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Xue H, Yu A, Chen L, Guo Q, Zhang L, Lin N, Chen X, Xu L, Huang H. Prenatal genetic diagnosis of fetuses with dextrocardia using whole exome sequencing in a tertiary center. Sci Rep 2024; 14:16266. [PMID: 39009665 PMCID: PMC11251054 DOI: 10.1038/s41598-024-67164-w] [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: 01/31/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
To evaluate the genetic etiology of fetal dextrocardia, associated ultrasound anomalies, and perinatal outcomes, we investigated the utility of whole exome sequencing (WES) for prenatal diagnosis of dextrocardia. Fetuses with dextrocardia were prospectively collected between January 2016 and December 2022. Trio-WES was performed on fetuses with dextrocardia, following normal karyotyping and/or chromosomal microarray analysis (CMA) results. A total of 29 fetuses with dextrocardia were collected, including 27 (93.1%) diagnosed with situs inversus totalis and 2 (6.9%) with situs inversus partialis. Cardiac malformations were present in nine cases, extra-cardiac anomalies were found in seven cases, and both cardiac and extra-cardiac malformations were identified in one case. The fetal karyotypes and CMA results of 29 cases were normal. Of the 29 cases with dextrocardia, 15 underwent WES, and the other 14 cases refused. Of the 15 cases that underwent WES, clinically relevant variants were identified in 5/15 (33.3%) cases, including the diagnostic variants DNAH5, DNAH11, LRRC56, PEX10, and ZIC3, which were verified by Sanger sequencing. Of the 10 cases with non-diagnostic results via WES, eight (80%) chose to continue the pregnancies. Of the 29 fetuses with dextrocardia, 10 were terminated during pregnancy, and 19 were live born. Fetal dextrocardia is often accompanied by cardiac and extra-cardiac anomalies, and fetal dextrocardia accompanied by situs inversus is associated with a high risk of primary ciliary dyskinesia. Trio-WES is recommended following normal karyotyping and CMA results because it can improve the diagnostic utility of genetic variants of fetal dextrocardia, accurately predict fetal prognosis, and guide perinatal management and the reproductive decisions of affected families.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
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Schubert C, Milverton J, Goodall S, Merlin T. A systematic review to assess the utility of genomic autopsy using exome or genome sequencing in cases of congenital anomalies and perinatal death. Genet Med 2024; 26:101159. [PMID: 38704678 DOI: 10.1016/j.gim.2024.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
PURPOSE Exome or genome sequencing (ES or GS) can identify genetic causes of otherwise unexplained congenital anomaly and perinatal death (PND) but is not routine practice. The evidence base for "genomic autopsy" after termination of pregnancy for fetal anomaly (TOPFA) and PND has been synthesized to determine the value of this investigation. METHODS We conducted a systematic review and meta-analysis of studies meeting prespecified inclusion criteria and containing ≥10 cases of TOPFA or PND (with or without major congenital abnormality), in which ES or GS was conducted. We determined test performance, including diagnostic yield, accuracy, and reliability. We also reported outcomes associated with clinical utility and harms, where described. RESULTS From 2245 potentially eligible studies, 32 publications were eligible and had data extracted, representing 2120 cases that could be meta-analyzed. No diagnostic accuracy or comparative studies were identified, although some analysis of concordance between different ES/GS methodologies could be performed. Studies reporting parent-related outcomes or long-term follow-up did not do so in a systematic or quantifiable manner. CONCLUSION Evidence suggests that approximately one-fourth to one-third of fetal losses associated with TOPFA or unexplained PND are associated with a genetic cause identifiable on ES or GS-albeit this estimate varies depending on phenotypic and background risk factors. Despite the large body of evidence on ES and GS, little research has attempted to validate the accuracy of testing, nor measure the clinical or societal outcomes in families that follow the diagnostic investigation in this context.
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Affiliation(s)
- Camille Schubert
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Milverton
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Goodall
- Centre for Health Economics Research and Evaluation, Faculty of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Tracy Merlin
- Adelaide Health Technology Assessment (AHTA), School of Public Health, University of Adelaide, Adelaide, SA, Australia
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Zhang F, Guo H, Zhou X, Deng Z, Xu Q, Wang Q, Yuan H, Luo J. Novel PIP5K1C variant identified in a Chinese pedigree with lethal congenital contractural syndrome 3. BMC Pediatr 2024; 24:182. [PMID: 38491417 PMCID: PMC10941444 DOI: 10.1186/s12887-024-04674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Biallelic pathogenic variants in PIP5K1C (MIM #606,102) lead to lethal congenital contractural syndrome 3 (LCCS3, MIM #611,369), a rare autosomal recessive genetic disorder characterized by small gestational age, severe multiple joint contractures and muscle atrophy, early death due to respiratory failure. Currently, 5 individuals with LCCS3 were reported and 5 pathogenic variants in PIP5K1C were identified. Here, we reported the two fetuses in a Chinese pedigree who displayed multiple joint contractures and other congenital anomalies. METHODS Trio-based whole-exome sequencing (WES) was performed for the parents and the recent fetus to detect the genetic cause for fetus phenotype. RESULTS A novel variant, NM_012398.3: c.949_952dup, p.S318Ifs*28 and a previously reported variant, c.688_689del, p.G230Qfs*114 (ClinVar database) in PIP5K1C, were detected in the individuals, and these variants were inherited from the mother and father, respectively. We described the features of multiple joint contractures in our fetuses, including bilateral talipes equinovarus, stiffness in the limbs, extended knees, persistently closed hands and overlapping fingers, which have not been delineated detailedly in previously reported LCCS3 individuals. Furthermore, novel phenotype, bilateral dilated lateral ventricles, was revealed in one fetus. CONCLUSIONS These findings expanded the genetic variant spectrum of PIP5K1C and enriched the clinical features of LCCS3, which will help with the prenatal diagnosis and genetic counseling for this family.
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Affiliation(s)
- Fang Zhang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Hongmei Guo
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Xinlong Zhou
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Key Laboratory for Precision Diagnosis and Treatment of Severe Infectious Diseases in Children, Dongguan, 523120, China
| | - Zhengxi Deng
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Qiuhong Xu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Qingming Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
| | - Jianhua Luo
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
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Liu F, Dai L, Li Z, Yin’s X. Novel variants of NEK9 associated with neonatal arthrogryposis: Two case reports and a literature review. Front Genet 2023; 13:989215. [PMID: 36712877 PMCID: PMC9879004 DOI: 10.3389/fgene.2022.989215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Objective: Pathogenic variants in NEK9 (MIM: 609798) have been identified in patients with lethal congenital contracture syndrome 10 (OMIM: 617022) and arthrogryposis, Perthes disease, and upward gaze palsy (APUG and OMIM: 614262). The shared core phenotype is multiple joint contractures or arthrogryposis. In the present study, three novel variants of NEK9 associated with neonatal arthrogryposis were reported. Methods: The clinical data of two premature infants and their parents were collected. The genomic DNA was extracted from their peripheral blood samples and subjected to trio-whole-exome sequencing (trio-WES) and copy number variation analysis. Results: Using trio-WES, a total of three novel pathogenic variants of NEK9 were detected in the two families. Patient 1 carried compound heterozygous variations of c.717C > A (p. C239*741) and c.2824delA (p.M942Cfs*21), which were inherited from his father and mother, respectively. Patient 2 also carried compound heterozygous variations of c.61G > T (p. E21*959) and c. 2824delA (p. M942Cfs*21), which were inherited from his father and mother, respectively. These variants have not been previously reported in the ClinVar, HGMD, or gnomAD databases. Conclusion: This is the first report about NEK9-related arthrogryposis in neonatal patients. The findings from this study suggest that different types of mutations in NEK9 lead to different phenotypes. Our study expanded the clinical phenotype spectrum and gene spectrum of NEK9-associated arthrogryposis.
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Affiliation(s)
- Fang Liu
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China,*Correspondence: Fang Liu,
| | - Liying Dai
- Department of Neonatology, Anhui Children’s Hospital, Hefei, China
| | - Zhi Li
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China
| | - Xiaowei Yin’s
- Department of Pediatrics, NICU, the 980th Hospital of the People’s Liberation Army Joint Service Support Force, Bethune International Peace Hospital, Shijiazhuang, China
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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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Falb RJ, Müller AJ, Klein W, Grimmel M, Grasshoff U, Spranger S, Stöbe P, Gauck D, Kuechler A, Dikow N, Schwaibold EMC, Schmidt C, Averdunk L, Buchert R, Heinrich T, Prodan N, Park J, Kehrer M, Sturm M, Kelemen O, Hartmann S, Horn D, Emmerich D, Hirt N, Neumann A, Kristiansen G, Gembruch U, Haen S, Siebert R, Hentze S, Hoopmann M, Ossowski S, Waldmüller S, Beck-Wödl S, Gläser D, Tekesin I, Distelmaier F, Riess O, Kagan KO, Dufke A, Haack TB. Bi-allelic loss-of-function variants in KIF21A cause severe fetal akinesia with arthrogryposis multiplex. J Med Genet 2023; 60:48-56. [PMID: 34740919 PMCID: PMC9811090 DOI: 10.1136/jmedgenet-2021-108064] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/14/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fetal akinesia (FA) results in variable clinical presentations and has been associated with more than 166 different disease loci. However, the underlying molecular cause remains unclear in many individuals. We aimed to further define the set of genes involved. METHODS We performed in-depth clinical characterisation and exome sequencing on a cohort of 23 FA index cases sharing arthrogryposis as a common feature. RESULTS We identified likely pathogenic or pathogenic variants in 12 different established disease genes explaining the disease phenotype in 13 index cases and report 12 novel variants. In the unsolved families, a search for recessive-type variants affecting the same gene was performed; and in five affected fetuses of two unrelated families, a homozygous loss-of-function variant in the kinesin family member 21A gene (KIF21A) was found. CONCLUSION Our study underlines the broad locus heterogeneity of FA with well-established and atypical genotype-phenotype associations. We describe KIF21A as a new factor implicated in the pathogenesis of severe neurogenic FA sequence with arthrogryposis of multiple joints, pulmonary hypoplasia and facial dysmorphisms. This hypothesis is further corroborated by a recent report on overlapping phenotypes observed in Kif21a null piglets.
