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Moya R, Angée C, Hanein S, Jabot-Hanin F, Kaplan J, Perrault I, Rozet JM, Fares Taie L. Four Unique Genetic Variants in Three Genes Account for 62.7% of Early-Onset Severe Retinal Dystrophy in Chile: Diagnostic and Therapeutic Consequences. Int J Mol Sci 2024; 25:6151. [PMID: 38892339 PMCID: PMC11172861 DOI: 10.3390/ijms25116151] [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: 04/04/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Leber congenital amaurosis (LCA)/early-onset severe retinal dystrophy (EOSRD) stand as primary causes of incurable childhood blindness. This study investigates the clinical and molecular architecture of syndromic and non-syndromic LCA/EOSRD within a Chilean cohort (67 patients/60 families). Leveraging panel sequencing, 95.5% detection was achieved, revealing 17 genes and 126 variants (32 unique). CRB1, LCA5, and RDH12 dominated (71.9%), with CRB1 being the most prevalent (43.8%). Notably, four unique variants (LCA5 p.Glu415*, CRB1 p.Ser1049Aspfs*40 and p.Cys948Tyr, RDH12 p.Leu99Ile) constituted 62.7% of all disease alleles, indicating their importance for targeted analysis in Chilean patients. This study underscores a high degree of inbreeding in Chilean families affected by pediatric retinal blindness, resulting in a limited mutation repertoire. Furthermore, it complements and reinforces earlier reports, indicating the involvement of ADAM9 and RP1 as uncommon causes of LCA/EOSRD. These data hold significant value for patient and family counseling, pharmaceutical industry endeavors in personalized medicine, and future enrolment in gene therapy-based treatments, particularly with ongoing trials (LCA5) or advancing preclinical developments (CRB1 and RDH12).
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Affiliation(s)
- Rene Moya
- Department of Ophthalmology, Hospital del Salvador, Universidad de Chile, Santiago 7500922, Chile;
| | - Clémentine Angée
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Sylvain Hanein
- Bioinformatic Platform, INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
| | - Lucas Fares Taie
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France (I.P.)
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Armirola-Ricaurte C, Zonnekein N, Koutsis G, Amor-Barris S, Pelayo-Negro AL, Atkinson D, Efthymiou S, Turchetti V, Dinopoulos A, Garcia A, Karakaya M, Moris G, Polat AI, Yiş U, Espinos C, Van de Vondel L, De Vriendt E, Karadima G, Wirth B, Hanna M, Houlden H, Berciano J, Jordanova A. Alternative splicing expands the clinical spectrum of NDUFS6-related mitochondrial disorders. Genet Med 2024; 26:101117. [PMID: 38459834 PMCID: PMC11180951 DOI: 10.1016/j.gim.2024.101117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024] Open
Abstract
PURPOSE We describe 3 families with Charcot-Marie-Tooth neuropathy (CMT), harboring a homozygous NDUFS6 NM_004553.6:c.309+5G>A variant previously linked to fatal Leigh syndrome. We aimed to characterize clinically and molecularly the newly identified patients and understand the mechanism underlying their milder phenotype. METHODS The patients underwent extensive clinical examinations. Exome sequencing was done in 4 affected individuals. The functional effect of the c.309+5G>A variant was investigated in patient-derived EBV-transformed lymphoblasts at the complementary DNA, protein, and mitochondrial level. Alternative splicing was evaluated using complementary DNA long-read sequencing. RESULTS All patients presented with early-onset, slowly progressive axonal CMT, and nystagmus; some exhibited additional central nervous system symptoms. The c.309+5G>A substitution caused the expression of aberrantly spliced transcripts and negligible levels of the canonical transcript. Immunoblotting showed reduced levels of mutant isoforms. No detectable defects in mitochondrial complex stability or bioenergetics were found. CONCLUSION We expand the clinical spectrum of NDUFS6-related mitochondrial disorders to include axonal CMT, emphasizing the clinical and pathophysiologic overlap between these 2 clinical entities. This work demonstrates the critical role that alternative splicing may play in modulating the severity of a genetic disorder, emphasizing the need for careful consideration when interpreting splice variants and their implications on disease prognosis.
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Affiliation(s)
- Camila Armirola-Ricaurte
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Noortje Zonnekein
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Georgios Koutsis
- Neurogenetics Unit, 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Silvia Amor-Barris
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ana Lara Pelayo-Negro
- University Hospital Marqués de Valdecilla (IFIMAV), University of Cantabria, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Santander, Spain
| | - Derek Atkinson
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Valentina Turchetti
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Argyris Dinopoulos
- 3rd Department of Pediatrics, Attiko Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonio Garcia
- Service of Clinical Neurophysiology, University Hospital Marqués de Valdecilla, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Santander, Spain
| | - Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases, University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - German Moris
- Service of Neurology, University Hospital Central de Asturias, University of Oviedo, Oviedo, Spain
| | - Ayşe Ipek Polat
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Uluç Yiş
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Carmen Espinos
- Rare Neurodegenerative Disease Laboratory, Centro de Investigación Príncipe Felipe (CIPF), CIBER on Rare Diseases (CIBERER), Valencia, Spain
| | - Liedewei Van de Vondel
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Els De Vriendt
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Georgia Karadima
- Neurogenetics Unit, 1st Department of Neurology, Eginitio Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases, University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Michael Hanna
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, United Kingdom
| | - Jose Berciano
- University Hospital Marqués de Valdecilla (IFIMAV), University of Cantabria, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Santander, Spain
| | - Albena Jordanova
- Molecular Neurogenomics group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium; Molecular Neurogenomics group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Medical Chemistry and Biochemistry, Medical University-Sofia, Sofia, Bulgaria.
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Fusaro M, Coustal C, Barnabei L, Riller Q, Heller M, Ho Nhat D, Fourrage C, Rivière S, Rieux-Laucat F, Maria ATJ, Picard C. A large deletion in a non-coding regulatory region leads to NFKB1 haploinsufficiency in two adult siblings. Clin Immunol 2024; 261:110165. [PMID: 38423196 DOI: 10.1016/j.clim.2024.110165] [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: 10/10/2023] [Revised: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Mutations in NFkB pathway genes can cause inborn errors of immunity (IEI), with NFKB1 haploinsufficiency being a significant etiology for common variable immunodeficiency (CVID). Indeed, mutations in NFKB1 are found in 4 to 5% of in European and United States CVID cohorts, respectively; CVID representing almost ¼ of IEI patients in European countries registries. This case study presents a 49-year-old patient with respiratory infections, chronic diarrhea, immune thrombocytopenia, hypogammaglobulinemia, and secondary lymphoma. Comprehensive genetic analysis, including high-throughput sequencing of 300 IEI-related genes and copy number variation analysis, identified a critical 2.6-kb deletion spanning the first untranslated exon and its upstream region. The region's importance was confirmed through genetic markers indicative of enhancers and promoters. The deletion was also found in the patient's brother, who displayed similar but milder symptoms. Functional analysis supported haploinsufficiency with reduced mRNA and protein expression in both patients. This case underscores the significance of copy number variation (CNV) analysis and targeting noncoding exons within custom gene panels, emphasizing the broader genomic approaches needed in medical genetics.
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Affiliation(s)
- Mathieu Fusaro
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France; Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital - Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.
| | - Cyrille Coustal
- Internal Medicine and Multi-Organic Diseases Department, Hôpital Saint Éloi, CHU Montpellier, Montpellier, France
| | - Laura Barnabei
- Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Institut Imagine, INSERM UMR 1163, F-75015 Paris, France
| | - Quentin Riller
- Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Institut Imagine, INSERM UMR 1163, F-75015 Paris, France
| | - Marion Heller
- Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital - Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Duong Ho Nhat
- Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Institut Imagine, INSERM UMR 1163, F-75015 Paris, France
| | - Cécile Fourrage
- INSERM-UMR 1163, Imagine Institute, Paris, France; Bioinformatics Core Facility, INSERM-UMR 1163, Imagine Institute, Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Service 3633, INSERM, University Paris Cité, Paris, France
| | - Sophie Rivière
- Internal Medicine and Multi-Organic Diseases Department, Hôpital Saint Éloi, CHU Montpellier, Montpellier, France
| | - Frédéric Rieux-Laucat
- Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Institut Imagine, INSERM UMR 1163, F-75015 Paris, France
| | - Alexandre Thibault Jacques Maria
- Internal Medicine & Onco-Immunology (MedI2O), Institute for Regenerative Medicine and Biotherapy (IRMB), Montpellier University Hospital, Montpellier, France; IRMB, University of Montpellier, INSERM, CHU Montpellier, Montpellier, France
| | - Capucine Picard
- Université Paris Cité, INSERM UMR1163, Imagine Institute, Paris, France; Study Center for Primary Immunodeficiencies, Necker-Enfants Malades Hospital - Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; French National Reference Center for Primary Immune Deficiencies CEREDIH, Necker University, Hospital for Sick Children - AP-HP, Paris, France
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Jordan P, Dorval G, Arrondel C, Morinière V, Tournant C, Audrezet MP, Michel-Calemard L, Putoux A, Lesca G, Labalme A, Whalen S, Loeuillet L, Martinovic J, Attie-Bitach T, Bessières B, Schaefer E, Scheidecker S, Lambert L, Beneteau C, Patat O, Boute-Benejean O, Molin A, Guimiot F, Fontanarosa N, Nizon M, Lefebvre M, Jeanpierre C, Saunier S, Heidet L. Targeted next-generation sequencing in a large series of fetuses with severe renal diseases. Hum Mutat 2022; 43:347-361. [PMID: 35005812 DOI: 10.1002/humu.24324] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 11/07/2022]
Abstract
We report the screening of a large panel of genes in a series of 100 fetuses (98 families) affected with severe renal defects. Causative variants were identified in 22% of cases, greatly improving genetic counseling. The percentage of variants explaining the phenotype was different according to the type of phenotype. The highest diagnostic yield was found in cases affected with the ciliopathy-like phenotype (11/15 families and, in addition, a single heterozygous or a homozygous Class 3 variant in PKHD1 in three unrelated cases with autosomal recessive polycystic kidney disease). The lowest diagnostic yield was observed in cases with congenital anomalies of the kidney and urinary tract (9/78 families and, in addition, Class 3 variants in GREB1L in three unrelated cases with bilateral renal agenesis). Inheritance was autosomal recessive in nine genes (PKHD1, NPHP3, CEP290, TMEM67, DNAJB11, FRAS1, ACE, AGT, and AGTR1), and autosomal dominant in six genes (PKD1, PKD2, PAX2, EYA1, BICC1, and MYOCD). Finally, we developed an original approach of next-generation sequencing targeted RNA sequencing using the custom capture panel used for the sequencing of DNA, to validate one MYOCD heterozygous splicing variant identified in two male siblings with megabladder and inherited from their healthy mother.
