo
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; Service de Biochimie et Génétique Moléculaire, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Gwendoline Soler
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Eleonore Eymard-Pierre
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Hélène Laurichesse
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Amélie Delabaere
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Denis Gallot
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Pamela Bouchet
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Céline Pebrel-Richard
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Laetitia Gouas
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Gaëlle Salaun
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Jérôme Salse
- UMR 1095 INRAE/UCA Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Genotyping and Sequencing Plateform Gentyane, Clermont-Ferrand, France
| | - Lauren Véronèse
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
| | - Andrei Tchirkov
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
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Greenberg ABW, Mehta NH, Allington G, Jin SC, Moreno-De-Luca A, Kahle KT. Molecular Diagnostic Yield of Exome Sequencing in Patients With Congenital Hydrocephalus: A Systematic Review and Meta-Analysis. JAMA Netw Open 2023; 6:e2343384. [PMID: 37991765 PMCID: PMC10665979 DOI: 10.1001/jamanetworkopen.2023.43384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023] Open
Abstract
Importance Exome sequencing (ES) has been established as the preferred first line of diagnostic testing for certain neurodevelopmental disorders, such as global developmental delay and autism spectrum disorder; however, current recommendations are not specific to or inclusive of congenital hydrocephalus (CH). Objective To determine the diagnostic yield of ES in CH and whether ES should be considered as a first line diagnostic test for CH. Data Sources PubMed, Cochrane Library, and Google Scholar were used to identify studies published in English between January 1, 2010, and April 10, 2023. The following search terms were used to identify studies: congenital hydrocephalus, ventriculomegaly, cerebral ventriculomegaly, primary ventriculomegaly, fetal ventriculomegaly, prenatal ventriculomegaly, molecular analysis, genetic cause, genetic etiology, genetic testing, exome sequencing, whole exome sequencing, genome sequencing, microarray, microarray analysis, and copy number variants. Study Selection Eligible studies included those with at least 10 probands with the defining feature of CH and/or severe cerebral ventriculomegaly that had undergone ES. Studies with fewer than 10 probands, studies of mild or moderate ventriculomegaly, and studies using genetic tests other than ES were excluded. A full-text review of 68 studies was conducted by 2 reviewers. Discrepancies were resolved by consensus. Data Extraction and Synthesis Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and Meta-Analysis of Observational Studies in Epidemiology guidelines were used by 2 reviewers to extract data. Data were synthesized using a random-effects model of single proportions. Data analysis occurred in April 2023. Main Outcomes and Measures The primary outcome was pooled diagnostic yield. Additional diagnostic yields were estimated for specific subgroups on the basis of clinical features, syndromic presentation, and parental consanguinity. For each outcome, a 95% CI and estimate of interstudy heterogeneity (I2 statistic) was reported. Results From 498 deduplicated and screened records, 9 studies with a total of 538 CH probands were selected for final inclusion. The overall diagnostic yield was 37.9% (95% CI, 20.0%-57.4%; I2 = 90.1). The yield was lower for isolated and/or nonsyndromic cases (21.3%; 95% CI, 12.8%-31.0%; I2 = 55.7). The yield was higher for probands with reported consanguinity (76.3%; 95% CI, 65.1%-86.1%; I2 = 0) than those without (16.2%; 95% CI, 12.2%-20.5%; I2 = 0). Conclusions and Relevance In this systematic review and meta-analysis of the diagnostic yield of ES in CH, the diagnostic yield was concordant with that of previous recommendations for other neurodevelopmental disorders, suggesting that ES should also be recommended as a routine diagnostic adjunct for patients with CH.