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Affiliation(s)
- Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Petra Stöbe
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Darja Gauck
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | | | - Luisa Averdunk
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University Dusseldorf, Dusseldorf, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Natalia Prodan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Denise Horn
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dirk Emmerich
- Practice for Ultrasound and Prenatal Medicine, Freiburg, Germany
| | - Nina Hirt
- Institute of Human Genetics, University Medical Center Freiburg, Freiburg, Germany
| | | | - Glen Kristiansen
- Institute of Pathology, Center for Integrated Oncology, University of Bonn, Bonn, Germany
| | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University Hospital Bonn, Bonn, Germany
| | - Susanne Haen
- Institute of Pathology and Neuropathology, University of Tuebingen, Tuebingen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | | | - Markus Hoopmann
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | | | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University Dusseldorf, Dusseldorf, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
| | - Karl-Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
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Gómez-Conde S, Dunand O, Hummel A, Morinière V, Gauthier M, Mesnard L, Heidet L. Bi-allelic pathogenic variants in ITGA8 cause slowly progressive renal disease of unknown etiology. Clin Genet 2023; 103:114-118. [PMID: 36089563 DOI: 10.1111/cge.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Integrin Subunit Alpha 8 gene (ITGA8) encodes an integrin chain that is known to be critical in the early stage of the kidney development. Bi-allelic pathogenic variants in ITGA8 are associated with bilateral renal agenesis, as well as anomalies involving urogenital system. Here, we report two unrelated patients presenting with slowly progressing chronic kidney disease associated with bilateral renal hypodysplasia carrying homozygous loss of function variants in the ITGA8 gene. These results broaden the clinical and genotypic spectrum of ITGA8 defects, revealing the high and unexpected degree of phenotypic heterogeneity of this autosomal recessive disease. Our study emphasizes the usefulness of Next-Generation Sequencing in unraveling the genetic cause of chronic kidney disease of unknown etiology, and raises the question of genetic modifiers involved in the variation of the phenotypes associated with autosomal recessive ITGA8 pathogenic variants.
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Affiliation(s)
- Sara Gómez-Conde
- APHP-Centre, Service de Néphrologie Pédiatrique, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Universitaire Necker-Enfants malades, Institut Imagine, Université Paris-Cité, Paris, France
| | - Olivier Dunand
- Service de Néphrologie Pédiatrique, Centre Hospitalier Universitaire Felix Guyon, Saint Denis, France
| | - Aurélie Hummel
- APHP-Centre, Service de Néphrologie, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Universitaire Necker-Enfants malades, Paris, France
| | - Vincent Morinière
- APHP-Centre, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Universitaire Necker-Enfants malades, Paris, France
| | - Marion Gauthier
- Service de Néphrologie et Dialyse, Hôpital André Grégoire, Montreuil, France
| | - Laurent Mesnard
- APHP-Sorbonne Université, Département de Néphrologie, Hôpital Tenon, Service des Soins Intensifs Néphrologiques et Rein Aigu (SINRA), Paris, France
| | - Laurence Heidet
- APHP-Centre, Service de Néphrologie Pédiatrique, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Universitaire Necker-Enfants malades, Institut Imagine, Université Paris-Cité, Paris, France
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8
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Berkay EG, Şoroğlu CV, Kalaycı T, Uyguner ZO, Akçapınar GB, Başaran S. A new enrichment approach for candidate gene detection in unexplained recurrent pregnancy loss and implantation failure. Mol Genet Genomics 2023; 298:253-272. [PMID: 36385415 DOI: 10.1007/s00438-022-01972-5] [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: 06/11/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022]
Abstract
Recurrent pregnancy loss (RPL) and implantation failure (RIF) are obstacles to livebirth and multifactorial conditions in which nearly half of the cases remain unexplained, and we aimed to identify maternal candidate gene variants and pathways for RPL and RIF by analyzing whole-exome sequencing (WES) data via a new detailed bioinformatics approach. A retrospective cohort study was applied to 35 women with normal chromosomal configuration diagnosed with unexplained RPL and/or RIF. WES and comprehensive bioinformatics analyses were performed. Published gene expression datasets (n = 46) were investigated for candidate genes. Variant effects on protein structure were analyzed for 12 proteins, and BUB1B was visualized in silico. WES and bioinformatics analyses are effective and applicable for studying URPL and RIF to detect mutations, as we suggest new candidates to explain the etiology. Forty-three variants in 39 genes were detected in 29 women, 7 of them contributing to oligogenic inheritance. These genes were related to implantation, placentation, coagulation, metabolism, immune system, embryological development, cell cycle-associated processes, and ovarian functions. WES, genomic variant analyses, expression data, and protein configuration studies offer new and promising ways to investigate the etiology of URPL and RIF. Discovering etiology-identifying genetic factors can help manage couples' needs and develop personalized therapies and new pharmaceutical products in the future. The classical approach with chromosomal analysis and targeted gene panel testing is insufficient in these cases; the exome data provide a promising way to detect and understand the possible clinical effects of the variant and its alteration on protein structure.
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Affiliation(s)
- Ezgi Gizem Berkay
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, 34093, Istanbul, Turkey. .,Department of Basic Sciences, Dentistry Faculty, Istanbul Kent University, 34433, Istanbul, Turkey.
| | - Can Veysel Şoroğlu
- Department of Medical Biotechnology, Institute of Health Sciences, Acıbadem Mehmet Ali Aydınlar University, 34684, Istanbul, Turkey
| | - Tuğba Kalaycı
- Division of Medical Genetics, Department of Internal Medicine, Istanbul Medical Faculty, Istanbul University, 34093, Istanbul, Turkey
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, 34093, Istanbul, Turkey
| | - Günseli Bayram Akçapınar
- Department of Medical Biotechnology, Institute of Health Sciences, Acıbadem Mehmet Ali Aydınlar University, 34684, Istanbul, Turkey
| | - Seher Başaran
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, 34093, Istanbul, Turkey
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Premadeva I, Gardham A, Faller A, Selkirk L. Fifteen-minute consultation: How to approach the withdrawal of neonatal intensive care. Arch Dis Child Educ Pract Ed 2022; 107:338-343. [PMID: 34045287 DOI: 10.1136/archdischild-2021-321667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/03/2022]
Abstract
Withdrawal of life-sustaining support on the neonatal unit presents a set of unique challenges specific in this age group of patients. This article aims to provide an overview of the key factors that should be considered during this process. It explores the practicalities of care delivery that reflects the psychological impact of undergoing end-of-life care on parents and team members. It will also highlight the role of clinical genetics that can be used to understand the underlying disease pathology and therefore can be a valuable tool in the difficult decision-making process.
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Affiliation(s)
- Irnthu Premadeva
- Neonatal Unit, Luton and Dunstable Hospital NHS Foundation Trust, Luton, UK
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, London, UK
| | - Adele Faller
- Neonatal Unit, Luton and Dunstable Hospital NHS Foundation Trust, Luton, UK
| | - Lisa Selkirk
- Neonatal Unit, Luton and Dunstable Hospital NHS Foundation Trust, Luton, UK
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Walczak-Sztulpa J, Wawrocka A, Sikora W, Pawlak M, Bukowska-Olech E, Kopaczewski B, Urzykowska A, Arts HH, Gotz-Więckowska A, Grenda R, Latos-Bieleńska A, Glazar R. WDR35 variants in a cranioectodermal dysplasia patient with early onset end-stage renal disease and retinal dystrophy. Am J Med Genet A 2022; 188:3071-3077. [PMID: 35875935 DOI: 10.1002/ajmg.a.62903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/31/2023]
Abstract
Cranioectodermal dysplasia (CED) is rare heterogeneous condition. It belongs to a group of disorders defined as ciliopathies and is associated with defective cilia function and structure. To date six genes have been associated with CED. Here we describe a 4-year-old male CED patient whose features include dolichocephaly, multi-suture craniosynostosis, epicanthus, frontal bossing, narrow thorax, limb shortening, and brachydactyly. The patient presented early-onset chronic kidney disease and was transplanted at the age of 2 years and 5 months. At the age of 3.5 years a retinal degeneration was diagnosed. Targeted sequencing by NGS revealed the presence of compound heterozygous variants in the WDR35 gene. The variants are a novel missense change in exon 9 p.(Gly303Arg) and a previously described nonsense variant in exon 18 p.(Leu641*). Our findings suggest that patients with WDR35 defects may be at risk to develop early-onset retinal degeneration. Therefore, CED patients with pathogenic variation in this gene should be assessed at least once by the ophthalmologist before the age of 4 years to detect early signs of retinal degeneration.
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Affiliation(s)
| | - Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Weronika Sikora
- Students' Scientific Society of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Pawlak
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Bartłomiej Kopaczewski
- Department of Neurosurgery, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Urzykowska
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Heleen H Arts
- Department of Pathology and Laboratory Medicine, Dalhousie University, Halifax, Nova Scotia, Canada.,IWK Health Centre, Clinical Genomics Laboratory, Halifax, Nova Scotia, Canada
| | - Anna Gotz-Więckowska
- Department of Ophthalmology, Poznan University of Medical Sciences, Poznan, Poland
| | - Ryszard Grenda
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Renata Glazar
- Centers for Medical Genetics GENESIS, Poznan, Poland
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11
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Najjar D, Chikhaoui A, Zarrouk S, Azouz S, Kamoun W, Nassib N, Bouchoucha S, Yacoub-Youssef H. Combining Gene Mutation with Expression of Candidate Genes to Improve Diagnosis of Escobar Syndrome. Genes (Basel) 2022; 13:genes13101748. [PMID: 36292632 PMCID: PMC9601381 DOI: 10.3390/genes13101748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/24/2022] Open
Abstract
Escobar syndrome is a rare, autosomal recessive disorder that affects the musculoskeletal system and the skin. Mutations in the CHRNG and TPM2 genes are associated with this pathology. In this study, we conducted a clinical and genetic investigation of five patients and also explored via in silico and gene expression analysis their phenotypic variability. In detail, we identified a patient with a novel composite heterozygous variant of the CHRNG gene and two recurrent mutations in both CHRNG and TPM2 in the rest of the patients. As for the clinical particularities, we reported a list of modifier genes in a patient suffering from myopathy. Moreover, we identified decreased expression of IGF-1, which could be related to the short stature of Escobar patients, and increased expression of POLG1 specific to patients with TPM2 mutation. Through this study, we identified the genetic spectrum of Escobar syndrome in the Tunisian population, which will allow setting up genetic counseling and prenatal diagnosis for families at risk. In addition, we highlighted relevant biomarkers that could differentiate between patients with different genetic defects.
