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Aggarwal S, Vineeth VS, Padwal SS, Bhat SA, Singh A, Kulkarni A, Patil M, Tallapaka K, Pasumarthi D, Venkatapuram V, Thotakura PL, Dalal A, Bhandari R. SERPINA11 related novel serpinopathy - A perinatal lethal disorder. Clin Genet 2024. [PMID: 38831697 DOI: 10.1111/cge.14564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
SERPINA11 is a hitherto poorly characterised gene belonging to Clade A of the SERPIN superfamily, with unknown expression pattern and functional significance. We report a perinatal lethal phenotype in two foetuses from the same family associated with a biallelic loss of function variant in SERPINA11, and provide functional evidence to support its candidature as a Mendelian disorder. The SERPINA11 variant-associated foetal phenotype is characterised by gross and histopathological features of extracellular matrix disruption. Western blot and immunofluorescence analyses revealed SERPINA11 expression in multiple mouse tissues, with pronounced expression in the bronchiolar epithelium. We observed a significant decrease in SERPINA11 immunofluorescence in the affected foetal lung compared with a healthy gestation-matched foetus. Protein expression data from HEK293T cell lines following site-directed mutagenesis support the loss of function nature of the variant. Transcriptome analysis from the affected foetal liver indicated the possibility of reduced SERPINA11 transcript abundance. This novel serpinopathy appears to be a consequence of the loss of inhibition of serine proteases involved in extracellular matrix remodelling, revealing SERPINA11 as a protease inhibitor critical for embryonic development.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Venugopal Satidevi Vineeth
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrutika S Padwal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sameer Ahmed Bhat
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Aditya Kulkarni
- Department of Histopathology, Apollo Hospitals, Hyderabad, India
| | - Mallikarjun Patil
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | - Divya Pasumarthi
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vijayasree Venkatapuram
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Pragna Lakshmi Thotakura
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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2
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Skrypnyk C, AlHarmi R. Molecular autopsy by proxy: relevance for genetic counseling in rare genetic disorders. Front Genet 2024; 15:1400295. [PMID: 38859940 PMCID: PMC11163115 DOI: 10.3389/fgene.2024.1400295] [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: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 06/12/2024] Open
Abstract
Background Rare genetic disorders may result in death before a definitive clinical diagnosis is established. Aim This study aims to outline the processes and challenges in managing, from a genetic perspective, couples who lost children affected by rare genetic disorders. Results Six couples who experienced child loss due to rare genetic disorders, seen by the primary author at genetic evaluation and counseling sessions, were retrospectively analyzed. Four out of 6 couples reported consanguinity. Exome and genome sequencing were performed for the parents. Carrier status of two rare lethal metabolic disorders was confirmed in one consanguineous couple. Three couples were carriers of 3 other rare diseases. Variants of LYST, MPV17, HEXB, ITGB4, CD3E, ASPM, TK2, COL11A2, and LAMB3 genes were identified. Six out of 10 were pathogenic variants, out of which 4 correlated with the demised children's phenotypes. One couple was negative for pathogenic variants. The last couple did not undergo genetic testing since they were beyond the fertile window. Conclusion Appropriate parental genetic evaluation and counseling are mandatory for selecting the right genetic test to certify the diagnosis postmortem, by virtue of molecular autopsy by proxy. Clarifying a rare disorder diagnosis can help couples to avoid recurrence and plan early for their next pregnancies.
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Affiliation(s)
- Cristina Skrypnyk
- Assistant Professor, Molecular Genetics, Princess Al-Jawhara Al-Ibrahim Center for Molecular Medicine, Genetics, and Inherited Disorders and Molecular Medicine Department, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
- Consultant Medical Geneticist, University Medical Clinics, Manama, Bahrain
| | - Rawan AlHarmi
- Research Associate, Regenerative Medicine Unit, Arabian Gulf University, Manama, Bahrain
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3
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Garzon JP, Pardo AC, Raski CR, Prada CE. Dandy-Walker malformation in an individual with ABL1 variant. Am J Med Genet A 2024:e63718. [PMID: 38760987 DOI: 10.1002/ajmg.a.63718] [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: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024]
Abstract
Dandy-Walker malformation (DWM) is often sporadic, but there are a growing number of genetic disorders that have been associated with this condition. We present a female individual with a de novo variant in ABL1, c.734A>G (p.Y245), who was diagnosed prenatally with DWM. ABL1-related neurodevelopmental disorder was recently identified but brain malformations have not been well characterized to date. We reviewed the published literature and identified one additional individual with DWM and ABL1-related disorder, which suggests a possible association with this malformation.
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Affiliation(s)
- Jenny P Garzon
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Andrea C Pardo
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Neurology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Carolyn R Raski
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Carlos E Prada
- Division of Genetics, Genomics, and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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4
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Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. ASCC1 structures and bioinformatics reveal a novel Helix-Clasp-Helix RNA-binding motif linked to a two-histidine phosphodiesterase. J Biol Chem 2024; 300:107368. [PMID: 38750793 DOI: 10.1016/j.jbc.2024.107368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Activating signal co-integrator complex 1 (ASCC1) acts with ASCC-ALKBH3 complex in alkylation damage responses. ASCC1 uniquely combines two evolutionarily ancient domains: nucleotide-binding K-Homology (KH) (associated with regulating splicing, transcriptional, and translation) and two-histidine phosphodiesterase (PDE) (associated with hydrolysis of cyclic nucleotide phosphate bonds). Germline mutations link loss of ASCC1 function to spinal muscular atrophy with congenital bone fractures 2 (SMABF2). Herein analysis of The Cancer Genome Atlas (TCGA) suggests ASCC1 RNA overexpression in certain tumors correlates with poor survival, Signatures 29 and 3 mutations, and genetic instability markers. We determined crystal structures of Alvinella pompejana (Ap) ASCC1 and Human (Hs) PDE domain revealing high resolution details and features conserved over 500 million years of evolution. Extending understanding of the KH domain Gly-X-X-Gly sequence motif, we define a novel structural Helix-Clasp-Helix (HCH) nucleotide binding motif and show ASCC1 sequence-specific binding to CGCG-containing RNA. The V-shaped PDE nucleotide binding channel has two His-Φ-Ser/Thr-Φ (HXT) motifs (Φ being hydrophobic) positioned to initiate cyclic phosphate bond hydrolysis. A conserved atypical active-site histidine torsion angle implies a novel PDE substrate. Flexible active site loop and arginine-rich domain linker appear regulatory. Small angle X-ray scattering (SAXS) revealed aligned KH-PDE RNA binding sites with limited flexibility in solution. Quantitative evolutionary bioinformatic analyses of disease and cancer-associated mutations support implied functional roles for RNA binding, phosphodiesterase activity, and regulation. Collective results inform ASCC1 roles in transactivation and alkylation damage responses, its targeting by structure-based inhibitors, and how ASCC1 mutations may impact inherited disease and cancer.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Roopa Thapar
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Altaf H Sarker
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jennifer M Soll
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO 63110, United States
| | - Tanmoy Paul
- Department Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302 United States
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States
| | - Abhishek Asthana
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH, 44195, United States
| | - Miaw-Sheue Tsai
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Ivaylo Ivanov
- Department Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302 United States
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, United States
| | - Robert H Silverman
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH, 44195, United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO 63110, United States
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States.
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Efthymiou S, Scala M, Nagaraj V, Ochenkowska K, Komdeur FL, Liang RA, Abdel-Hamid MS, Sultan T, Barøy T, Van Ghelue M, Vona B, Maroofian R, Zafar F, Alkuraya FS, Zaki MS, Severino M, Duru KC, Tryon RC, Brauteset LV, Ansari M, Hamilton M, van Haelst MM, van Haaften G, Zara F, Houlden H, Samarut É, Nichols CG, Smeland MF, McClenaghan C. Novel loss-of-function variants expand ABCC9-related intellectual disability and myopathy syndrome. Brain 2024; 147:1822-1836. [PMID: 38217872 PMCID: PMC11068106 DOI: 10.1093/brain/awae010] [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: 06/25/2023] [Revised: 11/22/2023] [Accepted: 12/30/2023] [Indexed: 01/15/2024] Open
Abstract
Loss-of-function mutation of ABCC9, the gene encoding the SUR2 subunit of ATP sensitive-potassium (KATP) channels, was recently associated with autosomal recessive ABCC9-related intellectual disability and myopathy syndrome (AIMS). Here we identify nine additional subjects, from seven unrelated families, harbouring different homozygous loss-of-function variants in ABCC9 and presenting with a conserved range of clinical features. All variants are predicted to result in severe truncations or in-frame deletions within SUR2, leading to the generation of non-functional SUR2-dependent KATP channels. Affected individuals show psychomotor delay and intellectual disability of variable severity, microcephaly, corpus callosum and white matter abnormalities, seizures, spasticity, short stature, muscle fatigability and weakness. Heterozygous parents do not show any conserved clinical pathology but report multiple incidences of intra-uterine fetal death, which were also observed in an eighth family included in this study. In vivo studies of abcc9 loss-of-function in zebrafish revealed an exacerbated motor response to pentylenetetrazole, a pro-convulsive drug, consistent with impaired neurodevelopment associated with an increased seizure susceptibility. Our findings define an ABCC9 loss-of-function-related phenotype, expanding the genotypic and phenotypic spectrum of AIMS and reveal novel human pathologies arising from KATP channel dysfunction.
