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Gieldon L, Mackenroth L, Kahlert AK, Lemke JR, Porrmann J, Schallner J, von der Hagen M, Markus S, Weidensee S, Novotna B, Soerensen C, Klink B, Wagner J, Tzschach A, Jahn A, Kuhlee F, Hackmann K, Schrock E, Di Donato N, Rump A. Correction: Diagnostic value of partial exome sequencing in developmental disorders. PLoS One 2020; 15:e0239959. [PMID: 32970766 PMCID: PMC7514079 DOI: 10.1371/journal.pone.0239959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0201041.].
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Gieldon L, Mackenroth L, Kahlert AK, Lemke JR, Porrmann J, Schallner J, von der Hagen M, Markus S, Weidensee S, Novotna B, Soerensen C, Klink B, Wagner J, Tzschach A, Jahn A, Kuhlee F, Hackmann K, Schrock E, Di Donato N, Rump A. Diagnostic value of partial exome sequencing in developmental disorders. PLoS One 2018; 13:e0201041. [PMID: 30091983 PMCID: PMC6084857 DOI: 10.1371/journal.pone.0201041] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Although intellectual disability is one of the major indications for genetic counselling, there are no homogenous diagnostic algorithms for molecular testing. While whole exome sequencing is increasingly applied, we questioned whether analyzing a partial exome, enriched for genes associated with Mendelian disorders, might be a valid alternative approach that yields similar detection rates but requires less sequencing capacities. Within this context 106 patients with different intellectual disability forms were analyzed for mutations in 4.813 genes after pre-exclusion of copy number variations by array-CGH. Subsequent variant interpretation was performed in accordance with the ACMG guidelines. By this, a molecular diagnosis was established in 34% of cases and candidate mutations were identified in additional 24% of patients. Detection rates of causative mutations were above 30%, regardless of further symptoms, except for patients with seizures (23%). We did not detect an advantage from partial exome sequencing for patients with severe intellectual disability (36%) as compared to those with mild intellectual disability (44%). Specific clinical diagnoses pre-existed for 20 patients. Of these, 5 could be confirmed and an additional 6 cases could be solved, but showed mutations in other genes than initially suspected. In conclusion partial exome sequencing solved >30% of intellectual disability cases, which is similar to published rates obtained by whole exome sequencing. The approach therefore proved to be a valid alternative to whole exome sequencing for molecular diagnostics in this cohort. The method proved equally suitable for both syndromic and non-syndromic intellectual disability forms of all severity grades.
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Affiliation(s)
- Laura Gieldon
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
- * E-mail:
| | - Luisa Mackenroth
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
- Klinik für angeborene Herzfehler und Kinderkardiologie, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes R. Lemke
- Institut für Humangenetik, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Joseph Porrmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Jens Schallner
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maja von der Hagen
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Sabine Weidensee
- Mitteldeutscher Praxisverbund Humangenetik, Praxis Erfurt, Erfurt, Germany
| | - Barbara Novotna
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Charlotte Soerensen
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Barbara Klink
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Johannes Wagner
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Andreas Tzschach
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Arne Jahn
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Franziska Kuhlee
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Evelin Schrock
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Nataliya Di Donato
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Andreas Rump
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
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Sadowski CE, Kohlstedt D, Meisel C, Keller K, Becker K, Mackenroth L, Rump A, Schröck E, Wimberger P, Kast K. BRCA1/2 missense mutations and the value of in-silico analyses. Eur J Med Genet 2017; 60:572-577. [PMID: 28807866 DOI: 10.1016/j.ejmg.2017.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants. METHODS We conducted mutation analysis of BRCA1/2 in 523 index patients with suspected hereditary breast and ovarian cancer (HBOC). Classification of the genetic variants was performed according to the German Consortium (GC)-HBOC database. Additionally, all missense variants were classified by the following three in-silico prediction tools: SIFT, Mutation Taster (MT2) and PolyPhen2 (PPH2). RESULTS Overall 201 different variants, 68 of which constituted missense variants were ranked as pathogenic, neutral, or unknown. The classification of missense variants by in-silico tools resulted in a higher amount of pathogenic mutations (25% vs. 13.2%) compared to the GC-HBOC-classification. Altogether, more than fifty percent (38/68, 55.9%) of missense variants were ranked differently. Sensitivity of in-silico-tools for mutation prediction was 88.9% (PPH2), 100% (SIFT) and 100% (MT2). CONCLUSION We found a relevant discrepancy in variant classification by using in-silico prediction tools, resulting in potential overestimation and/or underestimation of cancer risk. More reliable, notably gene-specific, prediction tools and functional tests are needed to improve clinical counseling.