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Affiliation(s)
- Penelope Jordan
- APHP Service de Génétique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Guillaume Dorval
- APHP Service de Génétique, Hôpital Universitaire Necker-Enfants Malades, Paris, France.,Inserm U1163, Laboratoire des Maladies Rénales Héréditaires Institut Imagine, Université de Paris, Paris, France.,APHP Service de Néphrologie Pédiatrique, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Christelle Arrondel
- Inserm U1163, Laboratoire des Maladies Rénales Héréditaires Institut Imagine, Université de Paris, Paris, France
| | - Vincent Morinière
- APHP Service de Génétique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Carole Tournant
- APHP Service de Génétique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Marie-Pierre Audrezet
- Service de Génétique moléculaire, Génétique, Génomique et Biotechnologies, UMR 1078, Hôpital Universitaire de Brest, Brest, France
| | - Laurence Michel-Calemard
- Service Biochimie Biologie Moléculaire Grand Est, Hospices Civils de Lyon, Groupement Hospitalier Est, CBPE, Bron, France
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Gaethan Lesca
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Audrey Labalme
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier Est, Bron, France
| | - Sandra Whalen
- APHP UF de Génétique Clinique, Centre de Référence des Anomalies du Développement et Syndromes Malformatifs, APHP, Hôpital Armand Trousseau, ERN ITHACA, Sorbonne Université, Paris, France
| | - Laurence Loeuillet
- APHP Service d'Embryofœtopathologie, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Jelena Martinovic
- APHP Service de Fœtopathologie, Hôpital Universitaire Antoine Béclère, Clamart, France
| | - Tania Attie-Bitach
- APHP Service d'Embryofœtopathologie, Hôpital Universitaire Necker-Enfants Malades, Paris, France.,Inserm U 1163, Institut Imagine, Université de Paris, Paris, France
| | - Bettina Bessières
- APHP Service d'Embryofœtopathologie, Hôpital Universitaire Necker-Enfants Malades, Paris, France.,Inserm U 1163, Institut Imagine, Université de Paris, Paris, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sophie Scheidecker
- Service de Génétique Médicale, Institut de Génétique médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laetitia Lambert
- Service de Génétique Médicale, Centre Hospitalier Régional Universitaire de Nancy, Nancy, France
| | - Claire Beneteau
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Odile Boute-Benejean
- Service de Génétique Médicale, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Arnaud Molin
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Fabien Guimiot
- APHP Service d'Embryo-Fœtopathologie, Hôpital Universitaire Robert Debré, Paris, France
| | | | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, L'institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Mathilde Lefebvre
- APHP Service de Pathologie fœtale, Hôpital Universitaire Armand Trousseau, Paris, France
| | - Cécile Jeanpierre
- Inserm U1163, Laboratoire des Maladies Rénales Héréditaires Institut Imagine, Université de Paris, Paris, France
| | - Sophie Saunier
- Inserm U1163, Laboratoire des Maladies Rénales Héréditaires Institut Imagine, Université de Paris, Paris, France
| | - Laurence Heidet
- Inserm U1163, Laboratoire des Maladies Rénales Héréditaires Institut Imagine, Université de Paris, Paris, France.,APHP Service de Néphrologie Pédiatrique, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Universitaire Necker-Enfants Malades, Paris, France
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5
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Frydas A, Cacace R, van der Zee J, Van Broeckhoven C, Wauters E. Genetic variants in progranulin upstream open reading frames increase downstream protein expression. Neurobiol Aging 2021; 110:113-121. [PMID: 34620513 DOI: 10.1016/j.neurobiolaging.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/29/2021] [Accepted: 09/05/2021] [Indexed: 11/25/2022]
Abstract
Premature termination codon (PTC) mutations in the granulin gene (GRN) lead to loss-of-function (LOF) of the progranulin protein (PGRN), causing frontotemporal lobar degeneration (FTLD) by haploinsufficiency. GRN expression is regulated at multiple levels, including the 5' untranslated region (UTR). The main 5' UTR of GRN and an alternative 5' UTR, contain upstream open reading frames (uORFs). These mRNA elements generally act as cis-repressors of translation. Disruption of each uORF of the alternative 5' UTR, increases protein expression with the 2 ATG-initiated uORFs being capable of initiating translation. We performed targeted sequencing of the uORF regions in a Flanders-Belgian cohort of patients with frontotemporal dementia (FTD) and identified 2 genetic variants, one in each 5' UTR. Both variants increase downstream protein levels, with the main 5' UTR variant rs76783532 causing a significant 1.5-fold increase in protein expression. We observed that the presence of functional uORFs in the alternative 5' UTR act as potential regulators of PGRN expression and demonstrate that genetic variation within GRN uORFs can alter their function.
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Affiliation(s)
- Alexandros Frydas
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Cacace
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Julie van der Zee
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Eline Wauters
- VIB Center for Molecular Neurology, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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6
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Hoogmartens J, Hens E, Engelborghs S, De Deyn PP, van der Zee J, Van Broeckhoven C, Cacace R. Investigation of the role of matrix metalloproteinases in the genetic etiology of Alzheimer's disease. Neurobiol Aging 2021; 104:105.e1-105.e6. [PMID: 33892965 DOI: 10.1016/j.neurobiolaging.2021.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/26/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022]
Abstract
Matrix metalloproteinases (MMPs) are a multigene family of proteinases regulating the functions of a large number of signaling and scaffolding molecules that are involved in neuro-inflammation, synaptic dysfunction and neuronal death. MMPs have been associated with neurological conditions, such as Alzheimer's disease (AD), through a sudden and massive upregulation of particular members of the MMP family. Evidence for this hypothesis can be found in the clinical observation of increased MMP1 and MMP3 expression levels in plasma of AD patients compared to control individuals and in the pro-amyloidogenic effects that have been described for additional MMP family members like MMP13, MT1-MMP, and MT5-MMP. Consequently, we investigated the role of MMP1, 3, 13, MT1-MMP, and MT5-MMP in the genetic etiology of AD. We performed full exonic resequencing of these 5 MMPs in 1278 AD patients (mean age at onset [AAO]: 74.88 ± 9.10, range: 29-96) and 797 age-matched control individuals (mean age at inclusion [AAI]: 74.92 ± 6.48, range: 65-100) from Flanders-Belgium and identified MMP13 as most promising candidate gene. We identified 6 ultra-rare (≤0.01%) MMP13 missense mutations in 6 patients that were absent from the control cohort. We observed in one control individual a frameshift mutation (p.G269Qfs*2) leading to a premature termination codon. Based on previously described functional evidence, suggesting that MMP13 regulates BACE1 processing, and our genetic findings, we hypothesize a gain-of-function disease mechanism for the missense mutations found in patients. Functional experimental studies remain essential to assess the effect of these mutations on disease related processes and genetic replication studies are needed to corroborate our findings.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elisabeth Hens
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Edegem, Belgium; Department of Neurology, UZ Brussel and Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology, UZ Brussel and Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Paul De Deyn
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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8
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Perrault I, Hanein S, Gérard X, Mounguengue N, Bouyakoub R, Zarhrate M, Fourrage C, Jabot-Hanin F, Bocquet B, Meunier I, Zanlonghi X, Kaplan J, Rozet JM. Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort. Genes (Basel) 2021; 12:genes12020287. [PMID: 33670832 PMCID: PMC7922592 DOI: 10.3390/genes12020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023] Open
Abstract
Leber congenital amaurosis (LCA) encompasses the earliest and most severe retinal dystrophies and can occur as a non-syndromic or a syndromic disease. Molecular diagnosis in LCA is of particular importance in clinical decision-making and patient care since it can provide ocular and extraocular prognostics and identify patients eligible to develop gene-specific therapies. Routine high-throughput molecular testing in LCA yields 70%–80% of genetic diagnosis. In this study, we aimed to investigate the non-coding regions of one non-syndromic LCA gene, RPGRIP1, in a series of six families displaying one single disease allele after a gene-panel screening of 722 LCA families which identified 26 biallelic RPGRIP1 families. Using trio-based high-throughput whole locus sequencing (WLS) for second disease alleles, we identified a founder deep intronic mutation (NM_020366.3:c.1468-128T>G) in 3/6 families. We employed Sanger sequencing to search for the pathologic variant in unresolved LCA cases (106/722) and identified three additional families (two homozygous and one compound heterozygous with the NM_020366.3:c.930+77A>G deep intronic change). This makes the c.1468-128T>G the most frequent RPGRIP1 disease allele (8/60, 13%) in our cohort. Studying patient lymphoblasts, we show that the pathologic variant creates a donor splice-site and leads to the insertion of the pseudo-exon in the mRNA, which we were able to hamper using splice-switching antisense oligonucleotides (AONs), paving the way to therapies.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Correspondence:
| | - Sylvain Hanein
- Translational Genetics, Institute of Genetic Diseases, INSERM UMR1163, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Nelson Mounguengue
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Ryme Bouyakoub
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Mohammed Zarhrate
- Genomics Platform, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Cécile Fourrage
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
- Bioinformatics Core Facility, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Béatrice Bocquet
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
| | - Isabelle Meunier
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, Univ Montpellier, CHU, 34091 Montpellier, France
| | - Xavier Zanlonghi
- Eye Clinic Jules Verne, 44300 Nantes, France;
- CHU, 35000 Rennes, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Ophthalmology Department, University Hospital Henri Mondor, APHP, 94000 Créteil, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
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9
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Parobkova E, van der Zee J, Dillen L, Van Broeckhoven C, Rusina R, Matej R. Sporadic Creutzfeldt-Jakob Disease and Other Proteinopathies in Comorbidity. Front Neurol 2020; 11:596108. [PMID: 33329348 PMCID: PMC7735378 DOI: 10.3389/fneur.2020.596108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Sporadic Creutzfeldt–Jakob disease (sCJD) is the most common type of a group of transmissible spongiform encephalopathies (prion diseases). The etiology of the sporadic form of CJD is still unclear. sCJD can occur in combination with other neurodegenerative diseases, which further complicates the diagnosis. Alzheimer's disease (AD), e.g., is often seen in conjunction with sCJD. Method: In this study, we performed a systematic analysis of 15 genes related to the most important neurodegenerative diseases - AD, frontotemporal dementia, amyotrophic lateral sclerosis, prion disease, and Parkinson's disease - in a cohort of sCJD and sCJD in comorbidity with AD and primary age-related proteinopathy (PART). A total of 30 neuropathologically verified cases of sCJD with and without additional proteinopathies were included in the study. In addition, we compared microtubule-associated protein tau (MAPT) haplotypes between sCJD patients and patients with sCJD and PART or sCJD and AD. Then we studied the interaction between the Apolipoprotein E gene (APOE) and PRNP in sCJD patients. Results: We did not find any causal mutations in the neurodegenerative disease genes. We did detect a p.E318G missense variant of uncertain significance (VUS) in PSEN1 in three patients. In PRNP, we also found a previously described non-pathogenic insertion (p.P84_Q91Q). Conclusion: Our pilot study failed to find any critical differences between pure sCJD and sCJD in conjunction with other comorbid neurodegenerative diseases. Further investigations are needed to better understand this phenomenon.