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Affiliation(s)
- Dorra Najjar
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Sinda Zarrouk
- Genomics Platform, Institut Pasteur de Tunis (IPT), Tunis-Belvédère, Tunis 1002, Tunisia
| | - Saifeddine Azouz
- Genomics Platform, Institut Pasteur de Tunis (IPT), Tunis-Belvédère, Tunis 1002, Tunisia
| | - Wafa Kamoun
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Nabil Nassib
- Service Orthopédie Pédiatrique, Hôpital d’Enfant Béchir Hamza, Tunis 1000, Tunisia
| | - Sami Bouchoucha
- Service Orthopédie Pédiatrique, Hôpital d’Enfant Béchir Hamza, Tunis 1000, Tunisia
| | - Houda Yacoub-Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
- Correspondence:
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12
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Yang L, Li X, Zhu X, Gu N, Dai Y. Novel ADAMTS13 mutation in a family with three recurrent neonatal deaths: a case report and literature review. Transl Pediatr 2022; 11:766-773. [PMID: 35685080 PMCID: PMC9173869 DOI: 10.21037/tp-22-114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upshaw-Schulman syndrome (USS) is rare, autosomal recessive, hereditary thrombotic thrombocytopenic purpura (TTP) caused by variants in a disintegrin-like and metalloprotease with thrombospondin type 1 motif (ADAMTS13). USS has a heterogeneous clinical course, and most symptoms overlap with other diseases. Early diagnosis may have important implications for the patients. We found novel ADAMTS13 mutation and explored the clinical features and prognosis of newborn-onset USS to increase awareness of the disease. CASE DESCRIPTION The same, non-consanguineous couple had three unexplained neonatal deaths. The symptoms of the three infants were mainly severe jaundice, anemia and thrombocytopenia after birth, which was consistent with the reported USS symptoms of neonates and died rapidly suddenly in the during rescue efforts. By using whole-exome sequencing (WES) for the study family, we found a novel heterozygous compound in ADAMTS13 (c.1187 (exon10) G>A (p.C396Y)/c.1595 (exon14) G>T (p.C532F)) that was carried by the three newborns originating from father and mother respectively. We reviewed nine published studies of newborn-onset USS and compared our cases for clinical symptoms and laboratory testing. All nine published cases were diagnosed by ADAMTS13 activity; in seven cases gene mutation analysis was performed and eight cases were still alive at the time of publication. CONCLUSIONS The case has added clinicians' awareness of the diagnosis and treatment of USS. A novel rare mutation in ADAMTS13 broadens the spectrum of genetic causes of this rare disorder and expands the phenotypic spectrum.
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Affiliation(s)
- Ling Yang
- Department of Neonatology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinan Li
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiangyu Zhu
- Prenatal Diagnosis Center of Jiangsu Province, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ning Gu
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yimin Dai
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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13
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Van den Veyver IB, Chandler N, Wilkins-Haug L, Wapner RJ, Chitty LS. International Society for Prenatal Diagnosis Updated Position Statement on the use of genome-wide sequencing for prenatal diagnosis. Prenat Diagn 2022; 42:796-803. [PMID: 35583085 PMCID: PMC11220784 DOI: 10.1002/pd.6157] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022]
Abstract
The research and clinical use of genome-wide sequencing for prenatal diagnosis of fetuses at risk for genetic disorders have rapidly increased in recent years. Current data indicate that the diagnostic rate is comparable and for certain indications higher than that of standard testing by karyotype and chromosomal microarray. Responsible clinical implementation and diagnostic use of prenatal sequencing depends on standardized laboratory practices and detailed pre-test and post-test counseling. This Updated Position Statement on behalf of the International Society for Prenatal Diagnosis recommends best practices for the clinical use of prenatal exome and genome sequencing from an international perspective. We include several new points for consideration by researchers and clinical service and laboratory providers.
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Affiliation(s)
- Ignatia B. Van den Veyver
- Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine
- Texas Children’s Hospital, Houston TX 77030, USA
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, WC1N 3JH, UK
| | - Louise Wilkins-Haug
- Division of Maternal-Fetal Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ronald J. Wapner
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, WC1N 3JH, UK
- Genetics and Genomics, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
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14
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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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15
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Kotecha UH, Mistri M, Rayabarapu P, Shah P, Shah N. The diagnostic utility of exome-based carrier screening in families with a positive family history. Am J Med Genet A 2022; 188:1323-1333. [PMID: 34997808 DOI: 10.1002/ajmg.a.62633] [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: 04/27/2021] [Revised: 10/15/2021] [Accepted: 12/26/2021] [Indexed: 11/09/2022]
Abstract
Identification of disease-causing variants in families with a history of a suspected recessive disorder is essential for appropriate counseling and reproductive decision making. The present case series depicts the utility of whole exome-based phenotypes-driven carrier analysis in 14 families with a positive family history. A phenotype-based analysis revealed a putative diagnostic yield of 71.4%. Proband sample, though insufficient, was available in only one family, which allowed the diagnosis to be confirmed. In the remaining nine families, despite the detection of heterozygous pathogenic/likely pathogenic variants, only a putative diagnosis was possible due to incomplete proband phenotyping as well as nonavailability of proband samples. We describe the youngest known patient homozygous for a likely pathogenic variant in PPP1R21. He is currently asymptomatic at 7 days of life and has a simplified gyral pattern on neuroimaging. The case series, though small, captures the challenges in the diagnosis of genetic disorders in low to middle income countries with in-equitable health care access. It reinforces the significance of detailed phenotyping in the proband as well as the importance of DNA storage for a conclusive diagnosis. A recurring post-test counseling challenge was risk ascertainment and reproductive decision making in subsequent pregnancies if the detected pathogenic/likely pathogenic variants are co-inherited, in families with a putative diagnosis. When opted for, prenatal testing in such a scenario would be limited in its ability to comment on the fetal status with respect to the disorder in the proband.
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Affiliation(s)
| | - Mehul Mistri
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | | | - Parth Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
| | - Nidhi Shah
- Neuberg Centre for Genomic Medicine, Ahmedabad, India
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16
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Ryżko J, Walczak-Sztulpa J, Czubkowski P, Latos-Bieleńska A, Kowalski A, Stefanowicz M, Jarmużek W, Grenda R, Pawłowska J. Case Report: Sequential Liver After Kidney Transplantation in a Patient With Sensenbrenner Syndrome (Cranioectodermal Dysplasia). Front Pediatr 2022; 10:834064. [PMID: 35281231 PMCID: PMC8914039 DOI: 10.3389/fped.2022.834064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/02/2022] [Indexed: 11/29/2022] Open
Abstract
Sensenbrenner syndrome, also known as cranioectodermal dysplasia (CED), is a rare ciliopathy clinically characterized by congenital craniofacial, skeletal, and ectodermal defects. Chronic kidney and liver insufficiency are also present in this disorder. Cranioectodermal dysplasia is an autosomal recessive and heterogeneous genetic disease. Six genes (IFT122, WDR35, IFT140, IFT43, IFT52, and WDR19) are known to be associated with this syndrome. Until 2021 more than 70 patients have been reported with CED, however, an orthotopic liver transplantation has been reported only in one case. Here, we present a case report of sequential liver-after-kidney transplantation in a male patient affected by CED. The kidney and liver transplantation was performed at the age of 7 and 12 years, respectively. Patients with Sensenbrenner syndrome require a multidisciplinary medical management and should regularly be followed-up by hepatologists and nephrologists, as the liver and kidney diseases are the major cause of morbidity and mortality.
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Affiliation(s)
- Joanna Ryżko
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Piotr Czubkowski
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Adam Kowalski
- Department of Pediatric Surgery and Organ Transplantation, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marek Stefanowicz
- Department of Pediatric Surgery and Organ Transplantation, The Children's Memorial Health Institute, Warsaw, Poland
| | - Wioletta Jarmużek
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Ryszard Grenda
- Department of Nephrology, Kidney Transplantation and Hypertension, The Children's Memorial Health Institute, Warsaw, Poland
| | - Joanna Pawłowska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
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17
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Hwang N, Jang JH, Cho EH, Choi R, Choi SJ, Park HD. Prenatal diagnosis of combined methylmalonic acidemia and homocystinuria cobalamin C type using clinical exome sequencing and targeted gene analysis. Mol Genet Genomic Med 2021; 9:e1838. [PMID: 34655177 PMCID: PMC8606215 DOI: 10.1002/mgg3.1838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 01/23/2023] Open
Abstract
Background Combined methylmalonic acidemia and homocystinuria is a rare inherited disorder of intracellular cobalamin metabolism caused by biallelic variants in one of the following genes: MMACHC (cblC), MMADHC (cblD), LMBRD1 (cblF), ABCD4 (cblJ), THAP11 (cblX‐like), and ZNF143 (cblX‐like), or a hemizygous variant in HCFC1 (cblX). Prenatal diagnosis of combined methylmalonic acidemia with homocystinuria is crucial for high‐risk couples since the disorder can be life‐threatening for offspring. We would like to describe two infant deaths both of which are likely attributable to cblC despite not having a genetic confirmation, and subsequent pregnancy and prenatal genetic testing. Methods Parental clinical exome sequencing and targeted Sanger sequencing of MMACHC gene in amniotic fluid was performed to check the carrier status of the fetus. Results Parental clinical exome sequencing revealed a heterozygous pathogenic variant [NM_015506.2:c.217C>T (p.Arg73*)] in the MMACHC gene of the mother and [NM_015506.2:c.609G>A (p.Trp203*)] in the MMACHC gene of the father. Targeted Sanger sequencing of MMACHC gene in amniotic fluid revealed that the fetus carried only one nonsense variant [NM_015506.2:c.609G>A (p.Trp203*)], which was inherited from the father. The mother delivered a healthy baby and the neonate did not show any symptoms or signs of combined methylmalonic acidemia and homocystinuria after birth. Conclusion We present a case of prenatal diagnosis with parental exome sequencing, which successfully diagnosed the carrier status of the fetus and parents in a combined methylmalonic acidemia and homocystinuria family.