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Affiliation(s)
| | - Neel H. Mehta
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Garrett Allington
- Department of Neurosurgery, Massachusetts General Hospital, Boston
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri
| | - Andrés Moreno-De-Luca
- Department of Radiology, Neuroradiology Section, Kingston Health Sciences Centre, Queen’s University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Kristopher T. Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Harvard Center for Hydrocephalus and Neurodevelopmental Disorders, Massachusetts General Hospital, Boston
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11
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Slavotinek A, Rego S, Sahin-Hodoglugil N, Kvale M, Lianoglou B, Yip T, Hoban H, Outram S, Anguiano B, Chen F, Michelson J, Cilio RM, Curry C, Gallagher RC, Gardner M, Kuperman R, Mendelsohn B, Sherr E, Shieh J, Strober J, Tam A, Tenney J, Weiss W, Whittle A, Chin G, Faubel A, Prasad H, Mavura Y, Van Ziffle J, Devine WP, Hodoglugil U, Martin PM, Sparks TN, Koenig B, Ackerman S, Risch N, Kwok PY, Norton ME. Diagnostic yield of pediatric and prenatal exome sequencing in a diverse population. NPJ Genom Med 2023; 8:10. [PMID: 37236975 PMCID: PMC10220040 DOI: 10.1038/s41525-023-00353-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The diagnostic yield of exome sequencing (ES) has primarily been evaluated in individuals of European ancestry, with less focus on underrepresented minority (URM) and underserved (US) patients. We evaluated the diagnostic yield of ES in a cohort of predominantly US and URM pediatric and prenatal patients suspected to have a genetic disorder. Eligible pediatric patients had multiple congenital anomalies and/or neurocognitive disabilities and prenatal patients had one or more structural anomalies, disorders of fetal growth, or fetal effusions. URM and US patients were prioritized for enrollment and underwent ES at a single academic center. We identified definitive positive or probable positive results in 201/845 (23.8%) patients, with a significantly higher diagnostic rate in pediatric (26.7%) compared to prenatal patients (19.0%) (P = 0.01). For both pediatric and prenatal patients, the diagnostic yield and frequency of inconclusive findings did not differ significantly between URM and non-URM patients or between patients with US status and those without US status. Our results demonstrate a similar diagnostic yield of ES between prenatal and pediatric URM/US patients and non-URM/US patients for positive and inconclusive results. These data support the use of ES to identify clinically relevant variants in patients from diverse populations.
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Affiliation(s)
- Anne Slavotinek
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Shannon Rego
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nuriye Sahin-Hodoglugil
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Billie Lianoglou
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Tiffany Yip
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Hoban
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Simon Outram
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Beatrice Anguiano
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Flavia Chen
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy Michelson
- Institute of Human Nutrition, Columbia University Medical Center, New York, NY, USA
| | - Roberta M Cilio
- Division of Pediatric Neurology, Department of Pediatrics, University of Louvain, Brussels, Belgium
| | - Cynthia Curry
- Genetic Medicine, University of California, San Francisco, Fresno, CA, USA
| | - Renata C Gallagher
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marisa Gardner
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Rachel Kuperman
- Department of Neurology, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
- Eysz, Inc, Piedmont, CA, USA
| | - Bryce Mendelsohn
- Division of Genetics, Kaiser Permanente Oakland Medical Center, Oakland, CA, USA
| | - Elliott Sherr
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Shieh
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Strober
- Division of Child Neurology, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Allison Tam
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Jessica Tenney
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - William Weiss
- Division of Child Neurology, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Amy Whittle
- Division of Pediatrics, Zuckerberg San Francisco General Hospital, San Francisco, San Francisco, CA, USA
| | - Garrett Chin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Amanda Faubel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Hannah Prasad
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Yusuph Mavura
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Ugur Hodoglugil
- Genomic Medicine Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Pierre-Marie Martin
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Teresa N Sparks
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
| | - Barbara Koenig
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Program in Bioethics, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Ackerman
- Institute for Health & Aging, School of Nursing, University of California San Francisco, San Francisco, CA, USA
- Department of Social & Behavioral Sciences, School of Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, San Francisco, USA
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Larson JK, Hunter‐Schlichting DN, Crowgey EL, Mills LJ, Druley TE, Marcotte EL. KMT2A‐D
pathogenicity, prevalence, and variation according to a population database. Cancer Med 2022; 12:7234-7245. [PMID: 36479909 PMCID: PMC10067056 DOI: 10.1002/cam4.5443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION The KMT2 family of genes is essential epigenetic regulators promoting gene expression. The gene family contains three subgroups, each with two paralogues: KMT2A and KMT2B; KMT2C and KMT2D; KMT2F and KMT2G. KMT2A-D are among the most frequent somatically altered genes in several different cancer types. Somatic KMT2A rearrangements are well-characterized in infant leukemia (IL), and growing evidence supports the role of additional family members (KMT2B, KMT2C, and KMT2D) in leukemogenesis. Enrichment of rare heterozygous frameshift variants in KMT2A and C has been reported in acute myeloid leukemia (AML), IL, and solid tumors. Currently, the non-synonymous variation, prevalence, and penetrance of these four genes are unknown. METHODS This study determined the prevalence of pathogenic/likely pathogenic (P/LP) germline KMT2A-D variants in a cancer-free adult population from the Genome Aggregation Database (gnomAD). Two methods of variant interpretation were utilized: a manual genomic variant interpretation and an automated ACMG pipeline. RESULTS The ACMG pipeline identified considerably fewer P/LP variants (n = 89) compared to the manual method (n = 660) in all 4 genes. Consequently, the total P/LP prevalence and allele frequency (AF) were higher in the manual method (1:112, AF = 4.46E-03) than in ACMG (1:832, AF = 6.01E-04). Multiple ancestry-exclusive P/LP variants were identified along with an increased frequency in males compared to females. Many of these variants identified in this population database are also associated with severe juvenile conditions. CONCLUSION These data demonstrate that putatively functional germline variation in these developmentally important genes is more common than previously appreciated and identification in cancer-free adults may indicate incomplete penetrance for many of these variants. Future research should examine a genetic predisposing role in IL and other pediatric cancers.