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Affiliation(s)
- Eva Parobkova
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia.,National Reference Laboratory for Human Prion Diseases, Thomayer Hospital, Prague, Czechia
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Vlaams Instituut voor Biotechnologie (VIB), Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Lubina Dillen
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Vlaams Instituut voor Biotechnologie (VIB), Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Vlaams Instituut voor Biotechnologie (VIB), Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Robert Rusina
- National Reference Laboratory for Human Prion Diseases, Thomayer Hospital, Prague, Czechia.,Department of Neurology, Third Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia
| | - Radoslav Matej
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czechia.,National Reference Laboratory for Human Prion Diseases, Thomayer Hospital, Prague, Czechia.,Department of Pathology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia.,Department of Pathology, Third Faculty of Medicine, Charles University and Kralovske Vinohrady University Hospital, Prague, Czechia
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10
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Hoogmartens J, Hens E, Engelborghs S, Vandenberghe R, De Deyn PP, Cacace R, Van Broeckhoven C. Contribution of homozygous and compound heterozygous missense mutations in VWA2 to Alzheimer's disease. Neurobiol Aging 2020; 99:100.e17-100.e23. [PMID: 33023779 DOI: 10.1016/j.neurobiolaging.2020.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease is the most frequent diagnosis of neurodegenerative dementia with early (≤65 years) and late (>65 years) onset ages in familial and sporadic patients. Causal mutations in 3 autosomal dominant Alzheimer genes, i.e. amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2), explain only 5%-10% of early-onset patients leaving the majority of patients genetically unresolved. To discover potential missing genetics, we used whole genome sequencing data of 17 early-onset patients with well-documented clinical diagnosis of Alzheimer's disease. In the discovery group, the mean onset age was 55.71 ± 6.83 years (range 37-65). Six patients had a brain autopsy and neuropathology confirmed Alzheimer's disease. Analysis of the genetic data identified in one patient a homozygous p.V366M missense mutation in the Von Willebrand factor A domain containing 2 gene (VWA2). Resequencing of the VWA2 coding region in an Alzheimer's disease patient cohort from Flanders-Belgium (n = 1148), including 152 early and 996 late onset patients, identified additional homozygous and compound heterozygous missense mutations in 1 early and 3 late-onset patients. Allele-sharing analysis identified common haplotypes among the compound heterozygous VWA2 mutation carriers, suggesting shared ancestors. Overall, we identified 5 patient carriers of homozygous or compound heterozygous missense mutations (5/1165; 0.43 %), 2 in early (2/169; 1.18 %) and 3 in late-onset (3/996; 0.30 %) patients. The frequencies of the homozygous and compound heterozygous missense mutations in patients are higher than expected from the frequencies calculated based on their combined single alleles. None of the homozygous/compound heterozygous missense mutation carriers had a family history of autosomal dominant Alzheimer's disease. Our findings suggest that homozygous and compound heterozygous missense mutations in VWA2 might contribute to the risk of Alzheimer's disease in sporadic patients.
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Affiliation(s)
- Julie Hoogmartens
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elisabeth Hens
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology, University Hospital Antwerp, Edegem, Belgium; Department of Neurology, University Hospital Brussel and Center for Neurosciences, Free University Brussels, Brussels, Belgium
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology, University Hospital Brussel and Center for Neurosciences, Free University Brussels, Brussels, Belgium
| | - Rik Vandenberghe
- Department of Neurology, University Hospitals Leuven and Department of Neurosciences, KU Leuven, Belgium
| | - Peter-P De Deyn
- Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp, Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium; Institute Born-Bunge, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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11
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Mutated ATP10B increases Parkinson's disease risk by compromising lysosomal glucosylceramide export. Acta Neuropathol 2020; 139:1001-1024. [PMID: 32172343 PMCID: PMC7244618 DOI: 10.1007/s00401-020-02145-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative brain disease presenting with a variety of motor and non-motor symptoms, loss of midbrain dopaminergic neurons in the substantia nigra pars compacta and the occurrence of α-synuclein-positive Lewy bodies in surviving neurons. Here, we performed whole exome sequencing in 52 early-onset PD patients and identified 3 carriers of compound heterozygous mutations in the ATP10B P4-type ATPase gene. Genetic screening of a Belgian PD and dementia with Lewy bodies (DLB) cohort identified 4 additional compound heterozygous mutation carriers (6/617 PD patients, 0.97%; 1/226 DLB patients, 0.44%). We established that ATP10B encodes a late endo-lysosomal lipid flippase that translocates the lipids glucosylceramide (GluCer) and phosphatidylcholine (PC) towards the cytosolic membrane leaflet. The PD associated ATP10B mutants are catalytically inactive and fail to provide cellular protection against the environmental PD risk factors rotenone and manganese. In isolated cortical neurons, loss of ATP10B leads to general lysosomal dysfunction and cell death. Impaired lysosomal functionality and integrity is well known to be implicated in PD pathology and linked to multiple causal PD genes and genetic risk factors. Our results indicate that recessive loss of function mutations in ATP10B increase risk for PD by disturbed lysosomal export of GluCer and PC. Both ATP10B and glucocerebrosidase 1, encoded by the PD risk gene GBA1, reduce lysosomal GluCer levels, emerging lysosomal GluCer accumulation as a potential PD driver.
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12
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Low Prevalence of GSC Gene Mutations in a Large Cohort of Predominantly Caucasian Patients with Hidradenitis Suppurativa. J Invest Dermatol 2020; 140:2085-2088.e14. [PMID: 32142795 DOI: 10.1016/j.jid.2019.10.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/23/2019] [Accepted: 10/01/2019] [Indexed: 11/21/2022]
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13
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Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A. NPJ Genom Med 2019; 4:31. [PMID: 31814998 PMCID: PMC6889285 DOI: 10.1038/s41525-019-0106-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/01/2019] [Indexed: 12/21/2022] Open
Abstract
The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for a lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 putative transcript models. Our annotations increase the transcriptional 'footprint' of these genes by over 674 kb. Using SCN1A as a case study, due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome or a similar phenotype with a panel of exon sequences representing eight established genes and identified two de novo SCN1A variants that now - through improved gene annotation - are ascribed to residing among our exons. These two (from 122 screened people, 1.6%) molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously classified SCN1A intronic Dravet syndrome-associated variant that now lies within a deeply conserved exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders.
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14
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Wang H, Wan Y, Yang Y, Li H, Mao L, Gao S, Xu J, Wang J. Novel compound heterozygous mutations in OCA2 gene associated with non-syndromic oculocutaneous albinism in a Chinese Han patient: a case report. BMC MEDICAL GENETICS 2019; 20:130. [PMID: 31345173 PMCID: PMC6659248 DOI: 10.1186/s12881-019-0850-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/19/2019] [Indexed: 11/24/2022]
Abstract
Background Oculocutaneous albinism (OCA) is a group of rare genetically heterogeneous disorders. The present study aimed to identify the genetic cause of a Chinese Han family with non-syndromic oculocutaneous albinism (OCA). Case presentation Here, we report an 11-month-old male proband from a Chinese Han non-consanguineous family, who presented with milky skin, yellow white hair, nystagmus, astigmatism, and hypermetropia. We performed the targeted next-generation sequencing (NGS) on the proband and identified two novel compound heterozygous variants (c.1865 T > C (p.Leu622Pro) and exons 17–21 deletion) in OCA2 gene associated with OCA type 2 (OCA2, OMIM 203200). Meanwhile, a previously reported heterozygous mutation (c.4805G > A) in MYO7 gene related with Usher syndrome type 1B was found. The online tools SIFT, PolyPhen-2, and Mutation Taster predicted variant c.1865 T > C was probably damaging. The residue p.Leu622 was in a highly conserved region among species by CLUSTALW. Three-dimensional homology model with I-TASSER indicated that p.Leu622Pro variant disturbed the formation of the α-helix, resulting in a random coil structure. The gross deletion (exons 17–21) in OCA2 gene has was not been reported previously. These two novel variants in OCA2 gene were inherited from each parent respectively, after verification by Sanger sequencing and quantitative PCR (qPCR) in the family. Conclusions This study indicates the two novel compound heterozygous mutations in OCA2 gene may be responsible for clinical manifestations of OCA2. It expands the mutation spectrum of OCA2 gene and is helpful to screen for large deletions with targeted NGS protocol in monogenic disease. It also assists the genetic counselling, carrier screening and personalized healthcare of the disease. Electronic supplementary material The online version of this article (10.1186/s12881-019-0850-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hairong Wang
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China
| | - Yang Wan
- Department of Obstetrics and Gynecology, Fuyang People's Hospital, Fuyang, 236000, China
| | - Yun Yang
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hao Li
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China
| | - Liangwei Mao
- Anhui Clinical Laboratories, BGI-Anhui, BGI-Shenzhen, Weisan Road, Fuyang, 236000, China.,College of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shuyang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jingjing Xu
- Prenatal diagnosis center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230071, China
| | - Jing Wang
- Prenatal diagnosis center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China, Hefei, 230071, China.
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15
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Cacace R, Heeman B, Van Mossevelde S, De Roeck A, Hoogmartens J, De Rijk P, Gossye H, De Vos K, De Coster W, Strazisar M, De Baets G, Schymkowitz J, Rousseau F, Geerts N, De Pooter T, Peeters K, Sieben A, Martin JJ, Engelborghs S, Salmon E, Santens P, Vandenberghe R, Cras P, P. De Deyn P, C. van Swieten J, M. van Duijn C, van der Zee J, Sleegers K, Van Broeckhoven C. Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability. Acta Neuropathol 2019; 137:901-918. [PMID: 30874922 PMCID: PMC6531610 DOI: 10.1007/s00401-019-01976-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
Emerging evidence suggested a converging mechanism in neurodegenerative brain diseases (NBD) involving early neuronal network dysfunctions and alterations in the homeostasis of neuronal firing as culprits of neurodegeneration. In this study, we used paired-end short-read and direct long-read whole genome sequencing to investigate an unresolved autosomal dominant dementia family significantly linked to 7q36. We identified and validated a chromosomal inversion of ca. 4 Mb, segregating on the disease haplotype and disrupting the coding sequence of dipeptidyl-peptidase 6 gene (DPP6). DPP6 resequencing identified significantly more rare variants-nonsense, frameshift, and missense-in early-onset Alzheimer's disease (EOAD, p value = 0.03, OR = 2.21 95% CI 1.05-4.82) and frontotemporal dementia (FTD, p = 0.006, OR = 2.59, 95% CI 1.28-5.49) patient cohorts. DPP6 is a type II transmembrane protein with a highly structured extracellular domain and is mainly expressed in brain, where it binds to the potassium channel Kv4.2 enhancing its expression, regulating its gating properties and controlling the dendritic excitability of hippocampal neurons. Using in vitro modeling, we showed that the missense variants found in patients destabilize DPP6 and reduce its membrane expression (p < 0.001 and p < 0.0001) leading to a loss of protein. Reduced DPP6 and/or Kv4.2 expression was also detected in brain tissue of missense variant carriers. Loss of DPP6 is known to cause neuronal hyperexcitability and behavioral alterations in Dpp6-KO mice. Taken together, the results of our genomic, genetic, expression and modeling analyses, provided direct evidence supporting the involvement of DPP6 loss in dementia. We propose that loss of function variants have a higher penetrance and disease impact, whereas the missense variants have a variable risk contribution to disease that can vary from high to low penetrance. Our findings of DPP6, as novel gene in dementia, strengthen the involvement of neuronal hyperexcitability and alteration in the homeostasis of neuronal firing as a disease mechanism to further investigate.