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Affiliation(s)
- Narae Hwang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun-Hae Cho
- Green Cross Genome, Yongin, Republic of Korea
| | - Rihwa Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Green Cross Laboratories, Yongin, Republic of Korea
| | - Suk-Joo Choi
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyung-Doo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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18
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Mone F, Eberhardt RY, Hurles ME, Mcmullan DJ, Maher ER, Lord J, Chitty LS, Dempsey E, Homfray T, Giordano JL, Wapner RJ, Sun L, Sparks TN, Norton ME, Kilby MD. Fetal hydrops and the Incremental yield of Next-generation sequencing over standard prenatal Diagnostic testing (FIND) study: prospective cohort study and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:509-518. [PMID: 33847422 PMCID: PMC8487902 DOI: 10.1002/uog.23652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To determine the incremental yield of exome sequencing (ES) over chromosomal microarray analysis (CMA) or karyotyping in prenatally diagnosed non-immune hydrops fetalis (NIHF). METHODS A prospective cohort study (comprising an extended group of the Prenatal Assessment of Genomes and Exomes (PAGE) study) was performed which included 28 cases of prenatally diagnosed NIHF undergoing trio ES following negative CMA or karyotyping. These cases were combined with data from a systematic review of the literature. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov databases were searched electronically (January 2000 to October 2020) for studies reporting on the incremental yield of ES over CMA or karyotyping in fetuses with prenatally detected NIHF. Inclusion criteria for the systematic review were: (i) at least two cases of NIHF undergoing sequencing; (ii) testing initiated based on prenatal ultrasound-based phenotype; and (iii) negative CMA or karyotyping result. The incremental diagnostic yield of ES was assessed in: (i) all cases of NIHF; (ii) isolated NIHF; (iii) NIHF associated with an additional fetal structural anomaly; and (iv) NIHF according to severity (i.e. two vs three or more cavities affected). RESULTS In the extended PAGE study cohort, the additional diagnostic yield of ES over CMA or karyotyping was 25.0% (7/28) in all NIHF cases, 21.4% (3/14) in those with isolated NIHF and 28.6% (4/14) in those with non-isolated NIHF. In the meta-analysis, the pooled incremental yield based on 21 studies (306 cases) was 29% (95% CI, 24-34%; P < 0.00001; I2 = 0%) in all NIHF, 21% (95% CI, 13-30%; P < 0.00001; I2 = 0%) in isolated NIHF and 39% (95% CI, 30-49%; P < 0.00001; I2 = 1%) in NIHF associated with an additional fetal structural anomaly. In the latter group, congenital limb contractures were the most prevalent additional structural anomaly associated with a causative pathogenic variant, occurring in 17.3% (19/110) of cases. The incremental yield did not differ significantly according to hydrops severity. The most common genetic disorders identified were RASopathies, occurring in 30.3% (27/89) of cases with a causative pathogenic variant, most frequently due to a PTPN11 variant (44.4%; 12/27). The predominant inheritance pattern in causative pathogenic variants was autosomal dominant in monoallelic disease genes (57.3%; 51/89), with most being de novo (86.3%; 44/51). CONCLUSIONS Use of prenatal next-generation sequencing in both isolated and non-isolated NIHF should be considered in the development of clinical pathways. Given the wide range of potential syndromic diagnoses and heterogeneity in the prenatal phenotype of NIHF, exome or whole-genome sequencing may prove to be a more appropriate testing approach than a targeted gene panel testing strategy. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Mone
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | | | - D J Mcmullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Dempsey
- Molecular and Clinical Sciences, St George's University of London, London, UK
| | - T Homfray
- SW Thames Regional Genetics Department, St George's University Hospitals NHS Foundation Trust, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - L Sun
- Fetal Medicine Unit and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital of Tongji University, Shanghai, China
| | - T N Sparks
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M E Norton
- Center for Maternal-Fetal Precision Medicine, Division of Maternal-Fetal Medicine, University of California, San Francisco, CA, USA
| | - M D Kilby
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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19
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Qiao F, Wang Y, Zhang C, Zhou R, Wu Y, Wang C, Meng L, Mao P, Cheng Q, Luo C, Hu P, Xu Z. Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:377-387. [PMID: 33142350 DOI: 10.1002/uog.23532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups. METHODS This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES. RESULTS Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1. CONCLUSIONS Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - R Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wu
- Department of Ultrasound, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - L Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Mao
- Personnel Division, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Q Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Z Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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20
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De Biase I, Yuzyuk T, Hernandez A, Basinger A. An Unusually High Excretion of Ethylmalonic Acid in a Patient with Multiple Acyl-CoA Dehydrogenase Deficiency. Clin Chem 2021; 67:1290-1292. [PMID: 34470039 DOI: 10.1093/clinchem/hvab096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Irene De Biase
- Department of Pathology, University of Utah, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | - Tatiana Yuzyuk
- Department of Pathology, University of Utah, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
| | | | - Alice Basinger
- Department of Genetics, Cook Children's Physician Network, TX
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21
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Salter CG, Cai Y, Lo B, Helman G, Taylor H, McCartney A, Leslie JS, Accogoli A, Zara F, Traverso M, Fasham J, Lees JA, Ferla M, Chioza BA, Wenger O, Scott E, Cross HE, Crawford J, Warshawsky I, Keisling M, Agamanolis D, Melver CW, Cox H, Elawad M, Marton T, Wakeling M, Holzinger D, Tippelt S, Munteanu M, Valcheva D, Deal C, Van Meerbeke S, Vockley CW, Butte MJ, Acar U, van der Knaap MS, Korenke GC, Kotzaeridou U, Balla T, Simons C, Uhlig HH, Crosby AH, De Camilli P, Wolf NI, Baple EL. Biallelic PI4KA variants cause neurological, intestinal and immunological disease. Brain 2021; 144:3597-3610. [PMID: 34415310 PMCID: PMC8719846 DOI: 10.1093/brain/awab313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/14/2021] [Accepted: 08/01/2021] [Indexed: 11/22/2022] Open
Abstract
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα/PI4KA/OMIM:600286) is a lipid kinase generating phosphatidylinositol 4-phosphate (PI4P), a membrane phospholipid with critical roles in the physiology of multiple cell types. PI4KIIIα’s role in PI4P generation requires its assembly into a heterotetrameric complex with EFR3, TTC7 and FAM126. Sequence alterations in two of these molecular partners, TTC7 (encoded by TTC7A or TCC7B) and FAM126, have been associated with a heterogeneous group of either neurological (FAM126A) or intestinal and immunological (TTC7A) conditions. Here we show that biallelic PI4KA sequence alterations in humans are associated with neurological disease, in particular hypomyelinating leukodystrophy. In addition, affected individuals may present with inflammatory bowel disease, multiple intestinal atresia and combined immunodeficiency. Our cellular, biochemical and structural modelling studies indicate that PI4KA-associated phenotypical outcomes probably stem from impairment of PI4KIIIα-TTC7-FAM126's organ-specific functions, due to defective catalytic activity or altered intra-complex functional interactions. Together, these data define PI4KA gene alteration as a cause of a variable phenotypical spectrum and provide fundamental new insight into the combinatorial biology of the PI4KIIIα-FAM126-TTC7-EFR3 molecular complex.
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Affiliation(s)
- Claire G Salter
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Yiying Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Bernice Lo
- Research Branch, Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Henry Taylor
- Department of surgery and Cancer, Imperial College London, London, UK
| | - Amber McCartney
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph S Leslie
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | | | - James Fasham
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
| | - Joshua A Lees
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Matteo Ferla
- Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - Barry A Chioza
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | | | | | - Harold E Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Joanna Crawford
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia
| | | | | | | | | | - Helen Cox
- West Midlands Clinical Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - Mamoun Elawad
- Department of Gastroenterology, Sidra Medicine, Doha, Qatar
| | - Tamas Marton
- West Midlands Perinatal Pathology, Birmingham Women's Hospital, Edgbaston, Birmingham, UK
| | - Matthew Wakeling
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Dirk Holzinger
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Stephan Tippelt
- Department of Pediatric Haematology-Oncology, University of Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institute for Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Christin Deal
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Sara Van Meerbeke
- Children's Hospital of Pittsburgh, UPMC, Division of Pediatric Allergy and Immunology, Pittsburgh, USA
| | - Catherine Walsh Vockley
- Children's Hospital of Pittsburgh, UPMC, Division of Genetic and Genomic Medicine, Pittsburgh, USA
| | - Manish J Butte
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Utkucan Acar
- Department of Paediatrics, Division of Immunology, Allergy, and Rheumatology, UCLA, Los Angeles, CA, USA
| | - Marjo S van der Knaap
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - G Christoph Korenke
- Department of Neuropediatrics, University Children's Hospital, Klinikum Oldenburg, 26133 Oldenburg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxfordshire, UK.,Department of Paediatrics, University of Oxford, Oxfordshire, UK.,Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Andrew H Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Program in Cellular Neuroscience Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Center, VU University Amsterdam and Amsterdam Neuroscience, 1081 HV Amsterdam, The Netherlands.,Department of Functional Genomics, Centre for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Emma L Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, UK.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, UK
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22
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Seaby EG, Ennis S. Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies. Brief Funct Genomics 2021; 19:243-258. [PMID: 32393978 DOI: 10.1093/bfgp/elaa009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. On average, only ~30% of patients receive a molecular diagnosis. National sequencing projects launched in the last 5 years are integrating clinical diagnostic testing with research avenues to widen the spectrum of known genetic disorders. Consequently, efforts to diagnose genetic disorders in a clinical setting are now often shared with efforts to prioritise candidate variants for the detection of new disease genes. Herein we discuss some of the biggest obstacles precluding molecular diagnosis and discovery of new gene disorders. We consider bioinformatic and analytical challenges faced when interpreting next generation sequencing data and showcase some of the newest tools available to mitigate these issues. We consider how incomplete penetrance, non-coding variation and structural variants are likely to impact diagnostic rates, and we further discuss methods for uplifting novel gene discovery by adopting a gene-to-patient-based approach.