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Affiliation(s)
- Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Marcello Scala
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16147 Genoa, Italy
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Vini Nagaraj
- Center for Advanced Biotechnology and Medicine, and Departments of Pharmacology and Medicine, Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscatway, NJ 08854, USA
| | - Katarzyna Ochenkowska
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), and Department of Neuroscience, Université de Montréal, Montreal H2X 0A9, Quebec, Canada
| | - Fenne L Komdeur
- Section Clinical Genetics, Department of Human Genetics and Amsterdam Reproduction and Development, Amsterdam University Medical Centers, 1105 AZ, Amsterdam, The Netherlands
| | - Robin A Liang
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, 9019 Tromsø, Norway
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Tipu Sultan
- Department of Pediatric Neurology, Children Hospital, University of Child Health Sciences, Lahore, Punjab 54000, Pakistan
| | - Tuva Barøy
- Department of Medical Genetics, Oslo University Hospital, 0450 Oslo, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, 9019 Tromsø, Norway
| | - Barbara Vona
- Institute of Human Genetics and Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Faisal Zafar
- Department of Paediatric Neurology, Children’s Hospital and Institute of Child Health, Multan, Punjab 60000, Pakistan
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | | | - Kingsley C Duru
- Center for Advanced Biotechnology and Medicine, and Departments of Pharmacology and Medicine, Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscatway, NJ 08854, USA
| | - Robert C Tryon
- Department of Cell Biology and Physiology, and Center for the Investigation of Membrane Excitability Diseases (CIMED), Washington University, St Louis, MO 63110, USA
| | - Lin Vigdis Brauteset
- Division of Habilitation for Children, Innlandet Hospital Sanderud, Hamar 2312, Norway
| | - Morad Ansari
- South East Scotland Genetic Service, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Mark Hamilton
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Mieke M van Haelst
- Section Clinical Genetics, Department of Human Genetics and Amsterdam Reproduction and Development, Amsterdam University Medical Centers, 1105 AZ, Amsterdam, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center, Utrecht, 3584 CX, The Netherlands
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Éric Samarut
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), and Department of Neuroscience, Université de Montréal, Montreal H2X 0A9, Quebec, Canada
| | - Colin G Nichols
- Department of Cell Biology and Physiology, and Center for the Investigation of Membrane Excitability Diseases (CIMED), Washington University, St Louis, MO 63110, USA
| | - Marie F Smeland
- Department of Pediatric Rehabilitation, University Hospital of North Norway, 9019 Tromsø, Norway
- Institute of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway
| | - Conor McClenaghan
- Center for Advanced Biotechnology and Medicine, and Departments of Pharmacology and Medicine, Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscatway, NJ 08854, 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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7
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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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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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9
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Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [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: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
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Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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10
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Maksiutenko EM, Barbitoff YA, Nasykhova YA, Pachuliia OV, Lazareva TE, Bespalova ON, Glotov AS. The Landscape of Point Mutations in Human Protein Coding Genes Leading to Pregnancy Loss. Int J Mol Sci 2023; 24:17572. [PMID: 38139401 PMCID: PMC10743817 DOI: 10.3390/ijms242417572] [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: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Pregnancy loss is the most frequent complication of a pregnancy which is devastating for affected families and poses a significant challenge for the health care system. Genetic factors are known to play an important role in the etiology of pregnancy loss; however, despite advances in diagnostics, the causes remain unexplained in more than 30% of cases. In this review, we aggregated the results of the decade-long studies into the genetic risk factors of pregnancy loss (including miscarriage, termination for fetal abnormality, and recurrent pregnancy loss) in euploid pregnancies, focusing on the spectrum of point mutations associated with these conditions. We reviewed the evolution of molecular genetics methods used for the genetic research into causes of pregnancy loss, and collected information about 270 individual genetic variants in 196 unique genes reported as genetic cause of pregnancy loss. Among these, variants in 18 genes have been reported by multiple studies, and two or more variants were reported as causing pregnancy loss for 57 genes. Further analysis of the properties of all known pregnancy loss genes showed that they correspond to broadly expressed, highly evolutionary conserved genes involved in crucial cell differentiation and developmental processes and related signaling pathways. Given the features of known genes, we made an effort to construct a list of candidate genes, variants in which may be expected to contribute to pregnancy loss. We believe that our results may be useful for prediction of pregnancy loss risk in couples, as well as for further investigation and revealing genetic etiology of pregnancy loss.
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Affiliation(s)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
| | | | | | | | | | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, Mendeleevskaya Line 3, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.N.); (O.V.P.); (T.E.L.); (O.N.B.)
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11
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Saxena D, Tiwari AK, Prasad R, Srivastav S. Resolving fetal hydrops - A rare entity. Eur J Med Genet 2023; 66:104888. [PMID: 37993095 DOI: 10.1016/j.ejmg.2023.104888] [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: 05/08/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Non-immune hydrops fetalis (NIHF) is abnormal accumulation of serous fluid in ≥2 interstitial spaces with no evidence of maternal red cell alloimmunization. Leaving a few treatable conditions, it is generally considered as a sign of poor fetal outcome. Bi-allelic variants in THSD1 have been found to be to be associated with phenotypes ranging from lethal NIHF to persistent edema. Here, we report a family with non-immune hydrops in two successive pregnancies. Whole exome sequencing in second pregnancy identified a homozygous truncating variant in THSD1 (NM_018676:c.892G>T:p.Glu298Ter). Postnatal follow up showed gradual resolution of the accumulated fluid and normal development. This report further strengthens the association of variants in THSD1 with NIHF.
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Affiliation(s)
- Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India.
| | - Amit K Tiwari
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Rameshwar Prasad
- Department of Neonatology, Rajendra Institute of Medical Sciences, Ranchi, Jharkhand, India
| | - Saumya Srivastav
- Consultant Fetal Medicine, Sansrishti Clinic, Hazaribagh, Jharkhand, India
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12
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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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13
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Wang Y, Sheng F, Ying L, Lou Q, Yu Z, Wang K, Wang H. CEP55-associated lethal fetal syndrome: a case report of a Chinese family. Front Genet 2023; 14:1267241. [PMID: 37928238 PMCID: PMC10623345 DOI: 10.3389/fgene.2023.1267241] [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: 08/07/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Background: Research on fetal loss related to germline mutations in single genes remains limited. Disruption of CEP55 has recently been established in association with perinatal deaths characterized by hydranencephaly, renal dysplasia, oligohydramnios, and characteristic dysmorphisms. We herein present a Chinese family with recurrent fetal losses due to compound heterozygous nonsense CEP55 variants. Case presentations: The Chinese couple had a history of five pregnancies, with four of them proceeding abnormally. Two stillbirths (II:3 and II:4) sequentially occurred in the third and fourth pregnancy. Prenatal ultrasound scans revealed phenotypic similarities between fetuses II:3 and II:4, including oligohydramnios, bilateral renal dysplasia and hydrocephalus/hydranencephaly. Clubfoot and syndactyly were also present in both stillborn babies. Fetus II:3 presented with endocardial cushion defects while fetus II:4 did not. With the product of conception in the fourth pregnancy, whole exome sequencing (WES) on fetus II:4 identified compound heterozygous nonsense CEP55 variants comprised of c.190C>T(p.Arg64*) and c.208A>T(p.Lys70*). Both variants were expected to result in lack of the TSG101 and ALIX binding domain. Sanger sequencing confirmed the presence and cosegregation of both variants. Conclusion: This is the fifth reported family wherein biallelic CEP55 variants lead to multiple perinatal deaths. Our findings, taken together with previously described phenotypically similar cases and even those with a milder and viable phenotype, broaden the genotypic and phenotypic spectrum of CEP55-associated lethal fetal syndrome, highlighting the vital biomolecular function of CEP55.
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Affiliation(s)
- Yeping Wang
- Jinhua Maternity and Child Health Care Hospital, Jinhua, China
- Jinhua Municipal Central Hospital, Jinhua, China
| | - Fang Sheng
- Jinhua Maternity and Child Health Care Hospital, Jinhua, China
| | | | - Qiaoli Lou
- Wuyi County First People's Hospital, Jinhua, China
| | - Zhaonan Yu
- Medical School of Tianjin University, Tianjin, China
- Hangzhou D. A. Medical Laboratory, Hangzhou, China
| | - Kaixuan Wang
- Jinhua Municipal Central Hospital, Jinhua, China
| | - Haoyi Wang
- Hangzhou D. A. Medical Laboratory, Hangzhou, China
- Precision Diagnosis and Treatment Center of Jinhua City, Jinhua, China
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14
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Alkuraya FS, Gray KJ, Prakash SK, Wojcik MH, Lin AE. Correspondence on "Points to consider in the practice of postmortem genetic testing: A statement of the American College of Medical Genetics and Genomics (ACMG)" by Deignan, et al. Genet Med 2023; 25:100904. [PMID: 37382598 DOI: 10.1016/j.gim.2023.100904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Affiliation(s)
- Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Kathryn J Gray
- Division of Maternal-Fetal Medicine, Brigham and Women's Hospital, Boston, MA
| | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX
| | - Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Angela E Lin
- Medical Genetics, Department of Pediatrics, Mass General for Children, Boston, MA
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15
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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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16
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Monies D, Goljan E, Assoum M, Albreacan M, Binhumaid F, Subhani S, Boureggah A, Hashem M, Abdulwahab F, Abuyousef O, Temsah MH, Alsohime F, Kelaher J, Abouelhoda M, Meyer BF, Alkuraya FS. The clinical utility of rapid exome sequencing in a consanguineous population. Genome Med 2023; 15:44. [PMID: 37344829 DOI: 10.1186/s13073-023-01192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The clinical utility of exome sequencing is now well documented. Rapid exome sequencing (RES) is more resource-intensive than regular exome sequencing and is typically employed in specialized clinical settings wherein urgent molecular diagnosis is thought to influence acute management. Studies on the clinical utility of RES have been largely limited to outbred populations. METHODS Here, we describe our experience with rapid exome sequencing (RES) in a highly consanguineous population. Clinical settings included intensive care units, prenatal cases approaching the legal cutoff for termination, and urgent transplant decisions. RESULTS A positive molecular finding (a pathogenic or likely pathogenic variant that explains the phenotype) was observed in 80 of 189 cases (42%), while 15 (8%) and 94 (50%) received ambiguous (variant of uncertain significance (VUS)) and negative results, respectively. The consanguineous nature of the study population gave us an opportunity to observe highly unusual and severe phenotypic expressions of previously reported genes. Clinical utility was observed in nearly all (79/80) cases with positive molecular findings and included management decisions, prognostication, and reproductive counseling. Reproductive counseling is a particularly important utility in this population where the overwhelming majority (86%) of identified variants are autosomal recessive, which are more actionable in this regard than the de novo variants typically reported by RES elsewhere. Indeed, our cost-effectiveness analysis shows compelling cost savings in the study population. CONCLUSIONS This work expands the diversity of environments in which RES has a demonstrable clinical utility.