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Affiliation(s)
- Rita Cacace
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Bavo Heeman
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Sara Van Mossevelde
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Arne De Roeck
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Julie Hoogmartens
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Helena Gossye
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Kristof De Vos
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Greet De Baets
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Nathalie Geerts
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Karin Peeters
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Anne Sieben
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | | | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Eric Salmon
- Department of Neurology, Centre Hospitalier Universitaire de Liège and University of Liège, Liège, Belgium
| | - Patrick Santens
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Rik Vandenberghe
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Louvain, Belgium
- Laboratory of Cognitive Neurology, Department of Neurology, University Hospitals Leuven, Louvain, Belgium
| | - Patrick Cras
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
| | - Peter P. De Deyn
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - John C. van Swieten
- Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Julie van der Zee
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp, CDE, Universiteitsplein 1, 2610 Antwerp, Belgium
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16
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Cui Y, Wang Y, Zhang N, He J, Huang H, Liu F, Wei S, Dong Q, Wu J, Lin K, Chen W, Xiang J, Jin H, Peng Z, Zhao Q, Li W, Jiang D, Banerjee S. Novel loss-of-function mutation in BRCA2 gene identified in a Chinese female with a family history of ovarian cancer: A case report. Oncol Lett 2019; 17:3350-3354. [PMID: 30867769 PMCID: PMC6396105 DOI: 10.3892/ol.2019.9950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/08/2018] [Indexed: 12/03/2022] Open
Abstract
Inherited loss-of-function mutations in the tumor suppressor BRCA2 gene are associated with a high risk of ovarian cancer in the Chinese population. The current case report discusses a novel heterozygous insertion in BRCA2 gene, c.3195_3196insA, in a 54-year-old Chinese female with hereditary ovarian cancer. This frameshift mutation generates a premature stop codon at amino acid 1,076, which leads to a truncated BRCA2 protein instead of a wild-type BRCA2 protein with 3,418 amino acids. According to the Breast Cancer Information Core database, this mutation has not been previously reported. However, germline mutations of BRCA2 are a more prevalent cause of ovarian cancer in Chinese females compared with females in Western populations. The present study expands the mutational spectra of BRCA2 that is associated with ovarian cancer.
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Affiliation(s)
- Yanzhi Cui
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Yanyan Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Ningzhi Zhang
- Prenatal Diagnosis Center, Department of Obstetrics, Fuyang People's Hospital, Fuyang, Anhui 236000, P.R. China
| | - Jun He
- Changsha Hospital for Maternal and Child Health Care, Changsha, Hunan 410007, P.R. China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Fengling Liu
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Suju Wei
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Qian Dong
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Jing Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Keke Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Weixi Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Hui Jin
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Qiang Zhao
- Department of Obstetrics and Gynecology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong 529030, P.R. China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Da Jiang
- Department of Internal Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
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17
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Chen K, Dong SS, Wu N, Wu ZH, Zhou YX, Li K, Zhang F, Xiao JH. A novel multiplex fluorescent competitive PCR for copy number variation detection. Genomics 2018; 111:1745-1751. [PMID: 30529537 DOI: 10.1016/j.ygeno.2018.11.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
The copy number variation (CNV) is an important genetic marker in cancer and other diseases. To detect CNVs of specific genetic loci, the multiplex ligation-dependent probe amplification (MLPA) is an appropriate approach, but the experimental optimization and probe synthesis are still great challenges. The multiplex competitive PCR is an alternative method for CNV detection. However, the construction of internal competitive template and establishment of a stable multiplex PCR system are the main limiting factors for this method. Here, we introduce a novel multiplex fluorescent competitive PCR (NMFC-PCR) for detecting CNVs. In this method, the blunt hairpin primers are used to rapidly establish a stable multiplex PCR system due to the reduction of non-specific amplification, and limited cycles' amplification is used to obtain the internal competitive template instead of artificial synthesis. With this method, we tested 21 clinical samples with potential LIM homeobox 1 (LHX1) or T-box 6 (TBX6) deletion. Every three segments located on the LHX1 and TBX6 were selected as the target regions, while two segments located on X-chromosome and five segments located on autosome were selected as the reference regions for detecting CNVs. The results showed that the gender information of 21 samples can be accurately inferred by the copy number ratio (CNR) of X-chromosomal reference region to autosomal reference region (X/A), and 2 samples had one copy of LHX1 and 9 samples had one copy of TBX6. To evaluate the accuracy of NMFC-PCR, 5 random samples with CNV were also detected by array-based comparative genomic hybridization (aCGH), and the results of aCGH were consistent with the NMFC-PCR results. To further assess the performance of NMFC-PCR, 60 normal samples were simultaneously tested. The results showed that the gender results were exactly the same as known information, and CNVs of LHX1 or TBX6 were not found. In conclusion, the method is a cheap, efficient, accurate, and convenient competitive PCR method for CNV detection.
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Affiliation(s)
- Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, China
| | - Shuang-Shuang Dong
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Key Laboratory of Reproduction Regulation of NHFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China; Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhi-Hong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China; Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu-Xun Zhou
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Key Laboratory of Reproduction Regulation of NHFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.
| | - Jun-Hua Xiao
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, China.
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18
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Nishio S, Moteki H, Usami S. Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel. Mol Genet Genomic Med 2018; 6:678-686. [PMID: 29633566 PMCID: PMC6081219 DOI: 10.1002/mgg3.399] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent advances in molecular genetic analysis using next-generation sequencing (NGS) have drastically accelerated the identification of disease-causing gene mutations. Most next-generation sequencing analyses of inherited diseases have mainly focused on single-nucleotide variants and short indels, although, recently, structure variations including copy number variations have come to be considered an important cause of many different diseases. However, only a limited number of tools are available for multiplex PCR-based target genome enrichment. METHODS In this paper, we reported a simple and efficient copy number variation visualization method for Ion AmpliSeq™ target resequencing data. Unlike the hybridization capture-based target genome enrichment system, Ion AmpliSeq™ reads are multiplex PCR products, and each read generated by the same amplicon is quite uniform in length and position. Based on this feature, the depth of coverage information for each amplicon included in the barcode/amplicon coverage matrix file was used for copy number detection analysis. We also performed copy number analysis to investigate the utility of this method through the use of positive controls and a large Japanese hearing loss cohort. RESULTS Using this method, we successfully confirmed previously reported copy number loss cases involving the STRC gene and copy number gain in trisomy 21 cases. We also performed copy number analysis of a large Japanese hearing loss cohort (2,475 patients) and identified many gene copy number variants. The most prevalent copy number variation was STRC gene copy number loss, with 129 patients carrying this copy number variation. CONCLUSION Our copy number visualization method for Ion AmpliSeq™ data can be utilized in efficient copy number analysis for the comparison of a large number of samples. This method is simple and requires only easy calculations using standard spread sheet software.
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Affiliation(s)
- Shin‐ya Nishio
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
| | - Hideaki Moteki
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
| | - Shin‐ichi Usami
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
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19
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Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L. Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples. Oncotarget 2018; 7:61845-61859. [PMID: 27533253 PMCID: PMC5308695 DOI: 10.18632/oncotarget.11259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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Affiliation(s)
- Márton Zsolt Enyedi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | | | | | - Farkas Sükösd
- Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | - Adrienn Hajdu
- Delta Bio 2000 Ltd., Szeged 6726, Hungary.,Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | | | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
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20
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Philtjens S, Van Mossevelde S, van der Zee J, Wauters E, Dillen L, Vandenbulcke M, Vandenberghe R, Ivanoiu A, Sieben A, Willems C, Benussi L, Ghidoni R, Binetti G, Borroni B, Padovani A, Pastor P, Diez-Fairen M, Aguilar M, de Mendonça A, Miltenberger-Miltényi G, Hernández I, Boada M, Ruiz A, Nacmias B, Sorbi S, Almeida MR, Santana I, Clarimón J, Lleó A, Frisoni GB, Sanchez-Valle R, Lladó A, Gómez-Tortosa E, Gelpi E, Van den Broeck M, Peeters K, Cras P, De Deyn PP, Engelborghs S, Cruts M, Van Broeckhoven C. Rare nonsynonymous variants in SORT1 are associated with increased risk for frontotemporal dementia. Neurobiol Aging 2018; 66:181.e3-181.e10. [PMID: 29555433 DOI: 10.1016/j.neurobiolaging.2018.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 12/12/2022]
Abstract
We investigated the genetic role of sortilin (SORT1) in frontotemporal dementia (FTD). SORT1 is the neuronal receptor for granulin, encoded by the progranulin gene (GRN), a major causal gene for inherited FTD. In Belgian cohorts of 636 FTD patients and 1066 unaffected control individuals, we identified 5 patient-only nonsynonymous rare variants in SORT1. Rare variant burden analysis showed a significant increase in rare coding variants in patients compared to control individuals (p = 0.04), particularly in the β-propeller domain (p = 0.04), with 2 rare variants located in the predicted binding site for GRN (p = 0.001). We extended these observations by analyzing 3 independent patient/control cohorts sampled in Spain, Italy, and Portugal by partners of the European Early-Onset Dementia Consortium, together with 1155 FTD patients and 1161 control persons. An additional 7 patient-only nonsynonymous variants were observed in SORT1 in European patients. Meta-analysis of the rare nonsynonymous variants in the Belgian and European patient/control cohorts revealed a significant enrichment in FTD patients (p = 0.006), establishing SORT1 as a genetic risk factor for FTD.