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Affiliation(s)
- Carolin E Sadowski
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Kohlstedt
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelia Meisel
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katja Keller
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Becker
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Luisa Mackenroth
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Andreas Rump
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Evelin Schröck
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karin Kast
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Gieldon L, Mackenroth L, Betcheva-Krajcir E, Rump A, Beck-Wödl S, Schallner J, Di Donato N, Schröck E, Tzschach A. Skewed X-inactivation in a family with DLG3-
associated X-linked intellectual disability. Am J Med Genet A 2017; 173:2545-2550. [DOI: 10.1002/ajmg.a.38348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/03/2017] [Accepted: 06/14/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Laura Gieldon
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Luisa Mackenroth
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Elitza Betcheva-Krajcir
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Andreas Rump
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Stefanie Beck-Wödl
- Institut für Medizinische Genetik und Angewandte Genomik; Universitätsklinikum Tübingen; Tübingen
| | - Jens Schallner
- Klinik und Poliklinik für Kinder- und Jugendmedizin; Universitätsklinikum Carl Gustav Carus; Dresden Germany
| | - Nataliya Di Donato
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Evelin Schröck
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
| | - Andreas Tzschach
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus; Technische Universität Dresden; Dresden Germany
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Pinggera A, Mackenroth L, Rump A, Schallner J, Beleggia F, Wollnik B, Striessnig J. New gain-of-function mutation shows CACNA1D as recurrently mutated gene in autism spectrum disorders and epilepsy. Hum Mol Genet 2017; 26:2923-2932. [PMID: 28472301 PMCID: PMC5886262 DOI: 10.1093/hmg/ddx175] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 11/12/2022] Open
Abstract
CACNA1D encodes the pore-forming α1-subunit of Cav1.3, an L-type voltage-gated Ca2+-channel. Despite the recent discovery of two de novo missense gain-of-function mutations in Cav1.3 in two individuals with autism spectrum disorder (ASD) and intellectual disability CACNA1D has not been considered a prominent ASD-risk gene in large scale genetic analyses, since such studies primarily focus on likely-disruptive genetic variants. Here we report the discovery and characterization of a third de novo missense mutation in CACNA1D (V401L) in a patient with ASD and epilepsy. For the functional characterization we introduced mutation V401L into two major C-terminal long and short Cav1.3 splice variants, expressed wild-type or mutant channel complexes in tsA-201 cells and performed whole-cell patch-clamp recordings. Mutation V401L, localized within the channel's activation gate, significantly enhanced current densities, shifted voltage dependence of activation and inactivation to more negative voltages and reduced channel inactivation in both Cav1.3 splice variants. Altogether, these gating changes are expected to result in enhanced Ca2+-influx through the channel, thus representing a strong gain-of-function phenotype. Additionally, we also found that mutant channels retained full sensitivity towards the clinically available Ca2+ -channel blocker isradipine. Our findings strengthen the evidence for CACNA1D as a novel candidate autism risk gene and encourage experimental therapy with available channel-blockers for this mutation. The additional presence of seizures and neurological abnormalities in our patient define a novel phenotype partially overlapping with symptoms in two individuals with PASNA (congenital primary aldosteronism, seizures and neurological abnormalities) caused by similar Cav1.3 gain-of-function mutations.