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23
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Castleman JS, Wall E, Allen S, Williams D, Doyle S, Kilby MD. The prenatal exome - a door to prenatal diagnostics? Expert Rev Mol Diagn 2021; 21:465-474. [PMID: 33877000 DOI: 10.1080/14737159.2021.1920398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Prenatal exome sequencing (ES) allows parents the opportunity to obtain arapid molecular diagnosis of monogenic etiology when their fetus is found to have structural anomalies detected on prenatal ultrasound. Such information can improve antenatal and neonatal counseling, decision-making and management, and expand reproductive options in subsequent pregnancies.Areas covered: This review appraises the evidence, from acomprehensive search of bibliographic databases, for the introduction of ES into the fetal medicine care pathway when investigating congenital malformations. The perspectives of clinical geneticists, clinical scientists, fetal medicine specialists, and patients are explored in relation to the novel investigation and the benefits and challenges of its use in ongoing pregnancies with particular reference to UK medical practice.Expert opinion: ES provides agenetic diagnosis for more than 1 in 10 fetuses with structural differences on ultrasound and normal conventional tests (karyotype or chromosomal microarray) in carefully selected cases. The diagnostic rate increases for certain phenotypes and can range between 6% and 80% where conventional cytogenetics have not detected adiagnosis. Expert oversight is required to ensure that patients receive high-quality, evidence-based care and accurate counseling, supported by amultidisciplinary team familiar with the test and its implications.
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Affiliation(s)
- James S Castleman
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Wall
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Mindelsohn Way, Edgbaston. Birmingham, UK
| | - Denise Williams
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Samantha Doyle
- Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mark D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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24
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Yap ZY, Park YH, Wortmann SB, Gunning AC, Ezer S, Lee S, Duraine L, Wilichowski E, Wilson K, Mayr JA, Wagner M, Li H, Kini U, Black ED, Monaghan KG, Lupski JR, Ellard S, Westphal DS, Harel T, Yoon WH. Functional interpretation of ATAD3A variants in neuro-mitochondrial phenotypes. Genome Med 2021; 13:55. [PMID: 33845882 PMCID: PMC8042885 DOI: 10.1186/s13073-021-00873-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Background ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane-anchored protein involved in diverse processes including mitochondrial dynamics, mitochondrial DNA organization, and cholesterol metabolism. Biallelic deletions (null), recessive missense variants (hypomorph), and heterozygous missense variants or duplications (antimorph) in ATAD3A lead to neurological syndromes in humans. Methods To expand the mutational spectrum of ATAD3A variants and to provide functional interpretation of missense alleles in trans to deletion alleles, we performed exome sequencing for identification of single nucleotide variants (SNVs) and copy number variants (CNVs) in ATAD3A in individuals with neurological and mitochondrial phenotypes. A Drosophila Atad3a Gal4 knockin-null allele was generated using CRISPR-Cas9 genome editing technology to aid the interpretation of variants. Results We report 13 individuals from 8 unrelated families with biallelic ATAD3A variants. The variants included four missense variants inherited in trans to loss-of-function alleles (p.(Leu77Val), p.(Phe50Leu), p.(Arg170Trp), p.(Gly236Val)), a homozygous missense variant p.(Arg327Pro), and a heterozygous non-frameshift indel p.(Lys568del). Affected individuals exhibited findings previously associated with ATAD3A pathogenic variation, including developmental delay, hypotonia, congenital cataracts, hypertrophic cardiomyopathy, and cerebellar atrophy. Drosophila studies indicated that Phe50Leu, Gly236Val, Arg327Pro, and Lys568del are severe loss-of-function alleles leading to early developmental lethality. Further, we showed that Phe50Leu, Gly236Val, and Arg327Pro cause neurogenesis defects. On the contrary, Leu77Val and Arg170Trp are partial loss-of-function alleles that cause progressive locomotion defects and whose expression leads to an increase in autophagy and mitophagy in adult muscles. Conclusion Our findings expand the allelic spectrum of ATAD3A variants and exemplify the use of a functional assay in Drosophila to aid variant interpretation.
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Affiliation(s)
- Zheng Yie Yap
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Yo Han Park
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Saskia B Wortmann
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria.,Radboud Centre for Mitochondrial Medicine (RCMM), Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Adam C Gunning
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, UK.,Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, EX2 5DW, UK
| | - Shlomit Ezer
- Department of Genetics, Hadassah Medical Center, POB 12000, 9112001, Jerusalem, Israel.,Faculty of Medicine, Hebrew University of Jerusalem, POB 12000, 9112001, Jerusalem, Israel
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lita Duraine
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Ekkehard Wilichowski
- Department of Pediatrics and Pediatric Neurology, University Medical Center Göttingen, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Hong Li
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA.,Department of Pediatrics, School of Medicine, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emily Davis Black
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, UK.,Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, EX2 5DW, UK
| | - Dominik S Westphal
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Center, POB 12000, 9112001, Jerusalem, Israel. .,Faculty of Medicine, Hebrew University of Jerusalem, POB 12000, 9112001, Jerusalem, Israel.
| | - Wan Hee Yoon
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
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25
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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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26
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Mone F, Eberhardt RY, Morris RK, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Giordano JL, Wapner RJ, Kilby MD. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: prospective cohort study and systematic review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:43-51. [PMID: 32388881 DOI: 10.1002/uog.22072] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To determine the incremental yield of antenatal exome sequencing (ES) over chromosomal microarray analysis (CMA) or conventional karyotyping in prenatally diagnosed congenital heart disease (CHD). METHODS A prospective cohort study of 197 trios undergoing ES following CMA or karyotyping owing to CHD identified prenatally and a systematic review of the literature were performed. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov (January 2000 to October 2019) databases were searched electronically for studies reporting on the diagnostic yield of ES in prenatally diagnosed CHD. Selected studies included those with more than three cases, with initiation of testing based upon prenatal phenotype only and that included cases in which CMA or karyotyping was negative. The incremental diagnostic yield of ES was assessed in: (1) all cases of CHD; (2) isolated CHD; (3) CHD associated with extracardiac anomaly (ECA); and (4) CHD according to phenotypic subgroup. RESULTS In our cohort, ES had an additional diagnostic yield in all CHD, isolated CHD and CHD associated with ECA of 12.7% (25/197), 11.5% (14/122) and 14.7% (11/75), respectively (P = 0.81). The corresponding pooled incremental yields from 18 studies (encompassing 636 CHD cases) included in the systematic review were 21% (95% CI, 15-27%), 11% (95% CI, 7-15%) and 37% (95% CI, 18-56%), respectively. The results did not differ significantly when subanalysis was limited to studies including more than 20 cases, except for CHD associated with ECA, in which the incremental yield was greater (49% (95% CI, 17-80%)). In cases of CHD associated with ECA in the primary analysis, the most common extracardiac anomalies associated with a pathogenic variant were those affecting the genitourinary system (23/52 (44.2%)). The greatest incremental yield was in cardiac shunt lesions (41% (95% CI, 19-63%)), followed by right-sided lesions (26% (95% CI, 9-43%)). In the majority (68/96 (70.8%)) of instances, pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease genes. The most common (19/96 (19.8%)) monogenic syndrome identified was Kabuki syndrome. CONCLUSIONS There is an apparent incremental yield of prenatal ES in CHD. While the greatest yield is in CHD associated with ECA, consideration could also be given to performing ES in the presence of an isolated cardiac abnormality. A policy of routine application of ES would require the adoption of robust bioinformatic, clinical and ethical pathways. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- F Mone
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - R K Morris
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - D J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - M D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
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27
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Murray SL, Fennelly NK, Doyle B, Lynch SA, Conlon PJ. Integration of genetic and histopathology data in interpretation of kidney disease. Nephrol Dial Transplant 2020; 35:1113-1132. [PMID: 32777081 DOI: 10.1093/ndt/gfaa176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 12/22/2022] Open
Abstract
For many years renal biopsy has been the gold standard for diagnosis in many forms of kidney disease. It provides rapid, accurate and clinically useful information in most individuals with kidney disease. However, in recent years, other diagnostic modalities have become available that may provide more detailed and specific diagnostic information in addition to, or instead of, renal biopsy. Genomics is one of these modalities. Previously prohibitively expensive and time consuming, it is now increasingly available and practical in a clinical setting for the diagnosis of inherited kidney disease. Inherited kidney disease is a significant cause of kidney disease, in both the adult and paediatric populations. While individual inherited kidney diseases are rare, together they represent a significant burden of disease. Because of the heterogenicity of inherited kidney disease, diagnosis and management can be a challenge and often multiple diagnostic modalities are needed to arrive at a diagnosis. We present updates in genomic medicine for renal disease, how genetic testing integrates with our knowledge of renal histopathology and how the two modalities may interact to enhance patient care.