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Affiliation(s)
- Jenna K. Larson
- Deparatment of Genetic Counseling University of Minnesota Minneapolis Minnesota USA
| | - DeVon N. Hunter‐Schlichting
- Masonic Cancer Center University of Minnesota Minneapolis Minnesota USA
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
| | | | - Lauren J. Mills
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
| | | | - Erin L. Marcotte
- Masonic Cancer Center University of Minnesota Minneapolis Minnesota USA
- Division of Pediatric Epidemiology and Clinical Research, Department of Pediatrics University of Minnesota Minneapolis Minnesota USA
- Brain Tumor Program University of Minnesota Minneapolis Minnesota USA
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13
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Zhu X, Gao Z, Wang Y, Huang W, Li Q, Jiao Z, Liu N, Kong X. Utility of trio-based prenatal exome sequencing incorporating splice-site and mitochondrial genome assessment in pregnancies with fetal ultrasound anomalies: prospective cohort study. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 60:780-792. [PMID: 35726512 DOI: 10.1002/uog.24974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To evaluate the utility of trio-based prenatal exome sequencing (pES), incorporating splice-site and mitochondrial genome assessment, in the prenatal diagnosis of fetuses with ultrasound anomalies and normal copy-number variant sequencing (CNV-seq) results. METHODS This was a prospective study of 90 ongoing pregnancies with ultrasound anomalies that underwent trio-based pES after receiving normal CNV-seq results, from September 2020 to November 2021, in a single center in China. By using pES with a panel encompassing exome coding and splicing regions as well as mitochondrial genome for fetuses and parents, we identified the underlying genetic causes of fetal anomalies, incidental fetal findings and parental carrier status. Information on pregnancy outcome and the impact of pES findings on parental decision-making was collected. RESULTS Of the 90 pregnancies included, 28 (31.1%) received a diagnostic result that could explain the fetal ultrasound anomalies. The highest diagnostic yield was noted for brain abnormalities (3/6 (50.0%)), followed by hydrops (4/9 (44.4%)) and skeletal abnormalities (13/34 (38.2%)). Collectively, 34 variants of 20 genes were detected in the 28 diagnosed cases, with 55.9% (19/34) occurring de novo. Variants of uncertain significance (VUS) associated with fetal phenotypes were detected in six (6.7%) fetuses. Interestingly, fetal (n = 4) and parental (n = 3) incidental findings (IFs) were detected in seven (7.8%) cases. These included two fetuses carrying a de-novo likely pathogenic (LP) variant of the CIC and FBXO11 genes, respectively, associated with neurodevelopmental disorders, and one fetus with a LP variant in a mitochondrial gene. The remaining fetus presented with unilateral renal dysplasia and was incidentally found to carry a pathogenic PKD1 gene variant resulting in adult-onset polycystic kidney, which was later confirmed to be inherited from the mother. In addition, parental heterozygous variants associated with autosomal recessive diseases were detected in three families, including one with additional fetal diagnostic findings. Diagnostic results or fetal IFs contributed to parental decision-making about termination of the pregnancy in 26 families (26/72 (36.1%)), while negative pES results or identification of VUS encouraged 40 families (40/72 (55.6%)) to continue their pregnancy, which ended in a live birth in all cases. CONCLUSION Trio-based pES can provide additional genetic information for pregnancies with fetal ultrasound anomalies without a CNV-seq diagnosis. The incidental findings and parental carrier status reported by trio-based pES with splice-site and mitochondrial genome analysis extend its clinical application, but careful genetic counseling is warranted. © 2022 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- X Zhu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Gao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Y Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - W Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Q Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z Jiao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - N Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Fu F, Li R, Yu Q, Wang D, Deng Q, Li L, Lei T, Chen G, Nie Z, Yang X, Han J, Pan M, Zhen L, Zhang Y, Jing X, Li F, Li F, Zhang L, Yi C, Li Y, Lu Y, Zhou H, Cheng K, Li J, Xiang L, Zhang J, Tang S, Fang P, Li D, Liao C. Application of exome sequencing for prenatal diagnosis of fetal structural anomalies: clinical experience and lessons learned from a cohort of 1618 fetuses. Genome Med 2022; 14:123. [PMID: 36307859 PMCID: PMC9615232 DOI: 10.1186/s13073-022-01130-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background Exome sequencing (ES) is becoming more widely available in prenatal diagnosis. However, data on