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Chaudhari S, Ware AP, Jasti DB, Gorthi SP, Acharya LP, Bhat M, Mallya S, Satyamoorthy K. Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s). Mol Genet Genomics 2023; 298:965-976. [PMID: 37209156 DOI: 10.1007/s00438-023-02032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/04/2023] [Indexed: 05/22/2023]
Abstract
Choreoacanthocytosis, one of the forms of neuroacanthocytosis, is caused by mutations in vacuolar protein sorting-associated protein A (VPS13A), and is often misdiagnosed with other form of neuroacanthocytosis with discrete genetic defects. The phenotypic variations among the patients with VPS13A mutations significantly obfuscates the understanding of the disease and treatment strategies. In this study, two unrelated cases were identified, exhibiting the core phenotype of neuroacanthocytosis but with considerable clinical heterogeneity. Case 1 presented with an additional Parkinsonism phenotype, whereas seizures were evident in case 2. To decipher the genetic basis, whole exome sequencing followed by validation with Sanger sequencing was performed. A known homozygous pathogenic nonsense mutation (c.799C > T; p.R267X) in exon 11 of the VPS13A gene was identified in case 1 that resulted in a truncated protein. A novel missense mutation (c.9263T > G; p.M3088R) in exon 69 of VPS13A identified in case 2 was predicted as pathogenic. In silico analysis of the p.M3088R mutation at the C-terminus of VPS13A suggests a loss of interaction with TOMM40 and may disrupt mitochondrial localization. We also observed an increase in mitochondrial DNA copy numbers in case 2. Mutation analysis revealed benign heterozygous variants in interacting partners of VPS13A such as VAPA in case 1. Our study confirmed the cases as ChAc and identified the novel homozygous variant of VPS13A (c.9263T > G; p.M3088R) within the mutation spectrum of VPS13A-associated ChAc. Furthermore, mutations in VPS13A and co-mutations in its potential interacting partner(s) might contribute to the diverse clinical manifestations of ChAc, which requires further study.
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Affiliation(s)
- Sima Chaudhari
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dushyanth Babu Jasti
- Department of Neurology, Kasturba Medical College, Manipal, Karnataka, 576104, India
| | - Sankar Prasad Gorthi
- Department of Neurology, Kasturba Medical College, Manipal, Karnataka, 576104, India
- Department of Neurology, Bharati Hospital and Research Center, Bharati Vidyapeeth (Deemed to be University) Medical College and Hospital, Dhankawadi, Pune, Maharashtra, 411043, India
| | - Lavanya Prakash Acharya
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Manoj Bhat
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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3
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Tran Mau-Them F, Delanne J, Denommé-Pichon AS, Safraou H, Bruel AL, Vitobello A, Garde A, Nambot S, Bourgon N, Racine C, Sorlin A, Moutton S, Marle N, Rousseau T, Sagot P, Simon E, Vincent-Delorme C, Boute O, Colson C, Petit F, Legendre M, Naudion S, Rooryck C, Prouteau C, Colin E, Guichet A, Ziegler A, Bonneau D, Morel G, Fradin M, Lavillaureix A, Quelin C, Pasquier L, Odent S, Vera G, Goldenberg A, Guerrot AM, Brehin AC, Putoux A, Attia J, Abel C, Blanchet P, Wells CF, Deiller C, Nizon M, Mercier S, Vincent M, Isidor B, Amiel J, Dard R, Godin M, Gruchy N, Jeanne M, Schaeffer E, Maillard PY, Payet F, Jacquemont ML, Francannet C, Sigaudy S, Bergot M, Tisserant E, Ascencio ML, Binquet C, Duffourd Y, Philippe C, Faivre L, Thauvin-Robinet C. Prenatal diagnosis by trio exome sequencing in fetuses with ultrasound anomalies: A powerful diagnostic tool. Front Genet 2023; 14:1099995. [PMID: 37035737 PMCID: PMC10076577 DOI: 10.3389/fgene.2023.1099995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/24/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction: Prenatal ultrasound (US) anomalies are detected in around 5%-10% of pregnancies. In prenatal diagnosis, exome sequencing (ES) diagnostic yield ranges from 6% to 80% depending on the inclusion criteria. We describe the first French national multicenter pilot study aiming to implement ES in prenatal diagnosis following the detection of anomalies on US. Patients and methods: We prospectively performed prenatal trio-ES in 150 fetuses with at least two US anomalies or one US anomaly known to be frequently linked to a genetic disorder. Trio-ES was only performed if the results could influence pregnancy management. Chromosomal microarray (CMA) was performed before or in parallel. Results: A causal diagnosis was identified in 52/150 fetuses (34%) with a median time to diagnosis of 28 days, which rose to 56/150 fetuses (37%) after additional investigation. Sporadic occurrences were identified in 34/56 (60%) fetuses and unfavorable vital and/or neurodevelopmental prognosis was made in 13/56 (24%) fetuses. The overall diagnostic yield was 41% (37/89) with first-line trio-ES versus 31% (19/61) after normal CMA. Trio-ES and CMA were systematically concordant for identification of pathogenic CNV. Conclusion: Trio-ES provided a substantial prenatal diagnostic yield, similar to postnatal diagnosis with a median turnaround of approximately 1 month, supporting its routine implementation during the detection of prenatal US anomalies.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Aurore Garde
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nicolas Bourgon
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sébastien Moutton