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Affiliation(s)
- Dorota Monies
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ewa Goljan
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mirna Assoum
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muna Albreacan
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Faisal Binhumaid
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shazia Subhani
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdulmlik Boureggah
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohamad H Temsah
- Department of Pediatrics, Pediatric Critical Care Unit, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad Alsohime
- Department of Pediatrics, Pediatric Critical Care Unit, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - James Kelaher
- General Corporate Consultancy Department, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Computational Science, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Brian F Meyer
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, MBC-26, PO Box 3354, Riyadh, 11211, Saudi Arabia.
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17
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Bouasker S, Patel N, Greenlees R, Wellesley D, Fares Taie L, Almontashiri NA, Baptista J, Alghamdi MA, Boissel S, Martinovic J, Prokudin I, Holden S, Mudhar HS, Riley LG, Nassif C, Attie-Bitach T, Miguet M, Delous M, Ernest S, Plaisancié J, Calvas P, Rozet JM, Khan AO, Hamdan FF, Jamieson RV, Alkuraya FS, Michaud JL, Chassaing N. Bi-allelic variants in WNT7B disrupt the development of multiple organs in humans. J Med Genet 2023; 60:294-300. [PMID: 35790350 DOI: 10.1136/jmedgenet-2022-108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/11/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Pulmonary hypoplasia, Diaphragmatic anomalies, Anophthalmia/microphthalmia and Cardiac defects delineate the PDAC syndrome. We aim to identify the cause of PDAC syndrome in patients who do not carry pathogenic variants in RARB and STRA6, which have been previously associated with this disorder. METHODS We sequenced the exome of patients with unexplained PDAC syndrome and performed functional validation of candidate variants. RESULTS We identified bi-allelic variants in WNT7B in fetuses with PDAC syndrome from two unrelated families. In one family, the fetus was homozygous for the c.292C>T (p.(Arg98*)) variant whereas the fetuses from the other family were compound heterozygous for the variants c.225C>G (p.(Tyr75*)) and c.562G>A (p.(Gly188Ser)). Finally, a molecular autopsy by proxy in a consanguineous couple that lost two babies due to lung hypoplasia revealed that both parents carry the p.(Arg98*) variant. Using a WNT signalling canonical luciferase assay, we demonstrated that the identified variants are deleterious. In addition, we found that wnt7bb mutant zebrafish display a defect of the swimbladder, an air-filled organ that is a structural homolog of the mammalian lung, suggesting that the function of WNT7B has been conserved during evolution for the development of these structures. CONCLUSION Our findings indicate that defective WNT7B function underlies a form of lung hypoplasia that is associated with the PDAC syndrome, and provide evidence for involvement of the WNT-β-catenin pathway in human lung, tracheal, ocular, cardiac, and renal development.
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Affiliation(s)
- Samir Bouasker
- Research Center, University Hospital Centre Sainte-Justine, Montreal H3T 1C5, Québec, Canada
| | - Nisha Patel
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rebecca Greenlees
- Eye Genetics Research Unit, Children's Medical Research Institute, University of Sydney; The Children's Hospital at Westmead, Sydney Children's Hospitals Network; and Save Sight Institute, Sydney, New South Wales, Australia
| | - Diana Wellesley
- Wessex Clinical Genetic Service, University Hospital Southampton, Southampton, UK
| | - Lucas Fares Taie
- Laboratory Genetics in Ophthalmology, INSERM UMR1163, Imagine Institute for Genetic Diseases, Université Paris Descartes-Sorbonne, Paris, Île-de-France, France
| | - Naif A Almontashiri
- Center for Genetics and Inherited Diseases (CGID), Taibah University, Madinah, Al Madinah, Saudi Arabia.,Research Department, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, Plymouth, UK.,Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Malak Ali Alghamdi
- Medical Genetic Division, Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sarah Boissel
- Research Center, University Hospital Centre Sainte-Justine, Montreal H3T 1C5, Québec, Canada
| | - Jelena Martinovic
- Unit of Fetal Pathology, APHP Hopital Antoine-Beclere, Clamart, Île-de-France, France
| | - Ivan Prokudin
- Eye Genetics Research Unit, Children's Medical Research Institute, University of Sydney; The Children's Hospital at Westmead, Sydney Children's Hospitals Network; and Save Sight Institute, Sydney, New South Wales, Australia
| | - Samantha Holden
- Department of Cellular Pathology, University Hospital Southampton, Southampton, UK
| | - Hardeep-Singh Mudhar
- National Specialist Ophthalmic Pathology Service (NSOPS), Dept of Histopathology, Royal Hallamshire Hospital, Sheffield, UK
| | - Lisa G Riley
- Rare Diseases Functional Genomics Laboratory, The Children's Hospital at Westmead, Sydney Children's Hospitals Network, Children's Medical Research Institute, University of Sydney, Sydney, New South Wales, Australia.,Specialty of Paediatrics and Child Health, Faculty of Medicine and Health, University of Sydney, Sidney, New South Wales, Australia
| | - Christina Nassif
- Research Center, University Hospital Centre Sainte-Justine, Montreal H3T 1C5, Québec, Canada
| | - Tania Attie-Bitach
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute for Genetic Diseases, Paris, Île-de-France, France
| | - Marguerite Miguet
- Research Center, University Hospital Centre Sainte-Justine, Montreal H3T 1C5, Québec, Canada
| | - Marion Delous
- Equipe GENDEV, Centre de Recherche en Neurosciences de Lyon, Inserm U1028, CNRS UMR5292, Université Lyon 1, Université St Etienne, Lyon, Auvergne-Rhône-Alpes, France
| | - Sylvain Ernest
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM UMR 1163, Imagine Institute for Genetic Diseases, Paris, Île-de-France, France
| | - Julie Plaisancié
- Department of Medical Genetics, Purpan University Hospital, Toulouse, Midi-Pyrénées, France.,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, Purpan University Hospital, Toulouse, Midi-Pyrénées, France.,INSERM U1214, ToNIC, Université Toulouse III, Toulouse, France
| | - Patrick Calvas
- Department of Medical Genetics, Purpan University Hospital, Toulouse, Midi-Pyrénées, France.,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, Purpan University Hospital, Toulouse, Midi-Pyrénées, France
| | - Jean-Michel Rozet
- Laboratory Genetics in Ophthalmology, INSERM UMR1163, Imagine Institute for Genetic Diseases, Université Paris Descartes-Sorbonne, Paris, Île-de-France, France
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, Abu Dhabi, UAE
| | - Fadi F Hamdan
- Research Center, University Hospital Centre Sainte-Justine, Montreal H3T 1C5, Québec, Canada
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, University of Sydney; The Children's Hospital at Westmead, Sydney Children's Hospitals Network; and Save Sight Institute, Sydney, New South Wales, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Jacques L Michaud
- Departments of Pediatrics and Neurosciences, Université de Montréal, Montreal H3T 1J4, Québec, Canada .,Departments of Pediatrics and Neurosciences, Université de Montréal, Montreal, Québec, Canada
| | - Nicolas Chassaing
- Department of Medical Genetics, Purpan University Hospital, Toulouse, Midi-Pyrénées, France .,Centre de Référence des Affections Rares en Génétique Ophtalmologique CARGO, Site Constitutif, Purpan University Hospital, Toulouse, Midi-Pyrénées, France
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18
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Al-Kouatly HB, Shivashankar K, Mossayebi MH, Makhamreh M, Critchlow E, Gao Z, Fasehun LK, Alkuraya FS, Ryan EE, Hegde M, Wodoslawsky S, Hughes J, Berger SI. Diagnostic yield from prenatal exome sequencing for non-immune hydrops fetalis: A systematic review and meta-analysis. Clin Genet 2023; 103:503-512. [PMID: 36757664 DOI: 10.1111/cge.14309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Non-immune hydrops fetalis (NIHF) has multiple genetic etiologies diagnosable by exome sequencing (ES). We evaluated the yield of prenatal ES for NIHF, and the contribution of additional clinical findings and history. Systematic review was performed with PROSPERO tag 232951 using CINAHL, PubMed, and Ovid MEDLINE from January 1, 2000 through December 1, 2021. Selected studies performed ES to augment standard prenatal diagnostic approaches. Cases meeting a strict NIHF phenotype were tabulated with structured data imputed from papers or requested from authors. Genetic variants and diagnostic outcomes were harmonized across studies using current ACMG and ClinGen variant classification guidelines. Thirty-one studies reporting 445 NIHF cases had a 37% (95% CI: 32%-41%) diagnostic rate. There was no significant difference between isolated NIHF and NIHF with fetal malformations or between recurrent and simplex cases. Diagnostic rate was higher for consanguineous than non-consanguineous cases. Disease categories included RASopathies (24%), neuromuscular (21%), metabolic (17%), lymphatic (13%), other syndromes (9%), cardiovascular (5%), hematologic (2%), skeletal (2%), and other categories (7%). Inheritance patterns included recessive (55%), dominant (41%), and X-linked (4%). ES should be considered in the diagnostic workup of NIHF with and without associated ultrasound findings regardless of history of recurrence or consanguinity.