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Affiliation(s)
- Susan L Murray
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, Royal College of Surgeons, Dublin, Ireland
| | | | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Sally Ann Lynch
- National Rare Disease Office Mater Hospital Dublin, Dublin, Ireland
| | - Peter J Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland.,Department of Medicine, Royal College of Surgeons, Dublin, Ireland
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28
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Mone F, Doyle S, Ahmad A, Abu Subieh H, Hamilton S, Allen S, Marton T, Williams D, Kilby MD. Diagnostic and perinatal outcomes in consanguineous couples with a structural fetal anomaly: A cohort study. Acta Obstet Gynecol Scand 2020; 100:418-424. [PMID: 33128783 DOI: 10.1111/aogs.14036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Consanguineous unions occur when a couple are related outside marriage and is associated with adverse genetic and perinatal outcomes for affected offspring. The objectives of this study were to evaluate: (i) background characteristics, (ii) uptake of prenatal and postnatal investigation and (iii) diagnostic outcomes of UK consanguineous couples presenting with a fetal structural anomaly. MATERIAL AND METHODS This was a retrospective and partly prospective cohort study comparing consanguineous (n = 62) and non-consanguineous (n = 218) pregnancies with current or previous fetal structural anomalies reviewed in a UK prenatal genetic clinic from 2008 to 2019. Outcomes were compared using odds ratios (OR). RESULTS Most consanguineous couples were of Pakistani ethnicity (odds ratio [OR] 29, 95% confidence interval [95% CI] 13-62) and required use of an interpreter [OR 9, 95% CI 4-20). In the consanguineous group, the uptake of prenatal invasive testing was lower (OR 0.4, 95% CI 0.2-0.7) and the number declining follow up was greater (OR 10, 95% CI 3-34) than in the non-consanguineous group. This likely explained the lower proportion of consanguineous couples where a final definitive unifying diagnosis to explain the fetal structural anomalies was reached (OR 0.3, 95% CI 0.2-0.6). When a diagnosis was obtained in this group, it was always postnatal and most often using genomic sequencing technologies (OR 6, 95% CI 1-27). The risk of perinatal death was greater (OR 3, 95% CI 1-6) in the consanguineous group, as was the risk of fetal structural anomaly recurrence in a subsequent pregnancy (OR 4, 95% CI 1-13). There was no difference in the uptake of perinatal autopsy or termination of pregnancy between groups. CONCLUSIONS Consanguineous couples are a vulnerable group in the prenatal setting. Although adverse perinatal outcomes in this group are more common secondary to congenital anomalies, despite the evolution of genomic sequencing technologies, due to a lower uptake of prenatal testing it is less likely that a unifying diagnosis is obtained and recurrence can occur. There is a need for proactive genetic counseling and education from the multidisciplinary team, addressing language barriers as well as religious and cultural beliefs in an attempt to optimize reproductive options.
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Affiliation(s)
- Fionnuala Mone
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
| | - Samantha Doyle
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Asfa Ahmad
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Hala Abu Subieh
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Susan Hamilton
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Tamas Marton
- West Midland's Perinatal Pathology Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
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29
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Beecroft SJ, Lamont PJ, Edwards S, Goullée H, Davis MR, Laing NG, Ravenscroft G. The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders. Mol Diagn Ther 2020; 24:641-652. [PMID: 32997275 DOI: 10.1007/s40291-020-00495-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The impact of high-throughput sequencing in genetic neuromuscular disorders cannot be overstated. The ability to rapidly and affordably sequence multiple genes simultaneously has enabled a second golden age of Mendelian disease gene discovery, with flow-on impacts for rapid genetic diagnosis, evidence-based treatment, tailored therapy development, carrier-screening, and prevention of disease recurrence in families. However, there are likely many more neuromuscular disease genes and mechanisms to be discovered. Many patients and families remain without a molecular diagnosis following targeted panel sequencing, clinical exome sequencing, or even genome sequencing. Here we review how massively parallel, or next-generation, sequencing has changed the field of genetic neuromuscular disorders, and anticipate future benefits of recent technological innovations such as RNA-seq implementation and detection of tandem repeat expansions from short-read sequencing.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | | | - Samantha Edwards
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Hayley Goullée
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Mark R Davis
- Neurogenetic Unit, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.,Neurogenetic Clinic, Royal Perth Hospital, Perth, Australia
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
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30
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Sennaiyan UN, Phani NM, Deepak V, Appaswamy G, Krishna MR. Massive parallel sequencing of dried umbilical cord remnants. Am J Med Genet A 2020; 182:2778-2780. [PMID: 32902111 DOI: 10.1002/ajmg.a.61850] [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: 08/15/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 11/08/2022]
Abstract
Genetic diagnosis depends on having available tissue to test. This can be important for many reasons, such as related to familial diagnosis in the case of another pregnancy. When blood or DNA samples from affected family members are not available, accurate prenatal diagnosis may be much more difficult and hence additional effort may be needed to obtain a genetic diagnosis in such families. We report two families with suspected monogenic disorders where attempts were made to establish the genetic etiology in deceased offspring using dried umbilical cord remnants which had been preserved by the family.
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Affiliation(s)
| | | | - Vuppu Deepak
- Life cell Diagnostics Pvt Ltd, Chennai, Tamil Nadu, India
| | | | - Mani Ram Krishna
- Dr R.K. Hospital for Women and Children, Thanjavur, Tamil Nadu, India
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31
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Robinson HK, Zaklyazminskaya E, Povolotskaya I, Surikova Y, Mallin L, Armstrong C, Mabin D, Benke PJ, Chrisant MR, McDonald M, Marboe CC, Agre KE, Deyle DR, McWalter K, Douglas G, Balashova MS, Kaimonov V, Shirokova N, Pomerantseva E, Turner CL, Ellard S. Biallelic variants in PPP1R13L cause paediatric dilated cardiomyopathy. Clin Genet 2020; 98:331-340. [PMID: 32666529 DOI: 10.1111/cge.13812] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/12/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022]
Abstract
Childhood dilated cardiomyopathy (DCM) is a leading cause of heart failure requiring cardiac transplantation and approximately 5% of cases result in sudden death. Knowledge of the underlying genetic cause can aid prognostication and clinical management and enables accurate recurrence risk counselling for the family. Here we used genomic sequencing to identify the causative genetic variant(s) in families with children affected by severe DCM. In an international collaborative effort facilitated by GeneMatcher, biallelic variants in PPP1R13L were identified in seven children with severe DCM from five unrelated families following exome or genome sequencing and inheritance-based variant filtering. PPP1R13L encodes inhibitor of apoptosis-stimulating protein of p53 protein (iASPP). In addition to roles in apoptosis, iASPP acts as a regulator of desmosomes and has been implicated in inflammatory pathways. DCM presented early (mean: 2 years 10 months; range: 3 months-9 years) and was progressive, resulting in death (n = 3) or transplant (n = 3), with one child currently awaiting transplant. Genomic sequencing technologies are valuable for the identification of novel and emerging candidate genes. Biallelic variants in PPP1R13L were previously reported in a single consanguineous family with paediatric DCM. The identification here of a further five families now provides sufficient evidence to support a robust gene-disease association between PPP1R13L and severe paediatric DCM. The PPP1R13L gene should be included in panel-based genetic testing for paediatric DCM.
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Affiliation(s)
- H K Robinson
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - E Zaklyazminskaya
- Medical Genetics Laboratory, Petrovsky National Research Centre of Surgery, Moscow, Russia.,NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia
| | - I Povolotskaya
- NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia
| | - Y Surikova
- Medical Genetics Laboratory, Petrovsky National Research Centre of Surgery, Moscow, Russia
| | - L Mallin
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - C Armstrong
- Paediatric Cardiac Service, Bristol Royal Hospital for Children, Bristol, UK
| | - D Mabin
- Paediatrics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - P J Benke
- Clinical Genetics Dpt, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA.,Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, USA
| | - M R Chrisant
- Clinical Genetics Dpt, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - M McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - C C Marboe
- Department of Pathology and Cell Biology, Columbia University Medical Centre, New York, New York, USA
| | - K E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - D R Deyle
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - K McWalter
- Clinical Genomics, GeneDx Inc, Gaithersburg, Maryland, USA
| | - G Douglas
- Clinical Genomics, GeneDx Inc, Gaithersburg, Maryland, USA
| | - M S Balashova
- NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia.,Chair of Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | - V Kaimonov
- NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia
| | - N Shirokova
- NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia
| | - E Pomerantseva
- NGS Laboratory
- Genotyping Laboratory
- Genetic Counseling Department, Centre of Genetics and Reproductive Medicine "Genetico", Moscow, Russia
| | - C L Turner
- Peninsula Clinical Genetics Service, Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - S Ellard
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical and Clinical Science, College of Medicine and Health, Exeter, UK
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32
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Bianchi DW, Deprest J, Levy B, Chitty LS, Ghidini A, Hui L, van Mieghem T, George ST. The 2019 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2020; 40:763-765. [PMID: 32597540 DOI: 10.1002/pd.5763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Jan Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals, Leuven, Belgium
| | - Brynn Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lyn S Chitty
- Genetic and Genomic Medicine, University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Lisa Hui
- Departments of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
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33
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Rautengarten C, Quarrell OW, Stals K, Caswell RC, De Franco E, Baple E, Burgess N, Jokhi R, Heazlewood JL, Offiah AC, Ebert B, Ellard S. A hypomorphic allele of SLC35D1 results in Schneckenbecken-like dysplasia. Hum Mol Genet 2020; 28:3543-3551. [PMID: 31423530 PMCID: PMC6927460 DOI: 10.1093/hmg/ddz200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
We report the case of a consanguineous couple who lost four pregnancies associated with skeletal dysplasia. Radiological examination of one fetus was inconclusive. Parental exome sequencing showed that both parents were heterozygous for a novel missense variant, p.(Pro133Leu), in the SLC35D1 gene encoding a nucleotide sugar transporter. The affected fetus was homozygous for the variant. The radiological features were reviewed, and being similar, but atypical, the phenotype was classified as a ‘Schneckenbecken-like dysplasia.’ The effect of the missense change was assessed using protein modelling techniques and indicated alterations in the mouth of the solute channel. A detailed biochemical investigation of SLC35D1 transport function and that of the missense variant p.(Pro133Leu) revealed that SLC35D1 acts as a general UDP-sugar transporter and that the p.(Pro133Leu) mutation resulted in a significant decrease in transport activity. The reduced transport activity observed for p.(Pro133Leu) was contrasted with in vitro activity for SLC35D1 p.(Thr65Pro), the loss-of-function mutation was associated with Schneckenbecken dysplasia. The functional classification of SLC35D1 as a general nucleotide sugar transporter of the endoplasmic reticulum suggests an expanded role for this transporter beyond chondroitin sulfate biosynthesis to a variety of important glycosylation reactions occurring in the endoplasmic reticulum.