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nathalie Marle
- Laboratoire Génétique Chromosomique et Moléculaire, CHU Dijon Bourgogne, Dijon, France
| | - Thierry Rousseau
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Paul Sagot
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Emmanuel Simon
- Service de Gynécologie Obstétrique, Médecine Fœtale et Stérilité Conjugale, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Catherine Vincent-Delorme
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Odile Boute
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Cindy Colson
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Florence Petit
- CHU Lille, Clinique de Génétique Guy Fontaine, Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs” Nord-Ouest, FLille, France
| | - Marine Legendre
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Sophie Naudion
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Caroline Rooryck
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
| | - Clément Prouteau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Estelle Colin
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Agnès Guichet
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Alban Ziegler
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Dominique Bonneau
- Biochemistry and Genetics Department, University Hospital of Angers, Angers, France
| | - Godelieve Morel
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Alinoé Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Chloé Quelin
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Gabriella Vera
- Service de Génétique—Unité de Génétique Clinique, Rouen, France
| | | | | | | | - Audrey Putoux
- Service de Génétique—GH Est-Hôpital Femme Mère Enfant, Lyon, France
| | | | - Carine Abel
- Service de Génétique et Centre de Diagnostic Anténatal, CHU de Lyon HCL—GH Nord-Hôpital de La Croix Rousse, Lyon, France
| | - Patricia Blanchet
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Constance F. Wells
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Caroline Deiller
- Equipe Maladies Génétiques de L’Enfant et de L’Adulte, Département Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU de Montpellier, University Montpellier, Montpellier, France
| | - Mathilde Nizon
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Marie Vincent
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France
- Institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Jeanne Amiel
- Equipe “Embryologie et Génétiques des Malformations Congénitales", Institut Imagine—INSERM U1163, Institut des Maladies Génétiques, Paris, France
- Service de Génétique Médicale et Clinique, Hôpital Necker-Enfants Malades, Paris, France
| | - Rodolphe Dard
- Unité Fonctionnelle de Génétique Médicale, Cytogénétique, Génétique Médicale et Biologie de La Reproduction, Centre Hospitalier Intercommunal Poissy-Saint-Germain-en-Laye, Poissy, France
| | - Manon Godin
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Nicolas Gruchy
- Service de Génétique, CHU Caen Clemenceau, EA 7450 Biotargen, University Caen, Caen, France
| | - Médéric Jeanne
- Service de Génétique, CHU de Tours, Tours, France
- UMR 1253, IBrain, Université de Tours, Inserm, Tours, France
| | - Elise Schaeffer
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Pierre-Yves Maillard
- Service de Génétique Médicale, CHU de Strasbourg—Hôpital de Hautepierre, Strasbourg, France
| | - Frédérique Payet
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Marie-Line Jacquemont
- Service de Génétique Médicale, Pôle Femme, Mère, Enfants CHU de La Réunion—GH Sud Réunion—Saint-Pierre, Saint-Pierre, France
| | - Christine Francannet
- Service de Génétique Médicale, Pôle Femme et Enfant, CHU de Clermont-Ferrand—Hôpital D'Estaing, Clermont-Ferrand, France
| | - Sabine Sigaudy
- Unité de Génétique Clinique Prénatale, Département de Génétique Médicale, CHU de Marseille—Hôpital de La Timone, Marseille, France
| | - Marine Bergot
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | | | - Marie-Laure Ascencio
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Christine Binquet
- Centre D'Investigation Clinique CIC-EC Inserm CIC1432, UFR des Sciences de Santé, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- INSERM UMR1231 GAD, F-21000, Dijon, France
- Centre de Référence Maladies Rares “Anomalies Du Développement et Syndromes Malformatifs”, Centre de Génétique, FHU TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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5
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Belova V, Shmitko A, Pavlova A, Afasizhev R, Cheranev V, Tabanakova A, Ponikarovskaya N, Rebrikov D, Korostin D. Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing. BMC Genomics 2022; 23:582. [PMID: 35962321 PMCID: PMC9375261 DOI: 10.1186/s12864-022-08825-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Exome sequencing is becoming a routine in health care, because it increases the chance of pinpointing the genetic cause of an individual patient's condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+ 3.06%) and indels (+ 8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.
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Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation.
| | - Anna Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Anastasia Tabanakova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Natalya Ponikarovskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, Moscow, 117997, Russian Federation
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