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Affiliation(s)
- Stéphanie Philtjens
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sara Van Mossevelde
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Eline Wauters
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Lubina Dillen
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Mathieu Vandenbulcke
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Department of Old Age Psychiatry and Memory Clinic, University Hospitals Leuven, Leuven, Belgium
| | - Rik Vandenberghe
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Adrian Ivanoiu
- Department of Neurology, Saint-Luc University Hospital and Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | - Anne Sieben
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | | | - Luisa Benussi
- Molecular Markers Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy
| | - Giuliano Binetti
- Molecular Markers Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy; MAC Memory Center, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Centro San Giovanni di Dio-Fatebenefratelli, Brescia, Italy
| | | | | | - Pau Pastor
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Terrassa, Barcelona, Spain. Centro de Investigación Biomédica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain; Fundacio de Docencia i Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | - Monica Diez-Fairen
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Terrassa, Barcelona, Spain. Centro de Investigación Biomédica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain; Fundacio de Docencia i Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | - Miquel Aguilar
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, Terrassa, Barcelona, Spain. Centro de Investigación Biomédica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain; Fundacio de Docencia i Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Isabel Hernández
- Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Merce Boada
- Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Agustín Ruiz
- Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Benedetta Nacmias
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
| | - Sandro Sorbi
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy; IRCCS Don Gnocchi, Firenze, Italy
| | | | - Isabel Santana
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jordi Clarimón
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain; Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Alberto Lleó
- Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain; Center for Networker Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Giovanni B Frisoni
- Hôpitaux Universitaires de Genève et Université de Genève, Geneva, Switzerland; IRCCS Fatebenefratelli, Brescia, Italy
| | - Raquel Sanchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Ellen Gelpi
- Neurological Tissue Bank of the Biobanc - Hospital Clinic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marleen Van den Broeck
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Karin Peeters
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Patrick Cras
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Peter P De Deyn
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Sebastiaan Engelborghs
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Marc Cruts
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium; Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | -
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium
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- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology VIB, Antwerp, Belgium
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21
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Yang Z, Sun G. High-frequency, low-coverage "false positives" mutations may be true in GS Junior sequencing studies. Sci Rep 2017; 7:13751. [PMID: 29062110 PMCID: PMC5653793 DOI: 10.1038/s41598-017-13116-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
The GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
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Affiliation(s)
- Zhiliang Yang
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Guilian Sun
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China
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22
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Heidet L, Morinière V, Henry C, De Tomasi L, Reilly ML, Humbert C, Alibeu O, Fourrage C, Bole-Feysot C, Nitschké P, Tores F, Bras M, Jeanpierre M, Pietrement C, Gaillard D, Gonzales M, Novo R, Schaefer E, Roume J, Martinovic J, Malan V, Salomon R, Saunier S, Antignac C, Jeanpierre C. Targeted Exome Sequencing Identifies PBX1 as Involved in Monogenic Congenital Anomalies of the Kidney and Urinary Tract. J Am Soc Nephrol 2017; 28:2901-2914. [PMID: 28566479 PMCID: PMC5619971 DOI: 10.1681/asn.2017010043] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 04/20/2017] [Indexed: 01/01/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) occur in three to six of 1000 live births, represent about 20% of the prenatally detected anomalies, and constitute the main cause of CKD in children. These disorders are phenotypically and genetically heterogeneous. Monogenic causes of CAKUT in humans and mice have been identified. However, despite high-throughput sequencing studies, the cause of the disease remains unknown in most patients, and several studies support more complex inheritance and the role of environmental factors and/or epigenetics in the pathophysiology of CAKUT. Here, we report the targeted exome sequencing of 330 genes, including genes known to be involved in CAKUT and candidate genes, in a cohort of 204 unrelated patients with CAKUT; 45% of the patients were severe fetal cases. We identified pathogenic mutations in 36 of 204 (17.6%) patients. These mutations included five de novo heterozygous loss of function mutations/deletions in the PBX homeobox 1 gene (PBX1), a gene known to have a crucial role in kidney development. In contrast, the frequency of SOX17 and DSTYK variants recently reported as pathogenic in CAKUT did not indicate causality. These findings suggest that PBX1 is involved in monogenic CAKUT in humans and call into question the role of some gene variants recently reported as pathogenic in CAKUT. Targeted exome sequencing also proved to be an efficient and cost-effective strategy to identify pathogenic mutations and deletions in known CAKUT genes.
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Affiliation(s)
- Laurence Heidet
- Assistance Publique - Hôpitaux de Paris, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Paris, France
- Assistance Publique - Hôpitaux de Paris, Service de Néphrologie Pédiatrique
| | - Vincent Morinière
- Assistance Publique - Hôpitaux de Paris, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Paris, France
- Assistance Publique - Hôpitaux de Paris, Département de Génétique, and
| | - Charline Henry
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Lara De Tomasi
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
- Paris Diderot University, Paris, France
| | - Madeline Louise Reilly
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
- Paris Diderot University, Paris, France
| | - Camille Humbert
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Olivier Alibeu
- Genomic Platform, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Paris Descartes Sorbonne Paris Cité University, and
| | - Cécile Fourrage
- Assistance Publique - Hôpitaux de Paris, Département de Génétique, and
- Bioinformatic Plateform, Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Christine Bole-Feysot
- Genomic Platform, Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Paris Descartes Sorbonne Paris Cité University, and
| | - Patrick Nitschké
- Bioinformatic Plateform, Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Frédéric Tores
- Bioinformatic Plateform, Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marc Bras
- Bioinformatic Plateform, Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marc Jeanpierre
- Paris Descartes Sorbonne Paris Cité University, Paris, France
- Assistance Publique - Hôpitaux de Paris, Département de Génétique, Hôpital Cochin, Paris, France
| | | | - Dominique Gaillard
- Service de Génétique clinique, Centre Hospitalo-Universitaire de Reims, Reims, France
| | - Marie Gonzales
- Assistance Publique - Hôpitaux de Paris, Département de Génétique Médicale, Hôpital Armand Trousseau and Université Pierre et Marie Curie, Paris, France
| | - Robert Novo
- Centre Hospitalo-Universitaire de Lille, Hôpital Jeanne de Flandre, Service de Néphrologie Pédiatrique, Lille, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Joëlle Roume
- Unité de Génétique Médicale, Centre Hospitalier Intercommunal Poissy, St. Germain en Laye, Poissy, France; and
| | - Jelena Martinovic
- Assistance Publique - Hôpitaux de Paris, Unit of Fetal Pathology, Antoine Béclère Hospital, Clamart, France
| | - Valérie Malan
- Assistance Publique - Hôpitaux de Paris, Service de Cytogénétique, Hôpital Universitaire Necker-Enfants malades, Paris, France
| | - Rémi Salomon
- Assistance Publique - Hôpitaux de Paris, Centre de référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Paris, France
- Assistance Publique - Hôpitaux de Paris, Service de Néphrologie Pédiatrique
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Sophie Saunier
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Corinne Antignac
- Assistance Publique - Hôpitaux de Paris, Département de Génétique, and
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases
- Paris Descartes Sorbonne Paris Cité University, Paris, France
| | - Cécile Jeanpierre
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche 1163, Laboratory of Hereditary Kidney Diseases,
- Paris Descartes Sorbonne Paris Cité University, Paris, France
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Nguyen HP, Van Mossevelde S, Dillen L, De Bleecker JL, Moisse M, Van Damme P, Van Broeckhoven C, van der Zee J. NEK1 genetic variability in a Belgian cohort of ALS and ALS-FTD patients. Neurobiol Aging 2017; 61:255.e1-255.e7. [PMID: 28935222 DOI: 10.1016/j.neurobiolaging.2017.08.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/19/2017] [Indexed: 12/15/2022]
Abstract
We evaluated the genetic impact of the amyotrophic lateral sclerosis (ALS) risk gene never in mitosis gene a-related kinase 1 (NEK1) in a Belgian cohort of 278 patients with ALS (n = 245) or ALS with frontotemporal dementia (ALS-FTD, n = 33) and 609 control individuals. We identified 2 ALS patients carrying a loss-of-function (LOF) mutation, p.Leu854Tyrfs*2 and p.Tyr871Valfs*17, that was absent in the control group. A third LOF variant p.Ser1036* was present in 2 sibs with familial ALS but also in an unrelated control person. Missense variants were common in both patients (3.6%) and controls (3.0%). The missense variant, p.Arg261His, which was previously associated with ALS risk, was detected with a minor allele frequency of 0.90% in patients compared to 0.33% in controls. Taken together, NEK1 LOF variants accounted for 1.1% of patients, although interpretation of pathogenicity and penetrance is complicated by the observation of occasional LOF variants in unaffected individuals (0.16%). Furthermore, enrichment of additional ALS gene mutations was observed in NEK1 carriers, suggestive of a "second hit" model were NEK1 variants may modify disease presentation of driving mutations.
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Affiliation(s)
- Hung Phuoc Nguyen
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sara Van Mossevelde
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Lubina Dillen
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Jan L De Bleecker
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Laboratory of Neurobiology, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Laboratory of Neurobiology, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
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Perrone F, Nguyen HP, Van Mossevelde S, Moisse M, Sieben A, Santens P, De Bleecker J, Vandenbulcke M, Engelborghs S, Baets J, Cras P, Vandenberghe R, De Jonghe P, De Deyn PP, Martin JJ, Van Damme P, Van Broeckhoven C, van der Zee J. Investigating the role of ALS genes CHCHD10 and TUBA4A in Belgian FTD-ALS spectrum patients. Neurobiol Aging 2016; 51:177.e9-177.e16. [PMID: 28069311 DOI: 10.1016/j.neurobiolaging.2016.12.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/06/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
Abstract
Mutation screening and phenotypic profiling of 2 amyotrophic lateral sclerosis-(ALS) and frontotemporal dementia-(FTD) associated genes, CHCHD10 and TUBA4A, were performed in a Belgian cohort of 459 FTD, 28 FTD-ALS, and 429 ALS patients. In CHCHD10, we identified a novel nonsense mutation (p.Gln108*) in a patient with atypical clinical FTD and pathology-confirmed Parkinson's disease (1/459, 0.22%) leading to loss of transcript. We further observed 3 previously described missense variants (p.Pro34Ser, p.Pro80Leu, and p.Pro96Thr) that were also present in the matched control series. In TUBA4A, we detected a novel frameshift mutation (p.Arg64Glyfs*90) leading to a truncated protein in 1 FTD patient (1/459 of 0.22%) with family history of Parkinson's disease and cognitive impairment, and a novel missense mutation (p.Thr381Met) in 2 sibs with familial ALS and memory problems (1 index patient/429, 0.23%) in whom we previously identified a pathogenic Chromosome 9 open reading frame 72 repeat expansion mutation. The present study confirms the role of CHCHD10 and TUBA4A in the FTD-ALS spectrum, although genetic variations in these 2 genes are extremely rare in the Belgian population and often associated with symptomatology of related neurodegenerative diseases including Parkinson's disease and Alzheimer's disease.