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Affiliation(s)
| | - Oliver W Quarrell
- Department of Clinical Genetics, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Karen Stals
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Richard C Caswell
- University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
| | - Elisa De Franco
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Emma Baple
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
| | - Nadia Burgess
- Department of Histology, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield UK. S10 2TH, UK
| | - Roobin Jokhi
- Department of Obstetrics and Gynaecology, Sheffield Teaching Hospitals, Jessop Wing Tree Root Walk, Sheffield S10 2SF, UK
| | - Joshua L Heazlewood
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Amaka C Offiah
- University of Sheffield, Academic Unit of Child Health, Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield S10 2TH, UK
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.,University of Exeter School of Medicine, Barrack Road, Exeter EX2 5DW, UK
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34
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Bukowska-Olech E, Sowińska-Seidler A, Szczałuba K, Jamsheer A. A novel biallelic splice-site variant in the LRP4 gene causes sclerosteosis 2. Birth Defects Res 2020; 112:652-659. [PMID: 32286743 DOI: 10.1002/bdr2.1676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 02/05/2023]
Abstract
The LRP4 gene encodes the highly conserved low-density lipoprotein receptor-related protein 4 (LRP4), which acts as a co-receptor for sclerostin. Sclerostin and LRP4 negatively regulate WNT/β-catenin signaling pathway and lack of their inhibitory activity leads to constant osteoblastic differentiation. Consequently, increased bone formation occurs, which in the case of LRP4 mutations results in sclerosteosis type 2 (SOST2). Alterations within the LRP4 may also cause Cenani-Lenz syndactyly syndrome (CLSS), congenital myasthenia or isolated syndactyly. Here, we have reported a patient, in whom we found a novel homozygous splice-site variant c.1048+6T>C in LRP4 using whole exome sequencing. The patient was initially misdiagnosed with isolated CLSS-like or Malik-Percin-like syndactyly. However, we have finally refined the diagnosis after comprehensive radiological examination and molecularly confirmed SOST2. Additionally, we have pointed here to the splicing variants as important causative alterations that may be overlooked in the molecular analysis due to the lack of advanced, reliable algorithms, built-into the standard diagnostic pipelines. Using advanced in silico prediction tools of splice-site alterations, including Alamut Visual software, we have demonstrated that the c.1048+6T>C LRP4 variant affects the native donor site and impairs an SC35 enhancer activity. Based on our experience, we recommend comprehensive radiological imaging, including X-ray of the skull in each case of isolated syndactyly resulting from pathogenic variants of LRP4. We suggest that all previously reported patients carrying biallelic LRP4 mutations, who were diagnosed with isolated syndactyly, could actually present with SOST2 that had been unrecognized due to the incomplete clinical and radiological assessment.
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Affiliation(s)
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland.,Centers for Medical Genetics GENESIS, Poznan, Poland
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35
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Rinaldi B, Race V, Corveleyn A, Van Hoof E, Bauters M, Van Den Bogaert K, Denayer E, de Ravel T, Legius E, Baldewijns M, Aertsen M, Lewi L, De Catte L, Breckpot J, Devriendt K. Next-generation sequencing in prenatal setting: Some examples of unexpected variant association. Eur J Med Genet 2020; 63:103875. [PMID: 32058062 DOI: 10.1016/j.ejmg.2020.103875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 11/28/2019] [Accepted: 02/01/2020] [Indexed: 01/08/2023]
Abstract
The application of next-generation sequencing to fetal pathology has proved to increase the diagnostic yield in fetuses with abnormal ultrasounds. We retrospectively reviewed genetic data of 30 selected cases studied through targeted resequencing of OMIM genes. In our experience, clinical data proved to be essential to support diagnostic reasoning and enhance variants' assessment. The molecular diagnosis was reached in 19/30 (63%) cases. Only in 7/19 cases the molecular diagnosis confirmed the initial diagnostic hypothesis, showing the relevance of the genotype-first approach. According to the genotype-phenotype correlation, we were able to divide the solved cases into three groups: i) the correlation is well established but it was missed due to lack of specificity, unusual presentation or recent description; ii) the clinical presentation is much more severe than currently known for the underlying condition; iii) the correlation does not recapitulate the entire phenotype, possibly due to the fetal presentation or multiple coexisting conditions. Moreover, we found a higher proportion of recessive diagnosis in abnormal fetuses compared to cohorts of individuals with developmental delay. Our findings suggest that fetal pathology may be enriched in rare alleles and/or in unusual combinations, counter-selected in postnatal genomes and thus contributing to both phenotypic extremeness and atypical presentation.
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Affiliation(s)
| | - Valerie Race
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Evelien Van Hoof
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Marijke Bauters
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Ellen Denayer
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Thomy de Ravel
- Centre for Medical Genetics, Reproduction and Genetics, University Hospital Brussels, Brussels, Belgium
| | - Eric Legius
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Marcella Baldewijns
- Department of Pathological Anatomy, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Michael Aertsen
- Department of Radiology, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Liesbeth Lewi
- Department of Obstetrics & Gynaecology, Fetal Medicine, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Luc De Catte
- Department of Obstetrics & Gynaecology, Fetal Medicine, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven, Catholic University Leuven, Leuven, Belgium.
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36
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Aggarwal S, Vineeth VS, Das Bhowmik A, Tandon A, Kulkarni A, Narayanan DL, Bhattacherjee A, Dalal A. Exome sequencing for perinatal phenotypes: The significance of deep phenotyping. Prenat Diagn 2019; 40:260-273. [PMID: 31742715 DOI: 10.1002/pd.5616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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37
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Guo W, Lai Y, Yan Z, Wang Y, Nie Y, Guan S, Kuo Y, Zhang W, Zhu X, Peng M, Zhi X, Wei Y, Yan L, Qiao J. Trio-whole-exome sequencing and preimplantation genetic diagnosis for unexplained recurrent fetal malformations. Hum Mutat 2019; 41:432-448. [PMID: 31680349 DOI: 10.1002/humu.23935] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/19/2019] [Accepted: 10/16/2019] [Indexed: 01/18/2023]
Abstract
Whole-exome sequencing (WES) is widely used to detect genetic mutations that cause Mendelian diseases, and has been successfully applied in combination with preimplantation genetic diagnosis (PGD) to avoid the transmission of genetic defects. We investigated 40 nonconsanguineous families with unexplained, recurrent fetal malformations (two or more malformed fetuses) from May 2016 to December 2018. Using Trio-WES, we identified 32 disease-associated variants in 40 families (80% positive rate), which were subsequently verified. Known Mendelian diseases were identified in 12 families (30%), highly suspected Mendelian diseases in 12 families (30%), variants with uncertain significance in 8 families (20%), and no noticeable variants for 8 families (20%). Further analysis showed variants in 22 genes may cause fetal malformations. Four gene variants were detected in fetuses for the first time, which expanded the spectrum of the disease phenotype. Two novel candidate genes may be related to fetal malformations. Of 26 couples receiving PGD on disease-associated genes, 3 healthy newborns were delivered, and 4 couples are undergoing pregnancies. We reported the fetal data and developed an optimized genetic testing strategy. Our finding strongly suggests the presence of single gene Mendelian disorders in 60% of those families, and PGD services for couples to have healthy babies.
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Affiliation(s)
- Wei Guo
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yuchen Lai
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhiqiang Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yuqian Wang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yanli Nie
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Shuo Guan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Ying Kuo
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Wenxin Zhang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Xiaohui Zhu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | | | - Xu Zhi
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Liying Yan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China
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38
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Chitty LS. Ultrasound examination: The key to maximising the benefits of advances in molecular diagnostic technologies. Prenat Diagn 2019; 39:663-665. [DOI: 10.1002/pd.5537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Lyn S. Chitty
- Great Ormond Street Hospital for Children NHS Foundation Trust London UK
- Genetics and Genomic MedicineThe UCL Great Ormond Street Institute of Child Health London UK
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39
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Bianchi DW, Ghidini A, Levy B, Deprest J, van Mieghem T, Chitty LS, Hui L, McLean-Inglis A. The 2018 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2019; 39:835-837. [PMID: 31414475 DOI: 10.1002/pd.5533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Inova Alexandria Hospital, Alexandria, VA, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jan Deprest
- Academic Department of Development and Regeneration, Woman and Child, Biomedical Sciences, and Clinical Department of Obstetrics and Gynaecology, KU Leuven, Leuven, Belgium
| | - Tim van Mieghem
- Departments of Obstetrics and Gynaecology, Mount Sinai Hospital, Toronto, Canada
| | - Lyn S Chitty
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, Australia
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40
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Genetic testing and PGD for unexplained recurrent fetal malformations with MAGEL2 gene mutation. SCIENCE CHINA-LIFE SCIENCES 2019; 62:886-894. [PMID: 31152388 DOI: 10.1007/s11427-019-9541-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
Birth defects are caused by multiple factors, such as chromosome abnormality, environmental factors, and maternal factors. In this study, we focused on exploring the genetic causes of a non-consanguineous couple who suffered from four times of unsuccessful pregnancy due to unexplained recurrent fetal malformations with similar symptoms and normal chromosome copy number variations. Using trio-whole exome sequencing (trio-WES) for this couple and one of the affected fetuses, we found a mutation, c.1996delC on the maternal imprinted gene MAGEL2 that was carried by the affected fetus and husband, leading to Schaaf-Yang syndrome. To screen this mutation, we further performed preimplantation genetic diagnosis (PGD) strategy followed by a gene pedigree validation and pathogenicity analysis. After the transfer of a PGD-screened embryo, a normal newborn without previous abnormal symptoms was born (February 15, 2019). We present the first data that identified a pathogenic gene (MAGEL2 c.1996delC) in a fetus with Schaaf-Yang syndrome in the EAS (East Asian) database and overcame this genetic defect by using processed PGD for this couple based on the WES results.