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Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kavya Shivashankar
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, Illinois, USA
| | - Matthew H Mossayebi
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Mona Makhamreh
- Department of Obstetrics and Gynecology, Maimonides Medical Center, Brooklyn, New York, USA
| | - Elizabeth Critchlow
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Zimeng Gao
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Luther-King Fasehun
- Department of Epidemiology and Biostatistics, College of Public Health, Temple University, Philadelphia, Pennsylvania, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Erin E Ryan
- Genomic Data / Genetic Counseling, GeneDx, Gaithersburg, Maryland, USA
| | - Madhuri Hegde
- Global Lab Services, PerkinElmer Genomics, Atlanta, Georgia, USA
| | - Sascha Wodoslawsky
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Joel Hughes
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA
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19
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Genomic autopsy to identify underlying causes of pregnancy loss and perinatal death. Nat Med 2023; 29:180-189. [PMID: 36658419 DOI: 10.1038/s41591-022-02142-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/22/2022] [Indexed: 01/21/2023]
Abstract
Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.
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20
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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: 1.0] [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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21
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Alqarawi W, Alsaeed A, Alghamdi M, Hersi A, Kashour T, Aljerian K. Medical Autopsy for Sudden Unexplained Death in Saudi Arabia: A Call to Action. J Saudi Heart Assoc 2022; 34:142-147. [PMID: 36127933 PMCID: PMC9458319 DOI: 10.37616/2212-5043.1310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
Sudden unexplained death (SUD) is a sudden, unexpected, and unexplained death in an individual older than 1 year. It is one of the most devastating and tragic events to families and the community at large, particularly when it happens at a young age. Finding the cause of SUD is extremely important in order to prevent its recurrence in the family, and to help understand the epidemiology of SUD in the community. It has been well-established that the most effective way of finding the cause of SUD is by performing a medical autopsy. In many countries, medical autopsy is mandated in SUD cases. In others, however, medical autopsy is rarely performed for the purpose of identifying the cause of SUD, which is the case in Saudi Arabia. In this review, we discussed the importance of finding the cause of death in SUD cases, the role of different types of medical autopsies, and the state of medical autopsy in Saudi Arabia. Moreover, we proposed a clinical pathway to incorporate medical autopsy in the care of SUD cases, and to connect family members to the health care system in order to perform cascade screening.
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Affiliation(s)
- Wael Alqarawi
- Department of Cardiac Sciences, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulelah Alsaeed
- Department of Cardiac Sciences, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Malak Alghamdi
- Medical Genetics Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Hersi
- Department of Cardiac Sciences, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Tarek Kashour
- Department of Cardiac Sciences, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Khaldoon Aljerian
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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22
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Dawood Y, Honhoff C, van der Post A, Roosendaal SD, Coolen BF, Strijkers GJ, Pajkrt E, de Bakker BS. Comparison of postmortem whole-body contrast-enhanced microfocus computed tomography and high-field magnetic resonance imaging of human fetuses. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2022; 60:109-117. [PMID: 34826157 PMCID: PMC9328149 DOI: 10.1002/uog.24827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Although fetal autopsy is generally recommended to confirm or refute the antemortem diagnosis, parental acceptance of the procedure has fallen over time, mainly due to its invasiveness. Contrast-enhanced microfocus CT (micro-CT) and high-field magnetic resonance imaging (HF-MRI, ≥ 3 Tesla) have both been suggested as non-invasive alternatives to conventional fetal autopsy for fetuses < 20 weeks of gestation. The aim of this study was to compare these two modalities in postmortem whole-body fetal imaging. METHODS In this study, the imaging process and quality of micro-CT and HF-MRI were compared using both qualitative and quantitative assessments. For the qualitative evaluation, fetal anatomy experts scored 56 HF-MRI and 56 micro-CT images of four human fetuses aged 13-18 gestational weeks on two components: overall image quality and the ability to recognize and assess 21 anatomical structures. For the quantitative evaluation, participants segmented manually three organs with increasing complexity to assess interobserver variability. In addition, the signal-to-noise and contrast-to-noise ratios of five major organs were determined. RESULTS Both imaging techniques were able to reach submillimeter voxel size. The highest resolution of micro-CT was 22 µm (isotropic), while the highest resolution of HF-MRI was 137 µm (isotropic). The qualitative image assessment form was sent to 45 fetal anatomy experts, of whom 36 (80%) responded. It was observed that micro-CT scored higher on all components of the qualitative assessment compared with HF-MRI. In addition, the quantitative assessment showed that micro-CT had lower interobserver variability and higher signal-to-noise and contrast-to-noise ratios. CONCLUSIONS Our findings show that micro-CT outperforms HF-MRI in postmortem whole-body fetal imaging in terms of both quantitative and qualitative outcomes. Combined, these findings suggest that the ability to extract diagnostic information is greater when assessing micro-CT compared with HF-MRI images. We, therefore, believe that micro-CT is the preferred imaging modality as an alternative to conventional fetal autopsy for early gestation and is an indispensable tool in postmortem imaging services. © 2021 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)
- Y. Dawood
- Department of Obstetrics and GynecologyAmsterdam UMC, University of AmsterdamAmsterdamThe Netherlands
- Department of Medical Biology, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
| | - C. Honhoff
- Department of Medical Biology, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - A.‐S. van der Post
- Department of Radiology, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - S. D. Roosendaal
- Department of Radiology, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - B. F. Coolen
- Department of Biomedical Engineering and Physics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - G. J. Strijkers
- Department of Biomedical Engineering and Physics, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - E. Pajkrt
- Department of Obstetrics and GynecologyAmsterdam UMC, University of AmsterdamAmsterdamThe Netherlands
- Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
| | - B. S. de Bakker
- Department of Obstetrics and GynecologyAmsterdam UMC, University of AmsterdamAmsterdamThe Netherlands
- Department of Medical Biology, Amsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
- Department of Pediatric Surgery, Erasmus MC – Sophia Children's HospitalUniversity Medical Center RotterdamRotterdamThe Netherlands
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23
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Marais A, Bertoli-Avella AM, Beetz C, Altunoglu U, Alhashem A, Mohamed S, Alghamdi A, Willems P, Tsoutsou E, Fryssira H, Pons R, Almarzooq R, Karatoprak EY, Ayaz A, Ünverengil G, Calvo M, Yüksel Z, Bauer P. Further clinical and genetic evidence of ASC-1 complex dysfunction in congenital neuromuscular disease. Eur J Med Genet 2022; 65:104537. [PMID: 35690317 DOI: 10.1016/j.ejmg.2022.104537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/21/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022]
Abstract
Transcriptional coregulators modulate the efficiency of transcription factors. Bi-allelic variants in TRIP4 and ASCC1, two genes that encode members of the tetrameric coregulator ASC-1, have recently been associated with congenital bone fractures, hypotonia, and muscular dystrophy in a total of 22 unrelated families. Upon exome sequencing and data repository mining, we identified six new patients with pathogenic homozygous variants in either TRIP4 (n = 4, two novel variants) or ASCC1 (n = 2, one novel variant). The associated clinical findings confirm and extend previous descriptions. Considering all patients reported to date, we provide supporting evidence suggesting that ASCC1-related disease has a more severe phenotype compared to TRIP4-related disorder regarding higher incidence of perinatal bone fractures and shorter survival.