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Affiliation(s)
- Federica Perrone
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Hung Phuoc Nguyen
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Sara Van Mossevelde
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Laboratory of Neurobiology, Vesalius Research Center, VIB, Leuven, Belgium
| | - Anne Sieben
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Patrick Santens
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Jan De Bleecker
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Mathieu Vandenbulcke
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Department of Old Age Psychiatry and Memory Clinic, University of Leuven, Leuven, Belgium
| | - Sebastiaan Engelborghs
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Patrick Cras
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Rik Vandenberghe
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Peter De Jonghe
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium; Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Peter P De Deyn
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology and Memory Clinic, Hospital Network Antwerp Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Jean-Jacques Martin
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Leuven, Belgium; Laboratory of Neurobiology, Vesalius Research Center, VIB, Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, Center for Molecular Neurology, VIB, Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
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Cammaerts S, Strazisar M, Smets B, Weckhuysen S, Nordin A, De Jonghe P, Adolfsson R, De Rijk P, Del Favero J. Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets. PLoS One 2015; 10:e0144428. [PMID: 26714269 PMCID: PMC4695081 DOI: 10.1371/journal.pone.0144428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/18/2015] [Indexed: 11/19/2022] Open
Abstract
As regulators of gene expression, microRNAs (miRNAs) are likely to play an important role in the development of disease. In this study we present a large-scale strategy to identify miRNAs with a role in the regulation of neuronal processes. Thereby we found variant rs7861254 located near the MIR204 gene to be significantly associated with schizophrenia. This variant resulted in reduced expression of miR-204 in neuronal-like SH-SY5Y cells. Analysis of the consequences of the altered miR-204 expression on the transcriptome of these cells uncovered a new mode of action for miR-204, being the regulation of noncoding RNAs (ncRNAs), including several miRNAs, such as MIR296. Furthermore, pathway analysis showed downstream effects of miR-204 on neurotransmitter and ion channel related gene sets, potentially mediated by miRNAs regulated through miR-204.
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Affiliation(s)
- Sophia Cammaerts
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Mojca Strazisar
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Bart Smets
- University of Antwerp, Antwerp, Belgium
- Centralized Service Facility, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Sarah Weckhuysen
- University of Antwerp, Antwerp, Belgium
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Annelie Nordin
- Division of Psychiatry, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Peter De Jonghe
- University of Antwerp, Antwerp, Belgium
- Neurogenetics Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Antwerp University Hospital, Antwerp, Belgium
| | - Rolf Adolfsson
- Division of Psychiatry, Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Peter De Rijk
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
| | - Jurgen Del Favero
- University of Antwerp, Antwerp, Belgium
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Multiplicom N.V., Niel, Belgium
- * E-mail:
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Arsenic R, Treue D, Lehmann A, Hummel M, Dietel M, Denkert C, Budczies J. Comparison of targeted next-generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer. BMC Clin Pathol 2015; 15:20. [PMID: 26587011 PMCID: PMC4652376 DOI: 10.1186/s12907-015-0020-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/12/2015] [Indexed: 01/04/2023] Open
Abstract
Background Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha, PIK3CA, is one of the most frequently mutated genes in breast cancer, and the mutation status of PIK3CA has clinical relevance related to response to therapy. The aim of our study was to investigate the mutation status of PIK3CA gene and to evaluate the concordance between NGS and SGS for the most important hotspot regions in exon 9 and 20, to investigate additional hotspots outside of these exons using NGS, and to correlate the PIK3CA mutation status with the clinicopathological characteristics of the cohort. Methods In the current study, next-generation sequencing (NGS) and Sanger Sequencing (SGS) was used for the mutational analysis of PIK3CA in 186 breast carcinomas. Results Altogether, 64 tumors had PIK3CA mutations, 55 of these mutations occurred in exons 9 and 20. Out of these 55 mutations, 52 could also be detected by Sanger sequencing resulting in a concordance of 98.4 % between the two sequencing methods. The three mutations missed by SGS had low variant frequencies below 10 %. Additionally, 4.8 % of the tumors had mutations in exons 1, 4, 7, and 13 of PIK3CA that were not detected by SGS. PIK3CA mutation status was significantly associated with hormone receptor-positivity, HER2-negativity, tumor grade, and lymph node involvement. However, there was no statistically significant association between the PIK3CA mutation status and overall survival. Conclusions Based on our study, NGS is recommended as follows: 1) for correctly assessing the mutation status of PIK3CA in breast cancer, especially for cases with low tumor content, 2) for the detection of subclonal mutations, and 3) for simultaneous mutation detection in multiple exons. Electronic supplementary material The online version of this article (doi:10.1186/s12907-015-0020-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruza Arsenic
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Denise Treue
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
| | - Jan Budczies
- Institute of Pathology, Charité University Hospital Berlin, Berlin, Germany
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Janssens J, Philtjens S, Kleinberger G, Van Mossevelde S, van der Zee J, Cacace R, Engelborghs S, Sieben A, Banzhaf-Strathmann J, Dillen L, Merlin C, Cuijt I, Robberecht C, Schmid B, Santens P, Ivanoiu A, Vandenbulcke M, Vandenberghe R, Cras P, De Deyn PP, Martin JJ, Maudsley S, Haass C, Cruts M, Van Broeckhoven C. Investigating the role of filamin C in Belgian patients with frontotemporal dementia linked to GRN deficiency in FTLD-TDP brains. Acta Neuropathol Commun 2015; 3:68. [PMID: 26555887 PMCID: PMC4641381 DOI: 10.1186/s40478-015-0246-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 10/21/2015] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) inclusions are pathological hallmarks of patients with frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Loss of TDP-43 in zebrafish engenders a severe muscle and vascular phenotype with a concomitant elevation of filamin C (FLNC) levels, an observation confirmed in the frontal cortex of FTLD-TDP patients. Here, we aimed to further assess the contribution of FLNC to frontotemporal dementia (FTD) etiology. We conducted a mutational screening of FLNC in a cohort of 529 unrelated Belgian FTD and FTD-ALS patients, and a control cohort of 920 unrelated and age-matched individuals. Additionally we performed an in-depth characterization of FLNC expression levels in FTD patients and a murine FTD model. In total 68 missense variants were identified of which 19 (MAF < 1 %) were patient-only. Gene burden analysis demonstrated a significant association between the presence of rare variants in FLNC and disease (P = 0.0349, RR = 1.46 [95 % CI 1.03–2.07]). Furthermore, elevated FLNC expression levels, observed previously in FTLD-TDP patients, were mainly attributable to FTD patients with the progranulin (GRN) p.0(IVS1 + 5G > C) loss-of-function mutation. Increased FLNC levels were, to a lesser extent, also identified in a FLNC p.V831I variant carrier and in FTD patients with the p.R159H mutation in valosin-containing protein (VCP). The GRN-associated increase of FLNC was confirmed in the frontal cortex of aged Grn knockout mice starting at 16–18 months of age. Combined quantitative proteomic and bioinformatic analyses of the frontal cortex of FTD patients possessing elevated FLNC levels, identified multiple altered protein factors involved in accelerated aging, neurodegeneration and synaptogenesis. Our findings further support the involvement of aberrant FLNC expression levels in FTD pathogenesis. Identification of increased FLNC levels in aged Grn mice and impaired pathways related to aging and neurodegeneration, implies a potential role for FLNC in mediating or accelerating the aging process.
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Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
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Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
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Yang Y, Mao B, Wang L, Mao L, Zhou A, Cao J, Hu J, Zhou Y, Pan Y, Wei X, Yang S, Mu F, Liu Z. Targeted next generation sequencing reveals a novel intragenic deletion of the LAMA2 gene in a patient with congenital muscular dystrophy. Mol Med Rep 2014; 11:3687-93. [PMID: 25544356 DOI: 10.3892/mmr.2014.3135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 11/14/2014] [Indexed: 11/05/2022] Open
Abstract
Mutations in the LAMA2 gene cause laminin α‑2 (merosin)‑deficient congenital muscular dystrophies, which are autosomal recessive muscle disorders. Laminin α‑2 is widely expressed in the basement membrane of skeletal muscle, the myotendinous junctions and extra‑synaptically at neuromuscular synapses. In the present study, target next‑generation sequencing was used for mutation detection, and polymerase chain reaction (PCR) analysis and Sanger sequencing were used in the identification of small deletions. Subsequently, quantitative PCR (qPCR) was performed to characterize the identified deletion encompassing exon five of the LAMA2 gene. Two causative mutations were identified using target region sequencing which provided the additional information required to facilitate clinical diagnosis. One heterozygous mutation (p. Lys682LysfsX22) was identified and confirmed by Sanger sequencing, and another heterozygous mutation (Exon5del) was found and validated by qPCR. Co‑segregation analysis indicated that the Exon5del mutation originated from the proband's mother and the previously reported frameshift mutation (p. Lys682LysfsX22) was inherited from the proband's father. To the best of our knowledge, the present study was the first to report an entire exon five deletion in the LAMA2 gene.
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Affiliation(s)
- Yun Yang
- Department of Research and Development, BGI‑Central China, Wuhan East Lake High‑Tech Development Zone, Wuhan, Hubei 430075, P.R. China
| | - Bing Mao
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Lixia Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Liangwei Mao
- Department of Research and Development, BGI‑Central China, Wuhan East Lake High‑Tech Development Zone, Wuhan, Hubei 430075, P.R. China
| | - Aifen Zhou
- Department of Obstetrics, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Jiangxia Cao
- Department of Obstetrics, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Jiasheng Hu
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Yan Zhou
- Department of Obstetrics, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Yanhong Pan
- Department of Research and Development, BGI‑Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Xiaoming Wei
- Department of Research and Development, BGI‑Shenzhen, Shenzhen, Guangdong 518083, P.R. China
| | - Shuang Yang
- Department of Research and Development, BGI‑Central China, Wuhan East Lake High‑Tech Development Zone, Wuhan, Hubei 430075, P.R. China
| | - Feng Mu
- Department of Research and Development, BGI‑Central China, Wuhan East Lake High‑Tech Development Zone, Wuhan, Hubei 430075, P.R. China
| | - Zhisheng Liu
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
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Guan Y, Hu H, Peng Y, Gong Y, Yi Y, Shao L, Liu T, Li G, Wang R, Dai P, Bignon YJ, Xiao Z, Yang L, Mu F, Xiao L, Xie Z, Yan W, Xu N, Zhou D, Yi X. Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing. Fam Cancer 2014; 14:9-18. [DOI: 10.1007/s10689-014-9749-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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31
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Morinière V, Dahan K, Hilbert P, Lison M, Lebbah S, Topa A, Bole-Feysot C, Pruvost S, Nitschke P, Plaisier E, Knebelmann B, Macher MA, Noel LH, Gubler MC, Antignac C, Heidet L. Improving mutation screening in familial hematuric nephropathies through next generation sequencing. J Am Soc Nephrol 2014; 25:2740-51. [PMID: 24854265 DOI: 10.1681/asn.2013080912] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Alport syndrome is an inherited nephropathy associated with mutations in genes encoding type IV collagen chains present in the glomerular basement membrane. COL4A5 mutations are associated with the major X-linked form of the disease, and COL4A3 and COL4A4 mutations are associated with autosomal recessive and dominant forms (thought to be involved in 15% and 1%-5% of the families, respectively) and benign familial hematuria. Mutation screening of these three large genes is time-consuming and expensive. Here, we carried out a combination of multiplex PCR, amplicon quantification, and next generation sequencing (NGS) analysis of three genes in 101 unrelated patients. We identified 88 mutations and 6 variations of unknown significance on 116 alleles in 83 patients. Two additional indel mutations were found only by secondary Sanger sequencing, but they were easily identified retrospectively with the web-based sequence visualization tool Integrative Genomics Viewer. Altogether, 75 mutations were novel. Sequencing the three genes simultaneously was particularly advantageous as the mode of inheritance could not be determined with certainty in many instances. The proportion of mutations in COL4A3 and COL4A4 was notably high, and the autosomal dominant forms of Alport syndrome appear more frequently than reported previously. Finally, this approach allowed the identification of large COL4A3 and COL4A4 rearrangements not described previously. We conclude that NGS is efficient, reduces screening time and cost, and facilitates the provision of appropriate genetic counseling in Alport syndrome.