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41
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Update on the use of exome sequencing in the diagnosis of fetal abnormalities. Eur J Med Genet 2019; 62:103663. [PMID: 31085342 DOI: 10.1016/j.ejmg.2019.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/26/2019] [Accepted: 05/04/2019] [Indexed: 12/18/2022]
Abstract
Unexpected fetal abnormalities detected through ultrasound scanning in pregnancy may have a monogenic aetiology but are difficult to diagnose. Next generation sequencing now enables us to sequence fetal exomes, providing increased resolution and broader diagnostic capability compared to traditional cytogenetic prenatal tests, improving the yield and accuracy of diagnoses and allowing better counselling for expectant parents. Here we review published studies of exome sequencing (ES) for prenatal diagnosis over the last 5 years and address important questions for its clinical implementation, including clinical utility, which groups benefit most, and practical and ethical challenges for interpreting and reporting results. We observe that fetal ES substantially improves diagnostic yield relative to cytogenetic techniques. However, diagnostic rates vary widely between studies, largely attributable to differences in case selection. Recently several large studies report variations in diagnostic yield between phenotypic groups, with fetuses with multisystem abnormalities most likely to receive a diagnosis from fetal ES. Challenges for prenatal ES include the limitations of ultrasound-based fetal phenotyping, the need for rapid return of results in pregnancy, and technical limitations compared to whole genome sequencing. We also consider ethical issues around potential secondary findings and variants of uncertain significance and the complex counselling needs these present. Prenatal ES is a valuable tool to diagnose fetal abnormalities and, as it is implemented in the clinic, more large-scale research will serve to further delineate its clinical utility, as well as generating new knowledge about fetal phenotypes and informing guidelines for case selection, reporting results and genetic counselling.
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42
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Next generation sequencing in recurrent pregnancy loss-approaches and outcomes. Eur J Med Genet 2019; 63:103644. [PMID: 30991114 DOI: 10.1016/j.ejmg.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/26/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
Next generation sequencing (NGS) has revolutionized the diagnosis of postnatal genetic diseases, but so far has been used less frequently to study reproductive disorders. Here we provide an overview of approaches and outcomes of genome sequencing for identifying causes of recurrent pregnancy loss (RPL). This includes exome sequencing to look for pathogenic sequence changes in the whole exome or in a preselected list of genes considered important for early embryonic development and pregnancy maintenance, as well as low coverage whole genome sequencing useful for identifying cryptic balanced chromosome rearrangements and copy number variants (CNVs) in couples with RPL and miscarriages. For the purpose of this review only studies with at least 2 pregnancy losses were included with NGS performed on complete families, or only on miscarriages, couples or females with RPL. Overall, mutations in candidate genes responsible for recurrent embryonic/fetal loss were found in up to 60% of cases, opening the door for possible identification of affected future pregnancies at the preimplantation stage. Recurrence of specific mutations or affected genes in different studies was rare (e.g.DYNC2H1, KIF14, RYR1 and GLE1) however genes involved in cell division, cilia function or fetal movement were frequently identified as candidates, the later possibly reflecting the fact that a large number of studied cases had features of fetal akinesia deformation sequence (FADS). Genome sequencing of the couple and miscarriages is most informative, as it allows analysis of the individual mutations as well as their collective burden on the genome and biological processes. However genome sequencing of the couple with RPL with follow up of candidate parental mutations in miscarriages appears to be a promising avenue when miscarriage DNA amounts or quality are suboptimal for whole genome studies. In the future, increasing the number of studied families, establishment of a database cataloguing CNVs and mutations found in early pregnancy loss as well as their functional assessment in miscarriage cells and parental reproductive tissues is needed for improved understanding of their role in adverse pregnancy outcome.
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43
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Kosfeld A, Martens H, Hennies I, Haffner D, Weber RG. Kongenitale Anomalien der Nieren und ableitenden Harnwege (CA KUT). MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0226-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zusammenfassung
Der Begriff CAKUT (Congenital Anomalies of the Kidney and Urinary Tract) bezeichnet diverse angeborene Fehlbildungen der Nieren und ableitenden Harnwege. Da alle CAKUT-Phänotypen zusammengenommen etwa 15–30 % aller pränatal diagnostizierten Fehlbildungen ausmachen und etwa 40 % der Fälle mit terminalem Nierenversagen bei Kindern und Jugendlichen verursachen, sind diese Anomalien epidemiologisch hochrelevant. Die Diagnosestellung erfolgt mit radiologischen Verfahren, insbesondere mit Ultraschall, wobei bei vielen Patienten eine Kombination verschiedener CAKUT-Phänotypen nachgewiesen wird. CAKUT tritt zu etwa 85 % sporadisch auf, zu etwa 15 % familiär. Das Vererbungsmuster ist häufig dominant, kann aber auch rezessiv sein. CAKUT kann isoliert auftreten, aber auch als Teil einer syndromalen Erkrankung. Variable Expressivität und inkomplette Penetranz sind bei CAKUT häufig. CAKUT ist genetisch sehr heterogen. Im Mausmodell wurden bislang über 180 CAKUT-assoziierte Gene beschrieben. Da Mutationen in den etwa 50 bisher bekannten humanen CAKUT-Genen nur ca. 20 % der CAKUT-Fälle erklären und sich verschiedene chromosomale Aberrationen wie Mikrodeletionen in weiteren ca. 15 % der Patienten insbesondere mit syndromalen CAKUT finden, sind exom-/genomweite Screeningverfahren für die Aufklärung genetischer CAKUT-Ursachen besonders geeignet. Bei sporadischen Fällen ist eine Trio-basierte Analyse der Exome/Genome von Patienten-Eltern-Trios zur Identifizierung von De-novo-Aberrationen und biallelischen Varianten vielversprechend. Eine Abklärung der genetischen Ursache ist für die Präzisierung von Wiederholungsrisiken sowie eine gezielte Untersuchung von CAKUT-Patienten im Hinblick auf extrarenale Phänotypen von klinischer Bedeutung.
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Affiliation(s)
- Anne Kosfeld
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
| | - Helge Martens
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
| | - Imke Hennies
- Aff2 0000 0000 9529 9877 grid.10423.34 Klinik für Pädiatrische Nieren-, Leber- und Stoffwechselerkrankungen Medizinische Hochschule Hannover Hannover Deutschland
| | - Dieter Haffner
- Aff2 0000 0000 9529 9877 grid.10423.34 Klinik für Pädiatrische Nieren-, Leber- und Stoffwechselerkrankungen Medizinische Hochschule Hannover Hannover Deutschland
| | - Ruthild G. Weber
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
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44
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Chitty LS. Advances in the prenatal diagnosis of monogenic disorders. Prenat Diagn 2018; 38:3-5. [PMID: 29464795 DOI: 10.1002/pd.5208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 12/29/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Lyn S Chitty
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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45
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Ruark E, Holt E, Renwick A, Münz M, Wakeling M, Ellard S, Mahamdallie S, Yost S, Rahman N. ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series. Wellcome Open Res 2018; 3:108. [PMID: 30483600 PMCID: PMC6234721 DOI: 10.12688/wellcomeopenres.14754.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2018] [Indexed: 11/20/2022] Open
Abstract
Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing germline base substitution and indel calling performance using the ICR142 NGS validation series, a dataset of Illumina platform-based exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with DeepVariant versions 0.5.2 and 0.6.1. This showed that v0.6.1 improves variant calling performance, but there was evidence of minor changes in indel calling behaviour that may benefit from attention. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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46
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Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
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47
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Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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48
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Ruark E, Holt E, Renwick A, Münz M, Wakeling M, Ellard S, Mahamdallie S, Yost S, Rahman N. ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling using the ICR142 NGS validation series. Wellcome Open Res 2018; 3:108. [PMID: 30483600 PMCID: PMC6234721 DOI: 10.12688/wellcomeopenres.14754.1] [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] [Accepted: 08/23/2018] [Indexed: 10/05/2023] Open
Abstract
Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing variant calling performance using the ICR142 NGS validation series, a dataset of exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with versions 0.5.2 and 0.6.1 of DeepVariant. This showed that v0.6.1 improves variant calling performance, but there was evidence of some minor changes in indel calling behaviour that may benefit from attention in future updates. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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49
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Beecroft SJ, Lombard M, Mowat D, McLean C, Cairns A, Davis M, Laing NG, Ravenscroft G. Genetics of neuromuscular fetal akinesia in the genomics era. J Med Genet 2018; 55:505-514. [PMID: 29959180 DOI: 10.1136/jmedgenet-2018-105266] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/22/2018] [Accepted: 04/19/2018] [Indexed: 12/27/2022]
Abstract
Fetal hypokinesia or akinesia encompasses a broad spectrum of disorders, united by impaired movement in utero. Often, the underlying aetiology is genetic in origin, affecting part of the neuromuscular system. The affordable and high-throughput nature of next-generation DNA sequencing has led to an explosion in disease gene discovery across rare diseases, including fetal akinesias. A genetic diagnosis has clinical utility as it may affect management and prognosis and informs recurrence risk, facilitating family planning decisions. More broadly, knowledge of disease genes increasingly allows population-based preconception carrier screening, which has reduced the incidence of recessive diseases in several populations. Despite gains in knowledge of the genetics of fetal akinesia, many families lack a genetic diagnosis. In this review, we describe the developments in Mendelian genetics of neuromuscular fetal akinesia in the genomics era. We examine genetic diagnoses with neuromuscular causes, specifically including the lower motor neuron, peripheral nerve, neuromuscular junction and muscle.
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Affiliation(s)
- Sarah Jane Beecroft
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Marcus Lombard
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Catriona McLean
- Victorian Neuromuscular Laboratory, Alfred Health, Melbourne, Victoria, Australia
| | - Anita Cairns
- Department of Neurology, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Mark Davis
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Harry Perkins Institute of Medical Research, QQ Block, QEII Medical Centre, Nedlands, Western Australia, Australia
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50
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Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23:94-101. [PMID: 29305293 DOI: 10.1016/j.siny.2017.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.
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