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Affiliation(s)
| | | | | | - Umut Altunoglu
- Department of Medical Genetics, Koç University, School of Medicine, 34450, Istanbul, Turkey
| | - Amal Alhashem
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Sarar Mohamed
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Prince Abdullah Bin Khaled Coeliac Disease Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediarics, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abdulaziz Alghamdi
- Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Eirini Tsoutsou
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Helena Fryssira
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Roser Pons
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Reem Almarzooq
- Pediatric Department, Salmaniya Medical Complex, Manama, Bahrain
| | - Elif Yüksel Karatoprak
- Departments of Pediatric Neurology, İstanbul Medeniyet University Faculty of Medicine, Göztepe Training and Research Hospital, İstanbul, Turkey
| | - Akif Ayaz
- Istanbul Medipol University Faculty of Medicine, Department of Medical Genetics, Istanbul, Turkey
| | - Gökçen Ünverengil
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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24
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Saini N, Venkatapuram VS, Vineeth VS, Kulkarni A, Tandon A, Koppolu G, Patil SJ, Dalal A, Aggarwal S. Fetal phenotypes of Mendelian disorders: A descriptive study from India. Prenat Diagn 2022; 42:911-926. [PMID: 35587316 DOI: 10.1002/pd.6172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Exome sequencing(ES) based diagnosis of Mendelian diseases in the fetus is limited by paucity of phenotypic information. This study reports the comprehensive phenotypes of some fetuses with Mendelian disorders. METHODS Next generation technology based sequencing of all coding regions of the genome(Exome sequencing) or targeted gene sequencing using Sanger or next generation platforms was performed in a cohort of deeply phenotyped, cytogenetically normal fetuses with morphological defects. Prenatal ultrasonographic phenotypes and Postmortem details including dysmorphology, histopathology, radiography were ascertained. Novel candidate genes, novel/ unusual findings and unusual genotypes in cases with confirmed Mendelian disorders are described. RESULTS Of the 102 fetuses sequenced, 45 (44%) achieved definitive diagnosis of a Mendelian disorder with 50 pathogenic/likely pathogenic variants. The majority (87%) were autosomal recessive, 69% families were consanguineous and 54% variants were novel. Dysmorphic syndromes, skeletal dysplasias and metabolic disorders were the commonest disease categories, ciliopathies and dystroglycanopathies commonest molecular categories. We describe the first fetal description of six monogenic diseases, and nine cases with novel histological findings. Nineteen cases had novel/ unusual findings. CONCLUSION This cohort demonstrates how deep fetal phenotypes of some Mendelian disorders can show novel/unusual findings which have important implications for prenatal diagnosis of these conditions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Neelam Saini
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | | | | | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Siddaramappa Jagdish Patil
- Division of Medical Genetics, Mazumdar Shaw Medical Center, Narayana Hrudayalaya Hospitals, Bangalore, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting & Diagnostics, Hyderabad, India
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25
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Smogavec M, Gerykova Bujalkova M, Lehner R, Neesen J, Behunova J, Yerlikaya-Schatten G, Reischer T, Altmann R, Weis D, Duba HC, Laccone F. Singleton exome sequencing of 90 fetuses with ultrasound anomalies revealing novel disease-causing variants and genotype-phenotype correlations. Eur J Hum Genet 2022; 30:428-438. [PMID: 34974531 PMCID: PMC8991249 DOI: 10.1038/s41431-021-01012-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 11/08/2022] Open
Abstract
Exome sequencing has been increasingly implemented in prenatal genetic testing for fetuses with morphological abnormalities but normal rapid aneuploidy detection and microarray analysis. We present a retrospective study of 90 fetuses with different abnormal ultrasound findings, in which we employed the singleton exome sequencing (sES; 75 fetuses) or to a lesser extent (15 fetuses) a multigene panel analysis of 6713 genes as a primary tool for the detection of monogenic diseases. The detection rate of pathogenic or likely pathogenic variants in this study was 34.4%. The highest diagnostic rate of 56% was in fetuses with multiple anomalies, followed by cases with skeletal or renal abnormalities (diagnostic rate of 50%, respectively). We report 20 novel disease-causing variants in different known disease-associated genes and new genotype-phenotype associations for the genes KMT2D, MN1, CDK10, and EXOC3L2. Based on our data, we postulate that sES of fetal index cases with a concurrent sampling of parental probes for targeted testing of the origin of detected fetal variants could be a suitable tool to obtain reliable and rapid prenatal results, particularly in situations where a trio analysis is not possible.
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Affiliation(s)
- Mateja Smogavec
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
| | | | - Reinhard Lehner
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Jürgen Neesen
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Jana Behunova
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Gülen Yerlikaya-Schatten
- Division of Obstetrics and Feto-Maternal Medicine, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Theresa Reischer
- Division of Obstetrics and Feto-Maternal Medicine, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Reinhard Altmann
- Department of Prenatal Medicine, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Hans-Christoph Duba
- Department of Medical Genetics, Kepler University Hospital, School of Medicine, Johannes Kepler University, Linz, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
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26
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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27
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Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat Diagn 2022; 42:662-685. [PMID: 35170059 PMCID: PMC9325531 DOI: 10.1002/pd.6115] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/10/2022]
Abstract
Objectives We conducted a systematic review and meta‐analysis to determine the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies, where karyotype/chromosomal microarray (CMA) is normal. Methods Following electronic searches of four databases, we included studies with ≥10 structurally abnormal fetuses undergoing ES or whole genome sequencing. The incremental diagnostic yield of ES over CMA/karyotype was calculated and pooled in a meta‐analysis. Sub‐group analyses investigated effects of case selection and fetal phenotype on diagnostic yield. Results We identified 72 reports from 66 studies, representing 4350 fetuses. The pooled incremental yield of ES was 31% (95% confidence interval (CI) 26%–36%, p < 0.0001). Diagnostic yield was significantly higher for cases pre‐selected for likelihood of monogenic aetiology compared to unselected cases (42% vs. 15%, p < 0.0001). Diagnostic yield differed significantly between phenotypic sub‐groups, ranging from 53% (95% CI 42%–63%, p < 0.0001) for isolated skeletal abnormalities, to 2% (95% CI 0%–5%, p = 0.04) for isolated increased nuchal translucency. Conclusion Prenatal ES provides a diagnosis in an additional 31% of structurally abnormal fetuses when CMA/karyotype is non‐diagnostic. The expected diagnostic yield depends on the body system(s) affected and can be optimised by pre‐selection of cases following multi‐disciplinary review to determine that a monogenic cause is likely.
What's already known about this topic?
Prenatal exome sequencing (ES) increases genetic diagnoses in fetuses with structural abnormalities and a normal karyotype and chromosomal microarray. Published diagnostic yields from ES are varied and may be influenced by study size, case selection and fetal phenotype.
What does this study add?
This study provides a comprehensive systematic review of the literature to date and investigates the diagnostic yield of ES for a range of isolated system anomalies, to support clinical decision‐making on how to offer prenatal ES.
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Affiliation(s)
- Rhiannon Mellis
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | | | - Elizabeth Scotchman
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Lyn S Chitty
- North Thames Genomic Laboratory HubGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Genetics and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
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28
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Kowalczyk K, Smyk M, Bartnik-Głaska M, Plaskota I, Wiśniowiecka-Kowalnik B, Bernaciak J, Chojnacka M, Paczkowska M, Niemiec M, Dutkiewicz D, Kozar A, Magdziak R, Krawczyk W, Pietras G, Michalak E, Klepacka T, Obersztyn E, Bal J, Nowakowska BA. Application of array comparative genomic hybridization (aCGH) for identification of chromosomal aberrations in the recurrent pregnancy loss. J Assist Reprod Genet 2022; 39:357-367. [PMID: 35079943 PMCID: PMC8956756 DOI: 10.1007/s10815-022-02400-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Spontaneous abortion occurs in 8–20% of recognized pregnancies and usually takes place in the first trimester (7–11 weeks). There are many causes of pregnancy loss, but the most important (about 75%) is the presence of chromosomal aberrations. We present the results of oligonucleotide array application in a cohort of 62 miscarriage cases. The inclusion criteria for the study were the loss after 8th week of pregnancy and the appearance of recurrent miscarriages. DNA was extracted from trophoblast or fetal skin fibroblasts. In the 62 tested materials from recurrent miscarriages, the detection rate was 56.5% (35/62). The most commonly found were aneuploidies (65%) (chromosomal trisomy 14, 16, 18, 21, and 22), Turner syndrome, and triploidy (17.1%). Other chromosomal abnormalities included pathogenic and likely pathogenic structural aberrations: 1) pathogenic: deletion 7p22.3p12.3 and duplication 9p24.3p13.2 inherited from the normal father, deletion 3q13.31q22.2 and deletion 3q22.3q23 of unknown inheritance and duplication of 17p12 inherited from father with foot malformation; 2) likely pathogenic variants: deletion 17p13.1 inherited from normal mother, deletion 5q14.3 of unknown inheritance and de novo deletion 1q21.1q21.2. Among these aberrations, six CNVs (copy number variants) were responsible for the miscarriage: deletion 7p22.3p12.3 and duplication 9p24.3p13.2, deletion 3q13.31q22.2 and deletion 3q22.3q23, and deletion 17p13.1 and deletion 1q21.1q21.2. Other two findings were classified as incidental findings (deletion 5q14.3 and 17p12 duplication). Our research shows that 17% of the aberrations (6/35 abnormal results) that cannot be identified by the routine kariotype analysis are structural aberrations containing genes important for fetal development, the mutations of which may cause spontaneous abortion.
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Affiliation(s)
- Katarzyna Kowalczyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Izabela Plaskota
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Marta Chojnacka
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Daria Dutkiewicz
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Agata Kozar
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Róża Magdziak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Wojciech Krawczyk
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Pietras
- Department of Obstetrics and Perinatology, Medical University of Lublin, Lublin, Poland
| | - Elżbieta Michalak
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Teresa Klepacka
- Deparment of Pathomorphology, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Jerzy Bal
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
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29
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Huang X, Fan DS. Autosomal recessive spinocerebellar ataxia type 4 with a VPS13D mutation: A case report. World J Clin Cases 2022; 10:703-708. [PMID: 35097097 PMCID: PMC8771376 DOI: 10.12998/wjcc.v10.i2.703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/03/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autosomal recessive spinocerebellar ataxia type 4 (SCAR4) is a type of SCA that is a group of hereditary diseases characterized by gait ataxia. The main clinical features of SCAR4 are progressive cerebellar ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. To date, many gene dysfunctions have been reported to be associated with SCAR4.