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Affiliation(s)
- Vincent Morinière
- Departments of Genetics, and Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France
| | - Karin Dahan
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Pascale Hilbert
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Marieline Lison
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Said Lebbah
- Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France
| | - Alexandra Topa
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | | | - Patrick Nitschke
- Bioinformatics Platform, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Emmanuelle Plaisier
- Assistance Publique des Hôpitaux de Paris, Nephrology Service, Tenon Hospital, Paris, France
| | | | - Marie-Alice Macher
- Assistance Publique des Hôpitaux de Paris, Pediatric Nephrology Service, Robert Debré Hospital, Paris, France; and
| | | | - Marie-Claire Gubler
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Imagine Institute, Paris, France
| | - Corinne Antignac
- Departments of Genetics, and Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France; Institut National de la Santé et de la Recherche Médicale, Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Imagine Institute, Paris, France Paris Descartes-Sorbonne Paris Cité University, and
| | - Laurence Heidet
- Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France; Pediatric Nephrology Service, Assistance Publique des Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France
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Claes KBM, De Leeneer K. Dealing with pseudogenes in molecular diagnostics in the next-generation sequencing era. Methods Mol Biol 2014; 1167:303-15. [PMID: 24823787 DOI: 10.1007/978-1-4939-0835-6_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this chapter, we focus on issues related to the application of next-generation sequencing (NGS) strategies for the analysis of genes with pseudogenes in a clinical setting. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences, which are characterized by higher mutation rates than their functional parental genes. For the target enrichment strategies, we describe advantages and disadvantages of PCR- and capture-based enrichment methodologies. For the mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some concrete examples of genes with known pseudogenes and associated with Mendelian disorders that were analyzed by NGS on various platforms and starting from different library preparations.
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Vandrovcova J, Thomas ER, Atanur SS, Norsworthy PJ, Neuwirth C, Tan Y, Kasperaviciute D, Biggs J, Game L, Mueller M, Soutar AK, Aitman TJ. The use of next-generation sequencing in clinical diagnosis of familial hypercholesterolemia. Genet Med 2013; 15:948-57. [DOI: 10.1038/gim.2013.55] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/19/2013] [Indexed: 11/09/2022] Open
Abstract
Abstract
Purpose:
Familial hypercholesterolemia is a common Mendelian disorder associated with early-onset coronary heart disease that can be treated by cholesterol-lowering drugs. The majority of cases in the United Kingdom are currently without a molecular diagnosis, which is partly due to the cost and time associated with standard screening techniques. The main purpose of this study was to test the sensitivity and specificity of two next-generation sequencing protocols for genetic diagnosis of familial hypercholesterolemia.
Methods:
Libraries were prepared for next-generation sequencing by two target enrichment protocols; one using the SureSelect Target Enrichment System and the other using the PCR-based Access Array platform.
Results:
In the validation cohort, both protocols showed 100% specificity, whereas the sensitivity for short variant detection was 100% for the SureSelect Target Enrichment and 98% for the Access Array protocol. Large deletions/duplications were only detected using the SureSelect Target Enrichment protocol. In the prospective cohort, the mutation detection rate using the Access Array was highest in patients with clinically definite familial hypercholesterolemia (67%), followed by patients with possible familial hypercholesterolemia (26%).
Conclusion:
We have shown the potential of target enrichment methods combined with next-generation sequencing for molecular diagnosis of familial hypercholesterolemia. Adopting these assays for patients with suspected familial hypercholesterolemia could improve cost-effectiveness and increase the overall number of patients with a molecular diagnosis.
Genet Med
15 12, 948–957.
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Molecular diagnosis of congenital muscular dystrophies with defective glycosylation of alpha-dystroglycan using next-generation sequencing technology. Neuromuscul Disord 2013; 23:337-44. [PMID: 23453855 DOI: 10.1016/j.nmd.2013.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 01/08/2013] [Accepted: 01/15/2013] [Indexed: 01/29/2023]
Abstract
Targeted resequencing using next-generation sequencing technology is being rapidly applied to the molecular diagnosis of human genetic diseases. The group of muscular dystrophies may be an appropriate candidate for this approach because these diseases exhibit genotype-phenotype heterogeneity. To perform a proof-of-concept study, we selected four patients with congenital muscular dystrophies with defective glycosylation of alpha-dystroglycan. A custom-solution-based target enrichment kit was designed to capture whole-genic regions of the 26 muscular-dystrophy-related genes, including six genes implicated in alpha-dystroglycanopathies. Although approximately 95% of both coding and noncoding regions were covered with at least 15-read depth, parts of the coding exons of FKRP and POMT2 were insufficiently covered. Homozygous and compound heterozygous POMGnT1 mutations were found in two patients. Two novel noncoding variants of FKTN were identified in one patient who had a retrotransposon insertion mutation of FKTN in only one allele. The current targeted resequencing strategy yielded promising results for the extension of this method to other muscular dystrophies. As suboptimal coverage in a small subset of coding regions may affect the sensitivity of the method, complementary Sanger sequencing may be required.
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35
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Costa JL, Sousa S, Justino A, Kay T, Fernandes S, Cirnes L, Schmitt F, Machado JC. Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Hum Mutat 2013; 34:629-35. [PMID: 23315985 DOI: 10.1002/humu.22272] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/20/2012] [Indexed: 01/19/2023]
Abstract
The introduction of the benchtop massive parallel sequencers made it possible for the majority of clinical diagnostic laboratories to gain access to this fast evolving technology. In this study, using the Ion Torrent Personal Genome Machine, we present a strategy for the molecular diagnosis of hereditary breast and ovarian cancer and respective analytical validation. The methodology relies on a multiplex PCR amplification of the BRCA1 and BRCA2 genes combined with a variant prioritization pipeline, designed to minimize the number of false-positive calls without the introduction of false-negative results. A training set of samples was used to optimize the entire process, and a second set was used to validate and independently evaluate the performance of the workflow. Performing the study in a blind manner relative to the variants in the samples and using conventional Sanger sequencing as standard, the workflow resulted in a strategy with a maximum analytical sensitivity ≥98.6% with a confidence of 95% and a specificity of 96.9%. Importantly, no true variant was missed. This study presents a comprehensive massive parallel sequencing-Sanger sequencing based strategy, which results in a high analytical sensitivity assay that provides a time- and cost-effective strategy for the identification of mutations in the BRCA1 and BRCA2 genes.
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Affiliation(s)
- José Luis Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
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36
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Comprehensive mutation analysis for congenital muscular dystrophy: a clinical PCR-based enrichment and next-generation sequencing panel. PLoS One 2013; 8:e53083. [PMID: 23326386 PMCID: PMC3543442 DOI: 10.1371/journal.pone.0053083] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/23/2012] [Indexed: 11/19/2022] Open
Abstract
The congenital muscular dystrophies (CMDs) comprise a heterogeneous group of heritable muscle disorders with often difficult to interpret muscle pathology, making them challenging to diagnose. Serial Sanger sequencing of suspected CMD genes, while the current molecular diagnostic method of choice, can be slow and expensive. A comprehensive panel test for simultaneous screening of mutations in all known CMD-associated genes would be a more effective diagnostic strategy. Thus, the CMDs are a model disorder group for development and validation of next-generation sequencing (NGS) strategies for diagnostic and clinical care applications. Using a highly multiplexed PCR-based target enrichment method (RainDance) in conjunction with NGS, we performed mutation detection in all CMD genes of 26 samples and compared the results with Sanger sequencing. The RainDance NGS panel showed great consistency in coverage depth, on-target efficiency, versatility of mutation detection, and genotype concordance with Sanger sequencing, demonstrating the test's appropriateness for clinical use. Compared to single tests, a higher diagnostic yield was observed by panel implementation. The panel's limitation is the amplification failure of select gene-specific exons which require Sanger sequencing for test completion. Successful validation and application of the CMD NGS panel to improve the diagnostic yield in a clinical laboratory was shown.
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Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. Eur J Hum Genet 2012; 21:864-70. [PMID: 23249957 DOI: 10.1038/ejhg.2012.270] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/28/2012] [Accepted: 11/13/2012] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches.
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38
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Michils G, Hollants S, Dehaspe L, Van Houdt J, Bidet Y, Uhrhammer N, Bignon YJ, Vermeesch JR, Cuppens H, Matthijs G. Molecular Analysis of the Breast Cancer Genes BRCA1 and BRCA2 Using Amplicon-Based Massive Parallel Pyrosequencing. J Mol Diagn 2012; 14:623-30. [DOI: 10.1016/j.jmoldx.2012.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/17/2012] [Accepted: 05/17/2012] [Indexed: 01/31/2023] Open
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Theuns J, Crosiers D, Debaene L, Nuytemans K, Meeus B, Sleegers K, Goossens D, Corsmit E, Elinck E, Peeters K, Mattheijssens M, Pickut B, Del-Favero J, Engelborghs S, De Deyn PP, Cras P, Van Broeckhoven C. Guanosine triphosphate cyclohydrolase 1 promoter deletion causes dopa-responsive dystonia. Mov Disord 2012; 27:1451-6. [PMID: 22976901 DOI: 10.1002/mds.25147] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 06/22/2012] [Accepted: 07/17/2012] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Autosomal dominant dopa-responsive dystonia (AD-DRD) is caused by a biochemical defect primarily resulting from guanosine triphosphate cyclohydrolase 1 gene (GCH1) mutations. Few families have been reported without mutations in GCH1. METHODS Genome-wide linkage analysis and positional cloning to identify the genetic defect in a Belgian AD-DRD family was carried out. RESULTS AND CONCLUSION In this study, we report on the identification and characterization of a novel 24-kb deletion spanning exon 1 and the 5' regulatory region of GCH1 causing a wide spectrum of motor and nonmotor symptoms in a large Belgian AD-DRD family. This large-scale deletion of regulatory sequences leads to decreased GCH1 activity in all carriers, most probably resulting from allelic loss of transcription. We mapped the breakpoints of this deletion to the nucleotide level, allowing the development of a straightforward polymerase chain reaction assay for fast, efficient detection of this large deletion, which will prove valuable for preimplantation genetic diagnosis.
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Affiliation(s)
- Jessie Theuns
- Neurodegenerative Brain Diseases Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium.