its clinical utility and integration into clinical management remain limited in practice. Herein, we report our experience implementing prenatal ES (pES) in a large cohort of fetuses with anomalies detected by ultrasonography using a hospital-based in-house multidisciplinary team (MDT) facilitated by a three-step genotype-driven followed by phenotype-driven analysis framework. Methods We performed pES in 1618 fetal cases with positive ultrasound findings but negative for karyotyping and chromosome microarray analysis between January 2014 and October 2021, including both retrospective (n=565) and prospective (n=1053) cohorts. The diagnostic efficiency and its correlation to organ systems involved, phenotypic spectrum, and the clinical impacts of pES results on pregnancy outcomes were analyzed. Results A genotype-driven followed by phenotype-driven three-step approach was carried out in all trio pES. Step 1, a genotype-driven analysis resulted in a diagnostic rate of 11.6% (187/1618). Step 2, a phenotype-driven comprehensive analysis yielded additional diagnostic findings for another 28 cases (1.7%; 28/1618). In the final step 3, data reanalyses based on new phenotypes and/or clinical requests found molecular diagnosis in 14 additional cases (0.9%; 14/1618). Altogether, 229 fetal cases (14.2%) received a molecular diagnosis, with a higher positive rate in the retrospective than the prospective cohort (17.3% vs. 12.4%, p<0.01). The diagnostic rates were highest in fetuses with skeletal anomalies (30.4%) and multiple organ involvements (25.9%), and lowest in fetuses with chest anomalies (0%). In addition, incidental and secondary findings with childhood-onset disorders were detected in 11 (0.7%) cases. Furthermore, we described the prenatal phenotypes for the first time for 27 gene-associated conditions (20.0%, 27/135) upon a systematic analysis of the diagnosed cases and expanded the phenotype spectrum for 26 (19.3%) genes where limited fetal phenotypic information was available. In the prospective cohort, the combined prenatal ultrasound and pES results had significantly impacted the clinical decisions (61.5%, 648/1053). Conclusions The genotype-driven approach could identify about 81.7% positive cases (11.6% of the total cohort) with the initial limited fetal phenotype information considered. The following two steps of phenotype-driven analysis and data reanalyses helped us find the causative variants in an additional 2.6% of the entire cohort (18.3% of all positive findings). Our extensive phenotype analysis on a large number of molecularly confirmed prenatal cases had greatly enriched our current knowledge on fetal phenotype-genotype correlation, which may guide more focused prenatal ultrasound in the future. This is by far the largest pES cohort study that combines a robust trio sequence data analysis, systematic phenotype-genotype correlation, and well-established MDT in a single prenatal clinical setting. This work underlines the value of pES as an essential component in prenatal diagnosis in guiding medical management and parental decision making. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01130-x.
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Implementation of Exome Sequencing in Prenatal Diagnosis and Impact on Genetic Counseling: The Polish Experience. Genes (Basel) 2022; 13:genes13050724. [PMID: 35627109 PMCID: PMC9140952 DOI: 10.3390/genes13050724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Despite advances in routine prenatal cytogenetic testing, most anomalous fetuses remain without a genetic diagnosis. Exome sequencing (ES) is a molecular technique that identifies sequence variants across protein-coding regions and is now increasingly used in clinical practice. Fetal phenotypes differ from postnatal and, therefore, prenatal ES interpretation requires a large amount of data deriving from prenatal testing. The aim of our study was to present initial results of the implementation of ES to prenatal diagnosis in Polish patients and to discuss its possible clinical impact on genetic counseling. Methods: In this study we performed a retrospective review of all fetal samples referred to our laboratory for ES from cooperating centers between January 2017 and June 2021. Results: During the study period 122 fetuses were subjected to ES at our institution. There were 52 abnormal ES results: 31 in the group of fetuses with a single organ system anomaly and 21 in the group of fetuses with multisystem anomalies. The difference between groups was not statistically significant. There were 57 different pathogenic or likely pathogenic variants reported in 33 different genes. The most common were missense variants. In 17 cases the molecular diagnosis had an actual clinical impact on subsequent pregnancies or other family members. Conclusions: Exome sequencing increases the detection rate in fetuses with structural anomalies and improves genetic counseling for both the affected couple and their relatives.
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