CASE SUMMARY Here, we report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene in a young female Chinese patient. The patient found something wrong with her legs about 10 years ago and presented with the typical characteristics of SCAR4 when she came to the hospital, including ataxia, neuropathy, and positive pyramidal signs. She was then diagnosed with SCAR4 and went home with symptomatic schemes.
CONCLUSION SCAR4 is a hereditary disease characterized by ataxia, pyramidal signs, neuropathy, and macrosaccadic intrusions. We report a novel compound heterozygous mutation, c.3288delA (p.Asp1097ThrfsTer6), in the VPS13D gene, which enriches the gene mutation spectrum and provides additional information about SCAR4.
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Affiliation(s)
- Xin Huang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
| | - Dong-Sheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China
- Municipal Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
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30
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Shamseldin HE, AlAbdi L, Maddirevula S, Alsaif HS, Alzahrani F, Ewida N, Hashem M, Abdulwahab F, Abuyousef O, Kuwahara H, Gao X, Alkuraya FS. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13:161. [PMID: 34645488 PMCID: PMC8511862 DOI: 10.1186/s13073-021-00973-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. METHODS We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. RESULTS The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. CONCLUSIONS Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology, Riyadh, 12354, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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31
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Ali Alghamdi M, Alrasheedi A, Alghamdi E, Adly N, AlAali WY, Alhashem A, Alshahrani A, Shamseldin H, Alkuraya FS, Alfadhel M. Molecular autopsy by proxy in preconception counseling. Clin Genet 2021; 100:678-691. [PMID: 34406647 PMCID: PMC9290025 DOI: 10.1111/cge.14049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 01/06/2023]
Abstract
Monogenic diseases that result in early pregnancy loss or neonatal death are genetically and phenotypically highly variable. This often poses significant challenges in arriving at a molecular diagnosis for reproductive planning. Molecular autopsy by proxy (MABP) refers to the genetic testing of relatives of deceased individuals to deduce the cause of death. Here, we specifically tested couples who lost one or more children/pregnancies with no available DNA. We developed our testing strategy using whole exome sequencing data from 83 consanguineous Saudi couples. We detected the shared carrier state of 50 pathogenic variants/likely pathogenic variants in 43 families and of 28 variants of uncertain significance in 24 families. Negative results were seen in 16 couples after variant reclassification. In 10 families, the risk of more than one genetic disease was documented. Secondary findings were seen in 10 families: either genetic variants with potential clinical consequences for the tested individual or a female carrier for X‐linked conditions. This couple‐based approach has enabled molecularly informed genetic counseling for 52% (43/83 families). Given the predominance of autosomal recessive causes of pregnancy and child death in consanguineous populations, MABP can be a helpful approach to consanguineous couples who seek counseling but lack molecular data on their deceased offspring.
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Affiliation(s)
- Malak Ali Alghamdi
- Medical Genetic Division, Pediatric Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Medical Genetics Division, Department of Pediatrics, King Saud University Medical City, Riyadh, Saudi Arabia
| | - Ameinah Alrasheedi
- Department of Pediatrics, College of Medicine and Medical Sciences, Qassim University, Al Qassim, Saudi Arabia
| | - Esra Alghamdi
- College of Medicine, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nouran Adly
- College of Medicine Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Wajeih Y AlAali
- Dr. Sulaiman Al Habib Medical Group, Riyadh, Saudi Arabia.,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Hanan Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia.,Genetics and Precision Medicine department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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32
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Hurni Y, Marangoni M, Garofalo G, Cassart M, Tomasi L, Vandernoot I, Smits G, Gounongbé C. Spontaneous resolution of nonimmune hydrops fetalis in a fetus with TP63 gene mutation and LZTR1 gene variants. Clin Case Rep 2021; 9:e04624. [PMID: 34401172 PMCID: PMC8353418 DOI: 10.1002/ccr3.4624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
In cases of fetal hydrops, searching for an etiology is essential to evaluate the fetal prognosis and propose the most appropriate management.
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Affiliation(s)
- Yannick Hurni
- Department of Fetal MedicineCHU Saint‐PierreBrusselsBelgium
| | - Martina Marangoni
- Center of Human GeneticsHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
| | | | - Marie Cassart
- Department of Fetal MedicineCHU Saint‐PierreBrusselsBelgium
- Department of RadiologyHôpitaux Iris Sud and CHU Saint‐PierreBrusselsBelgium
| | - Lisa Tomasi
- Department of PediatricsCHU Saint‐PierreBrusselsBelgium
| | - Isabelle Vandernoot
- Center of Human GeneticsHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
| | - Guillaume Smits
- Center of Human GeneticsHôpital ErasmeUniversité Libre de BruxellesBrusselsBelgium
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33
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Wojcik MH, Stadelmaier R, Heinke D, Holm IA, Tan WH, Agrawal PB. The Unrecognized Mortality Burden of Genetic Disorders in Infancy. Am J Public Health 2021; 111:S156-S162. [PMID: 34314210 PMCID: PMC8495634 DOI: 10.2105/ajph.2021.306275] [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] [Accepted: 03/11/2021] [Indexed: 11/04/2022]
Abstract
Objectives. To determine how deaths of infants with genetic diagnoses are described in national mortality statistics. Methods. We present a retrospective cohort study of mortality data, obtained from the National Death Index (NDI), and clinical data for 517 infants born from 2011 to 2017 who died before 1 year of age in the United States. Results. Although 115 of 517 deceased infants (22%) had a confirmed diagnosis of a genetic disorder, only 61 of 115 deaths (53%) were attributed to International Classification of Diseases, 10th Revision codes representing congenital anomalies or genetic disorders (Q00-Q99) as the underlying cause of death because of inconsistencies in death reporting. Infants with genetic diagnoses whose underlying causes of death were coded as Q00-Q99 were more likely to have chromosomal disorders than monogenic conditions (43/61 [70%] vs 18/61 [30%]; P < .001), which reflects the need for improved accounting for monogenic disorders in mortality statistics. Conclusions. Genetic disorders, although a leading cause of infant mortality, are not accurately captured by vital statistics. Public Health Implications. Expanded access to genetic testing and further clarity in death reporting are needed to describe properly the contribution of genetic disorders to infant mortality.
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Affiliation(s)
- Monica H Wojcik
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Rachel Stadelmaier
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Dominique Heinke
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Ingrid A Holm
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Wen-Hann Tan
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
| | - Pankaj B Agrawal
- Monica H. Wojcik and Pankaj B. Agrawal are with the Division of Newborn Medicine and Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA. Rachel Stadelmaier is with the Department of Pediatrics, Boston Children's Hospital and Harvard Medical School. Dominique Heinke is with the Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health and Harvard T. H. Chan School of Public Health, Harvard University, Boston. Ingrid A. Holm and Wen-Hann Tan are with the Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School
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Nestander MA, Berryman K, Brady R, Aden J, Haischer-Rollo G. Differences in Postmortem Investigation Following Perinatal Death. Am J Perinatol 2021; 40:780-787. [PMID: 34126647 DOI: 10.1055/s-0041-1731276] [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] [Indexed: 10/21/2022]
Abstract
OBJECTIVE The study aimed to describe the postmortem investigation patterns for perinatal deaths and compare the degree of investigation between stillbirths and early neonatal deaths. STUDY DESIGN We conducted a single-center retrospective review of all perinatal deaths from 2011 to 2017. Perinatal death was defined as intrauterine fetal death at ≥20 weeks' gestation, plus neonatal deaths within the first 7 days of life. Rates of postmortem investigation were compared. RESULTS There were 97 perinatal deaths, with 54 stillbirths (56%) and 43 neonatal deaths (44%). Stillbirths were significantly more likely to receive autopsy (p = 0.013) and postmortem genetic testing (p = 0.0004) when compared with neonatal deaths. Maternal testing was also more likely in stillbirths than neonatal deaths. A total of 32 deaths (33%) had no postmortem evaluation beyond placental pathology. CONCLUSION Investigation following perinatal death is more likely in stillbirths than neonatal deaths. Methods to improve postmortem investigation following perinatal death are needed, particularly for neonatal deaths. KEY POINTS · Investigation into perinatal death is recommended.. · Rates of investigation remain low.. · Neonatal deaths with less investigation than stillbirths..