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40
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Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee ASG. Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J Mol Diagn 2012; 14:602-12. [PMID: 22921312 DOI: 10.1016/j.jmoldx.2012.06.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 06/07/2012] [Accepted: 06/20/2012] [Indexed: 12/30/2022] Open
Abstract
In a clinical setting, next-generation sequencing (NGS) approaches for the enrichment and resequencing of DNA targets may have limitations in throughput, cost, or accuracy. We evaluated an NGS workflow for targeted DNA sequencing for mutation detection. Targeted sequence data of the BRCA1 and BRCA2 genes, generated using a PCR-based, multiplexed NGS approach using the SOLiD 4 (n = 24) and Ion Torrent PGM (n = 20) next-generation sequencers, were evaluated against sequence data obtained by Sanger sequencing. The overall sensitivity for SOLiD and PGM were 97.8% (95% CI = 94.7 to 100.0) and 98.9% (95% CI = 96.8 to 100.0) respectively. The specificity for the SOLiD platform was high, at 100.0% (95% CI = 99.3 to 100.0). PGM correctly identified all 3 indels, but 68 false-positive indels were also called. Equimolar normalization of amplicons was not necessary for successful NGS. Both platforms are highly amenable to scale-up, potentially reducing the reagent cost for BRCA testing to <US$200. Only 325 ng of DNA per patient is required, with similar coverage and accuracy obtained using DNA derived from peripheral blood or buccal wash samples. The strategy described is accurate and easy to incorporate into conventional workflow, and shows potential for mutation screening of clinically important gene targets in genetic disorders.
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Affiliation(s)
- Maurice Chan
- Division of Medical Sciences, National Cancer Centre, Singapore, Singapore
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41
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Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R. Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis. Expert Rev Mol Diagn 2012; 12:159-73. [PMID: 22369376 DOI: 10.1586/erm.11.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The potential applications of next-generation sequencing technologies in diagnostic laboratories have become increasingly evident despite the various technical challenges that still need to be overcome to potentiate its widespread adoption in a clinical setting. Whole-genome sequencing is now both technically feasible and 'cost effective' using next-generation sequencing techniques. However, this approach is still considered to be 'expensive' for a diagnostic test. Although the goal of the US$1000 genome is fast approaching, neither the analytical hurdles nor the ethical issues involved are trivial. In addition, the cost of data analysis and storage has been much higher than initially expected. As a result, it is widely perceived that targeted sequencing and whole-exome sequencing are more likely to be adopted as diagnostic tools in the foreseeable future. However, the information-generating power of whole-exome sequencing has also sparked considerable debate in relation to its deployment in genetic diagnostics, particularly with reference to the revelation of incidental findings. In this review, we focus on the targeted sequencing approach and its potential as a genetic diagnostic tool.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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42
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Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol 2012; 71:5-14. [PMID: 22275248 DOI: 10.1002/ana.22647] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recent developments in high-throughput sequence capture methods and next-generation sequencing technologies have now made exome sequencing a viable approach to elucidate the genetic basis of Mendelian disorders with hitherto unknown etiology. In addition, exome sequencing is increasingly being employed as a diagnostic tool for specific genetic diseases, particularly in the context of those disorders characterized by significant genetic and phenotypic heterogeneity, for example, Charcot-Marie-Tooth disease and congenital disorders of glycosylation. Such disorders are challenging to interrogate with conventional polymerase chain reaction-Sanger sequencing methods, because of the inherent difficulty in prioritizing candidate genes for diagnostic testing. Here, we explore the value of exome sequencing as a diagnostic tool and discuss whether exome sequencing can come to serve a dual role in diagnosis and discovery. We summarize the current status of exome sequencing, the technical challenges facing it, and its adaptation to diagnostics, and make recommendations for the use of exome sequencing as a routine diagnostic tool. Finally, we discuss pertinent ethical concerns, such as the use of exome sequencing data, originally generated in a diagnostic context, in research investigations.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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43
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Rossetti S, Hopp K, Sikkink RA, Sundsbak JL, Lee YK, Kubly V, Eckloff BW, Ward CJ, Winearls CG, Torres VE, Harris PC. Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing. J Am Soc Nephrol 2012; 23:915-33. [PMID: 22383692 DOI: 10.1681/asn.2011101032] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Mutations in two large multi-exon genes, PKD1 and PKD2, cause autosomal dominant polycystic kidney disease (ADPKD). The duplication of PKD1 exons 1-32 as six pseudogenes on chromosome 16, the high level of allelic heterogeneity, and the cost of Sanger sequencing complicate mutation analysis, which can aid diagnostics of ADPKD. We developed and validated a strategy to analyze both the PKD1 and PKD2 genes using next-generation sequencing by pooling long-range PCR amplicons and multiplexing bar-coded libraries. We used this approach to characterize a cohort of 230 patients with ADPKD. This process detected definitely and likely pathogenic variants in 115 (63%) of 183 patients with typical ADPKD. In addition, we identified atypical mutations, a gene conversion, and one missed mutation resulting from allele dropout, and we characterized the pattern of deep intronic variation for both genes. In summary, this strategy involving next-generation sequencing is a model for future genetic characterization of large ADPKD populations.
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Affiliation(s)
- Sandro Rossetti
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA.
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44
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Ceulemans S, van der Ven K, Del-Favero J. Targeted screening and validation of copy number variations. Methods Mol Biol 2012; 838:311-28. [PMID: 22228019 DOI: 10.1007/978-1-61779-507-7_15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.
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Affiliation(s)
- Shana Ceulemans
- Applied Molecular Genomics Unit, VIB, Department of Molecular Genetics, Flanders, Belgium
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45
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Jia X, Wei X, Liu Q, Cao M, Wang L, Zheng M, Liu J. An assay of gene copy number and its application based on heteroduplex products. Exp Mol Pathol 2011; 91:429-33. [DOI: 10.1016/j.yexmp.2011.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Accepted: 04/19/2011] [Indexed: 10/18/2022]
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46
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Schlipf NA, Schüle R, Klimpe S, Karle KN, Synofzik M, Schicks J, Riess O, Schöls L, Bauer P. Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients. Clin Genet 2011; 80:148-60. [DOI: 10.1111/j.1399-0004.2011.01715.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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De Leeneer K, Hellemans J, De Schrijver J, Baetens M, Poppe B, Van Criekinge W, De Paepe A, Coucke P, Claes K. Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations. Hum Mutat 2011; 32:335-44. [PMID: 21305653 DOI: 10.1002/humu.21428] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 12/01/2010] [Indexed: 12/11/2022]
Abstract
This study describes how the new massive parallel sequencing technology can be implemented in a diagnostic setting for the breast cancer susceptibility genes (BRCA1 and BRCA2). The throughput was maximized by increasing uniformity in coverage, obtained by a multiplex approach, which outperformed pooling of singleplex PCRs. We evaluated the sensitivity by analysis of 133 distinct sequence variants; three (2%) deletions or duplications in homopolymers of greater than or equal to seven nucleotides remained undetected, illustrating a limitation of pyrosequencing. Furthermore, other limitations like nonrandom sequencing errors, pseudogene amplification, and failure to detect multiexon deletions are thoroughly described. Our workflow illustrates the potential of massive parallel sequencing of large genes in a diagnostic setting, which is of great importance to meet the increasing expectations of genetic testing. Implementation of this approach will hopefully lead to a strong reduction in turnaround times. As a consequence a wider spectrum of at risk women will be able to benefit from therapeutic interventions and prophylactic interventions.
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Affiliation(s)
- Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan, Belgium
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48
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Reliable resequencing of the human dystrophin locus by universal long polymerase chain reaction and massive pyrosequencing. Anal Biochem 2010; 406:176-84. [PMID: 20670611 DOI: 10.1016/j.ab.2010.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 01/07/2023]
Abstract
The X-linked dystrophin gene is well known for its involvement in Duchenne/Becker muscular dystrophies and for its exceptional megabase size. This locus at Xp21 is prone to frequent random molecular changes, including large deletions and duplications, but also smaller variations. To cope with such huge sequence analysis requirements in forthcoming diagnostic applications, we employed the power of the parallel 454 GS-FLX pyrosequencer to the dystrophin locus. We enriched the genomic region of interest by the robust amplification of 62 fragments under universal conditions by the long-PCR protocol yielding 244,707 bp of sequence. Pooled PCR products were fragmented and used for library preparation and DNA sequencing. To evaluate the entire procedure we analyzed four male DNA samples for sequence coverage and accuracy in DNA sequence variation and for any potential bias. We identified 562 known variations and 55 additional variants not yet reported, among which we detected a causative Arg1844Stop mutation in one sample. Sanger sequencing confirmed all changes. Unexpectedly, only 3 x coverage was sufficient for 99.9993% accuracy. Our results show that long PCR combined to massive pyrosequencing is very reliable for the analysis of the biggest gene of the human genome and open the doors to other demanding applications in molecular diagnostics.
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Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A 2010; 107:12629-33. [PMID: 20616022 PMCID: PMC2906584 DOI: 10.1073/pnas.1007983107] [Citation(s) in RCA: 359] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Inherited loss-of-function mutations in the tumor suppressor genes BRCA1, BRCA2, and multiple other genes predispose to high risks of breast and/or ovarian cancer. Cancer-associated inherited mutations in these genes are collectively quite common, but individually rare or even private. Genetic testing for BRCA1 and BRCA2 mutations has become an integral part of clinical practice, but testing is generally limited to these two genes and to women with severe family histories of breast or ovarian cancer. To determine whether massively parallel, "next-generation" sequencing would enable accurate, thorough, and cost-effective identification of inherited mutations for breast and ovarian cancer, we developed a genomic assay to capture, sequence, and detect all mutations in 21 genes, including BRCA1 and BRCA2, with inherited mutations that predispose to breast or ovarian cancer. Constitutional genomic DNA from subjects with known inherited mutations, ranging in size from 1 to >100,000 bp, was hybridized to custom oligonucleotides and then sequenced using a genome analyzer. Analysis was carried out blind to the mutation in each sample. Average coverage was >1200 reads per base pair. After filtering sequences for quality and number of reads, all single-nucleotide substitutions, small insertion and deletion mutations, and large genomic duplications and deletions were detected. There were zero false-positive calls of nonsense mutations, frameshift mutations, or genomic rearrangements for any gene in any of the test samples. This approach enables widespread genetic testing and personalized risk assessment for breast and ovarian cancer.
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Affiliation(s)
- Tom Walsh
- Departments of Medicine and Genome Sciences and
| | - Ming K. Lee
- Departments of Medicine and Genome Sciences and
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Zhou X, Ren L, Meng Q, Li Y, Yu Y, Yu J. The next-generation sequencing technology and application. Protein Cell 2010; 1:520-36. [PMID: 21204006 DOI: 10.1007/s13238-010-0065-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 05/29/2010] [Indexed: 12/11/2022] Open
Abstract
As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years. This is largely due to the advent of newer generations of sequencing platforms, offering ever-faster and cheaper ways to analyze sequences. In our previous review, we looked into technical characteristics of the next-generation sequencers and provided prospective insights into their future development. In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.
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Affiliation(s)
- Xiaoguang Zhou
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
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