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Affiliation(s)
- Matthew A Nestander
- Division of Neonatal, Department of Pediatrics, Carl R. Darnall Army Medical Center, Fort Hood, Texas
| | - Kathryn Berryman
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, Brooke Army Medical Center, Fort Sam Houston, Texas
| | - Robert Brady
- Department of Pathology, Brooke Army Medical Center, Fort Sam Houston, Texas
| | - James Aden
- Department of Graduate Medical Education, Brooke Army Medical Center, Fort Sam Houston, Texas
| | - Gayle Haischer-Rollo
- Department of Pediatrics, Neonatal Division, Brooke Army Medical Center, Fort Sam Houston, Texas
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Abstract
PURPOSE OF REVIEW The current review seeks to provide a comprehensive update on the revolutionary technology of whole exome sequencing (WES) which has been used to interrogate abnormal foetal phenotypes since the last few years, and is changing the paradigms of prenatal diagnosis, facilitating accurate genetic diagnosis and optimal management of pregnancies affected with foetal abnormalities, as well enabling delineation of novel Mendelian disorders. RECENT FINDINGS WES has contributed to identification of more than 1000 Mendelian genes and made rapid strides into clinical diagnostics in recent years. Diagnostic yield of WES in postnatal cohorts has ranged from 25 to 50%, and this test is now a first tier investigation for various clinical presentations. Various abnormal perinatal phenotypes have also been investigated using WES since 2014, with diagnostic yields ranging from 8.5 to 80%. Studies in foetal phenotypes have been challenging and guidelines in this cohort are still evolving. SUMMARY WES has proven to be a disrupting technology, enabling genetic diagnosis for pregnancies complicated by previously unexplained foetal abnormalities, and revealing a significant contribution of single gene disorders in these, thereby changing clinical diagnostic paradigms. The application of this technology in perinatal cohorts is also providing interesting insights into single gene defects presenting as previously unknown genetic syndromes, hence contributing to expansion of Mendelian genetics to encompass various foetal phenotypes.
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Najafi K, Mehrjoo Z, Ardalani F, Ghaderi-Sohi S, Kariminejad A, Kariminejad R, Najmabadi H. Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities. Sci Rep 2021; 11:6952. [PMID: 33772059 PMCID: PMC7997959 DOI: 10.1038/s41598-021-86309-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent miscarriages occur in about 5% of couples trying to conceive. In the past decade, the products of miscarriage have been studied using array comparative genomic hybridization (a-CGH). Within the last decade, an association has been proposed between miscarriages and single or multigenic changes, introducing the possibility of detecting other underlying genetic factors by whole exome sequencing (WES). We performed a-CGH on the products of miscarriage from 1625 Iranian women in consanguineous or non-consanguineous marriages. WES was carried out on DNA extracted from the products of miscarriage from 20 Iranian women in consanguineous marriages and with earlier normal genetic testing. Using a-CGH, a statistically significant difference was detected between the frequency of imbalances in related vs. unrelated couples (P < 0.001). WES positively identified relevant alterations in 11 genes in 65% of cases. In 45% of cases, we were able to classify these variants as pathogenic or likely pathogenic, according to the American College of Medical Genetics and Genomics guidelines, while in the remainder, the variants were classified as of unknown significance. To the best of our knowledge, our study is the first to employ WES on the products of miscarriage in consanguineous families with recurrent miscarriages regardless of the presence of fetal abnormalities. We propose that WES can be helpful in making a diagnosis of lethal disorders in consanguineous couples after prior genetic testing.
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Affiliation(s)
- Kimia Najafi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Zohreh Mehrjoo
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Fariba Ardalani
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Siavash Ghaderi-Sohi
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Ariana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Roxana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Hossein Najmabadi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran.
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran.
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Al-Kouatly HB, Makhamreh MM, Rice SM, Smith K, Harman C, Quinn A, Valcarcel BN, Firman B, Liu R, Hegde M, Critchlow E, Berger SI. High diagnosis rate for nonimmune hydrops fetalis with prenatal clinical exome from the Hydrops-Yielding Diagnostic Results of Prenatal Sequencing (HYDROPS) Study. Genet Med 2021; 23:1325-1333. [PMID: 33686258 DOI: 10.1038/s41436-021-01121-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Nonimmune hydrops fetalis (NIHF) presents as life-threatening fluid collections in multiple fetal compartments and can be caused by both genetic and non-genetic etiologies. We explored incremental diagnostic yield of testing with prenatal exome sequencing (ES) for NIHF following a negative standard NIHF workup. METHODS Participants enrolled into the Hydrops-Yielding Diagnostic Results of Prenatal Sequencing (HYDROPS) study met a strict definition of NIHF and had negative standard-of-care workup. Clinical trio ES from fetal samples and parental blood was performed at a CLIA-certified reference laboratory with clinical reports returned by geneticists and genetic counselors. Negative exomes were reanalyzed with information from subsequent ultrasounds and records. RESULTS Twenty-two fetal exomes reported 11 (50%) diagnostic results and five possible diagnoses (22.7%). Diagnosed cases comprised seven de novodominant disorders, three recessive disorders, and one inherited dominant disorder including four Noonan syndromes (PTPN11, RAF1, RIT1, and RRAS2), three musculoskeletal disorders (RYR1, AMER1, and BICD2), two metabolic disorders (sialidosis and multiple sulfatase deficiency), one Kabuki syndrome, and one congenital anemia (KLF1). CONCLUSION The etiology of NIHF predicts postnatal prognosis and recurrence risk in future pregnancies. ES provides high incremental diagnostic yield for NIHF after standard-of-care testing and should be considered in the workup.
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Affiliation(s)
- Huda B Al-Kouatly
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.
| | - Mona M Makhamreh
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Stephanie M Rice
- Division of Maternal-Fetal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Christopher Harman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea Quinn
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Breanna N Valcarcel
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Brandy Firman
- Department of Obstetrics and Gynecology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | - Elizabeth Critchlow
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Seth I Berger
- Center for Genetic Medicine Research/Rare Disease Institute, Children's National Medical Center, Washington, DC, USA.
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Morton CC. ASHG 2020 Curt Stern Award introduction: Fowzan Sami Alkuraya. Am J Hum Genet 2021; 108:392-394. [PMID: 33667392 DOI: 10.1016/j.ajhg.2020.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.
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Alkuraya FS. 2020 Curt Stern Award address: a more perfect clinical genome-how consanguineous populations contribute to the medical annotation of the human genome. Am J Hum Genet 2021; 108:395-399. [PMID: 33667393 DOI: 10.1016/j.ajhg.2020.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article is based on the address given by the author at the 2020 virtual meeting of the American Society of Human Genetics (ASHG) on October 26, 2020. The video of the original address can be found at the ASHG website.
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Abstract
PURPOSE OF REVIEW Human reproduction is remarkably inefficient; with pregnancy loss occurring in 10-30% of clinically recognized pregnancies. Of those, 3-5% of couples experience recurrent pregnancy loss (RPL), more than 50% of who never receive an underlying diagnosis. Herein, we review evidence that genetic changes, including pathogenic variant(s) in highly penetrant genes, may provide an explanation for a proportion of couples with pregnancy loss. RECENT FINDINGS Genetic abnormalities that may predispose to pregnancy loss include chromosomal aneuploidy, copy number variants, single-gene changes and others. Although previously limited by the need for hypothesis-driven assessment, advancement of various molecular technologies have sheparded in the opportunity to identify molecular cause of highly heterogeneous conditions, including RPL. The identification of causative genetic aberrations associated with RPL demonstrates a promising area of further research. SUMMARY The journey of human development from a single-cell zygote to a term infant is complex process. Early research into copy number variants and highly penetrant single-gene changes may provide diagnosis for a proportion of couples with RPL as well as inform genes critical for early human development.
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Affiliation(s)
- Christina G Tise
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California, USA
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Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
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Abstract
A systematic, effective stillbirth evaluation is important for identification of potential causes of fetal death. Knowledge of potential causes of fetal death facilitates emotional closure for patients and informs recurrence risk as well as future pregnancy management. The highest-yield components of a stillbirth evaluation for finding a cause of fetal death are fetal autopsy, placental pathology, and genetic testing. All patients should be offered these tests following a stillbirth. A clear plan for postpartum follow-up should be made with the patient in order to ensure ongoing support through the grief and recovery process.
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Mastromoro G, Guadagnolo D, Giancotti A, Di Gregorio MG, Marchionni E, Vena F, Lepri FR, Bargiacchi L, Ventriglia F, Di Gioia C, Novelli A, Pizzuti A. Recurrent prenatal PIEZO1-related lymphatic dysplasia: Expanding molecular and ultrasound findings. Eur J Med Genet 2020; 64:104106. [PMID: 33227434 DOI: 10.1016/j.ejmg.2020.104106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/24/2020] [Accepted: 11/15/2020] [Indexed: 12/16/2022]
Abstract
Generalized lymphatic dysplasia (GLD), characterized by lymphedema, lymphangiectasias, chylothorax, effusions, represents a recognized cause of fetal hydrops. We describe for the first time recurrent pregnancies showing different ultrasound presentations of lymphatic dysplasia. The first fetus displayed diffuse subcutaneous cysts and septations while the second one presented fetal hydrops. Exome sequencing results at 18 gestational weeks in the second pregnancy showed compound heterozygosity for two novel PIEZO1 variants, afterwards detected also in the first fetus and in the heterozygous parents. Both ultrasound and genetic findings expand the current knowledge of PIEZO1-related GLD. We suggest exome sequencing in hydropic fetuses with normal cytogenetics and in pregnancies with recurrent hydrops/lymphatic dysplasia.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
| | - Antonella Giancotti
- Department of Maternal and Child Health and Urologic Science, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
| | | | - Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
| | - Flaminia Vena
- Department of Maternal and Child Health and Urologic Science, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
| | | | - Lavinia Bargiacchi
- Department of Radiological, Oncological and Pathological Sciences, Sapienza, University of Rome, Rome, Italy
| | - Flavia Ventriglia
- Department of Pediatrics, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
| | - Cira Di Gioia
- Department of Radiological, Oncological and Pathological Sciences, Sapienza, University of Rome, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Policlinico Umberto I Hospital, Rome, Italy
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A systematic review of monogenic etiologies of nonimmune hydrops fetalis. Genet Med 2020; 23:3-12. [PMID: 33082562 PMCID: PMC7796968 DOI: 10.1038/s41436-020-00967-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Hydrops Fetalis (HF), accumulation of fluid in two or more fetal compartments, is life-threatening to the fetus. Genetic etiologies include many chromosomal and monogenic disorders. Despite this, the clinical workup typically evaluates limited genetic targets. To support broader molecular testing of pregnancies with HF, we cataloged the spectrum of monogenic disorders associated with nonimmune hydrops fetalis (NIHF). We performed a systematic literature review under PROSPERO tag CRD42018099495 of cases reporting NIHF meeting strict phenotypic criteria and well-defined genetic diagnosis. We ranked the evidence per gene based on number of reported cases, phenotype and molecular/biochemical diagnosis. We identified 131 genes with strong evidence for an association with NIHF and 46 genes with emerging evidence spanning the spectrum of multisystem syndromes, cardiac disorders, hematologic disorders, and metabolic disorders. Several genes previously implicated with NIHF did not have any reported cases in the literature with both fetal hydrops and molecular diagnosis. Many genes with strong evidence for association with NIHF would not be detected using current sequencing panels. Nonimmune HF has many possible monogenic etiologies, several with treatment implications, but current diagnostic approaches are not exhaustive. Studies are needed to assess if broad sequencing approaches like whole exome sequencing are useful in clinical management of HF.
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Wojcik MH, Agrawal PB. Deciphering congenital anomalies for the next generation. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005504. [PMID: 32826208 PMCID: PMC7552931 DOI: 10.1101/mcs.a005504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Congenital anomalies are common, with 2%-3% of infants estimated to have at least one major congenital malformation and countless others with minor malformations of lesser cosmetic or medical importance. As congenital malformations are major drivers of morbidity and mortality, representing the leading cause of infant mortality in the United States, there is substantial interest in understanding the underlying etiologies-particularly if modifiable causes may be identified or pre- or postnatal treatments can be offered. Recent research has begun to reveal the spectrum of monogenic disorders that commonly result in birth defects, and newer approaches have revealed non-Mendelian genetic contributions including gene-environment interactions. Our experience suggests that increased efforts to sequence and analyze cases of perinatal death, as well as continued global collaboration, will be essential in understanding the genomic landscape of structural anomalies.
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Affiliation(s)
- Monica H Wojcik
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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Yatsenko SA, Rajkovic A. Genetics of human female infertility†. Biol Reprod 2020; 101:549-566. [PMID: 31077289 DOI: 10.1093/biolre/ioz084] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/17/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
About 10% of women of reproductive age are unable to conceive or carry a pregnancy to term. Female factors alone account for at least 35% of all infertility cases and comprise a wide range of causes affecting ovarian development, maturation of oocytes, and fertilization competence, as well as the potential of a fertilized egg for preimplantation development, implantation, and fetal growth. Genetic abnormalities leading to infertility in females comprise large chromosome abnormalities, submicroscopic chromosome deletion and duplications, and DNA sequence variations in the genes that control numerous biological processes implicated in oogenesis, maintenance of ovarian reserve, hormonal signaling, and anatomical and functional development of female reproductive organs. Despite the great number of genes implicated in reproductive physiology by the study of animal models, only a subset of these genes is associated with human infertility. In this review, we mainly focus on genetic alterations identified in humans and summarize recent knowledge on the molecular pathways of oocyte development and maturation, the crucial role of maternal-effect factors during embryogenesis, and genetic conditions associated with ovarian dysgenesis, primary ovarian insufficiency, early embryonic lethality, and infertility.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Magee-Womens Research Institute, Pittsburgh, PA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Aleksandar Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA.,Institute of Human Genetics, University of California San Francisco, San Francisco, CA
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47
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Affiliation(s)
- Monica H Wojcik
- From the Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston
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48
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Stanley KE, Giordano J, Thorsten V, Buchovecky C, Thomas A, Ganapathi M, Liao J, Dharmadhikari AV, Revah-Politi A, Ernst M, Lippa N, Holmes H, Povysil G, Hostyk J, Parker CB, Goldenberg R, Saade GR, Dudley DJ, Pinar H, Hogue C, Reddy UM, Silver RM, Aggarwal V, Allen AS, Wapner RJ, Goldstein DB. Causal Genetic Variants in Stillbirth. N Engl J Med 2020; 383:1107-1116. [PMID: 32786180 PMCID: PMC7604888 DOI: 10.1056/nejmoa1908753] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND In the majority of cases, the cause of stillbirth remains unknown despite detailed clinical and laboratory evaluation. Approximately 10 to 20% of stillbirths are attributed to chromosomal abnormalities. However, the causal nature of single-nucleotide variants and small insertions and deletions in exomes has been understudied. METHODS We generated exome sequencing data for 246 stillborn cases and followed established guidelines to identify causal variants in disease-associated genes. These genes included those that have been associated with stillbirth and strong candidate genes. We also evaluated the contribution of 18,653 genes in case-control analyses stratified according to the degree of depletion of functional variation (described here as "intolerance" to variation). RESULTS We identified molecular diagnoses in 15 of 246 cases of stillbirth (6.1%) involving seven genes that have been implicated in stillbirth and six disease genes that are good candidates for phenotypic expansion. Among the cases we evaluated, we also found an enrichment of loss-of-function variants in genes that are intolerant to such variation in the human population (odds ratio, 2.15; 95% confidence interval [CI], 1.46 to 3.06). Loss-of-function variants in intolerant genes were concentrated in genes that have not been associated with human disease (odds ratio, 2.22; 95% CI, 1.41 to 3.34), findings that differ from those in two postnatal clinical populations that were also evaluated in this study. CONCLUSIONS Our findings establish the diagnostic utility of clinical exome sequencing to evaluate the role of small genomic changes in stillbirth. The strength of the novel risk signal (as generated through the stratified analysis) was similar to that in known disease genes, which indicates that the genetic cause of stillbirth remains largely unknown. (Funded by the Institute for Genomic Medicine.).
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Affiliation(s)
- Kate E Stanley
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Jessica Giordano
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Vanessa Thorsten
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Christie Buchovecky
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Amanda Thomas
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Mythily Ganapathi
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Jun Liao
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Avinash V Dharmadhikari
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Anya Revah-Politi
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Michelle Ernst
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Natalie Lippa
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Halie Holmes
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Gundula Povysil
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Joseph Hostyk
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Corette B Parker
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Robert Goldenberg
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - George R Saade
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Donald J Dudley
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Halit Pinar
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Carol Hogue
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Uma M Reddy
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Robert M Silver
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Vimla Aggarwal
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Andrew S Allen
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Ronald J Wapner
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - David B Goldstein
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
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Abstract
Many genetic disorders are detectable in the prenatal period, and the capacity to identify them has increased remarkably as molecular genetic testing techniques continue to improve and become incorporated into clinical practice. The indications for prenatal genetic testing vary widely, including follow-up of an anomaly found by routine ultrasound or maternal aneuploidy screening, a family history of genetic disease, advanced maternal or paternal age, or evaluation of a low-risk pregnancy due to parental concern. The interpretation of genetic variants identified in the prenatal period poses unique challenges due to the lack of ability for deep phenotyping as well as the option to make critical decisions regarding pregnancy continuation and perinatal management. In this review, we address the various modalities currently available and commonly used for genetic testing, including preimplantation genetic testing of embryos, cell-free DNA testing, and diagnostic procedures such as chorionic villous sampling, amniocentesis, or percutaneous umbilical blood sampling, from which samples may be sent for a wide variety of genetic tests. We discuss the difference between these modalities for the genetic diagnosis of a fetus, their strengths and weaknesses, and strategies for their optimal use in order to direct perinatal care.
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KIAA1109 gene mutation in surviving patients with Alkuraya-Kučinskas syndrome: a review of literature. BMC MEDICAL GENETICS 2020; 21:136. [PMID: 32590954 PMCID: PMC7318400 DOI: 10.1186/s12881-020-01074-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022]
Abstract
Background Alkuraya-Kučinskas syndrome is an autosomal recessive disorder characterized by brain abnormalities associated with cerebral parenchymal underdevelopment, arthrogryposis, club foot and global developmental delay. KIAA1109, a functionally uncharacterized gene is identified as the molecular cause for Alkuraya-Kučinskas syndrome. Most of the reported mutations in KIAA1109 gene result in premature termination of pregnancies or neonatal deaths while a few mutations have been reported in surviving patients with global developmental delay and intellectual disability. To our knowledge, only three surviving patients from two families have been reported with missense variants in KIAA1109. In this study, we describe four surviving patients from two related families (a multiplex family) with global developmental delay and mild to severe intellectual disability with no other systemic manifestations. There were no miscarriages or neonatal deaths reported in these families. Methods X-chromosome exome panel sequencing was carried out in one patient and whole exome sequencing was carried out on the remaining three affected individuals and the unaffected father of the index family. Data analysis was carried out followed by variant filtering and segregation analysis. Sanger sequencing was carried out to validate the segregation of mutation in all four affected siblings and unaffected parents from both families. Results A novel homozygous missense mutation in a conserved region of KIAA1109 protein was identified. Sanger sequencing confirmed the segregation of mutation in both families in an autosomal recessive fashion. Conclusion Our study is the second study reporting a KIAA1109 variant in surviving patients with Alkuraya-Kučinskas syndrome. Our study expands the spectrum of phenotypic features and mutations associated with Alkuraya-Kučinskas syndrome.
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