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Affiliation(s)
- Alexandra Pinggera
- Department of Pharmacology and Toxicology Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | | | | | - Jens Schallner
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Filippo Beleggia
- Department I of Internal Medicine, University Hospital of Cologne, 50923 Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
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Le Tanno P, Breton J, Bidart M, Satre V, Harbuz R, Ray PF, Bosson C, Dieterich K, Jaillard S, Odent S, Poke G, Beddow R, Digilio MC, Novelli A, Bernardini L, Pisanti MA, Mackenroth L, Hackmann K, Vogel I, Christensen R, Fokstuen S, Béna F, Amblard F, Devillard F, Vieville G, Apostolou A, Jouk PS, Guebre-Egziabher F, Sartelet H, Coutton C. PBX1 haploinsufficiency leads to syndromic congenital anomalies of the kidney and urinary tract (CAKUT) in humans. J Med Genet 2017; 54:502-510. [PMID: 28270404 DOI: 10.1136/jmedgenet-2016-104435] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/03/2017] [Accepted: 01/17/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) represent a significant healthcare burden since it is the primary cause of chronic kidney in children. CNVs represent a recurrent molecular cause of CAKUT but the culprit gene remains often elusive. Our study aimed to define the gene responsible for CAKUT in patients with an 1q23.3q24.1 microdeletion. METHODS We describe eight patients presenting with CAKUT carrying an 1q23.3q24.1 microdeletion as identified by chromosomal microarray analysis (CMA). Clinical features were collected, especially the renal and urinary tract phenotype, and extrarenal features. We characterised PBX1 expression and localisation in fetal and adult kidneys using quantitative RT-PCR and immunohistochemistry. RESULTS We defined a 276-kb minimal common region (MCR) that only overlaps with the PBX1 gene. All eight patients presented with syndromic CAKUT. CAKUT were mostly bilateral renal hypoplasia (75%). The most frequent extrarenal symptoms were developmental delay and ear malformations. We demonstrate that PBX1 is strongly expressed in fetal kidneys and brain and expression levels decreased in adult samples. In control fetal kidneys, PBX1 was localised in nuclei of medullary, interstitial and mesenchymal cells, whereas it was present in endothelial cells in adult kidneys. CONCLUSIONS Our results indicate that PBX1 haploinsufficiency leads to syndromic CAKUT as supported by the Pbx1-null mice model. Correct PBX1 dosage appears to be critical for normal nephrogenesis and seems important for brain development in humans. CMA should be recommended in cases of fetal renal anomalies to improve genetic counselling and pregnancy management.
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Affiliation(s)
- Pauline Le Tanno
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Julie Breton
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Marie Bidart
- Université Grenoble Alpes, Grenoble, France
- UF Clinatec, Pôle Recherche, CHU Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
| | - Radu Harbuz
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Pierre F Ray
- Université Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Caroline Bosson
- Laboratoire de Biochimie Génétique et Moléculaire, Institut de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Klaus Dieterich
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Sylvie Jaillard
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, Université de Rennes, Rennes, France
| | - Sylvie Odent
- CHU Rennes, Service de Génétique Clinique, Centre de Référence Anomalies du Développement CLAD-Ouest, Hôpital Sud, Rennes, France
| | - Gemma Poke
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | - Rachel Beddow
- Genetic Health Service New Zealand Central Hub, Wellington, New Zealand
| | | | - Antonio Novelli
- Department of Medical Genetics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Laura Bernardini
- Mendel Laboratory IRCCS "Casa Sollievo della Sofferenza" Hospital, Foggia, Italy
| | | | - Luisa Mackenroth
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Siv Fokstuen
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Frédérique Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Florence Amblard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Francoise Devillard
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Gaelle Vieville
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
| | - Alexia Apostolou
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | | | - Hervé Sartelet
- Département d'Anatomie et Cytologie Pathologiques, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Grenoble, France
| | - Charles Coutton
- Département de Génétique et Procréation, CHU Grenoble Alpes, Grenoble, France
- Equipe "Génétique, Epigénétique et Thérapies de l'Infertilité", Institut Albert Bonniot, La Tronche, France
- Université Grenoble Alpes, Grenoble, France
- Génétique et Procréation, Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
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Pinggera A, Mackenroth L, Striessnig J. Ca V 1.3 ( Cacna1d ) Gain-of-Function De Novo Missense Mutations are Associated with CNS Disorders. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Hackmann K, Kuhlee F, Betcheva-Krajcir E, Kahlert AK, Mackenroth L, Klink B, Di Donato N, Tzschach A, Kast K, Wimberger P, Schrock E, Rump A. Ready to clone: CNV detection and breakpoint fine-mapping in breast and ovarian cancer susceptibility genes by high-resolution array CGH. Breast Cancer Res Treat 2016; 159:585-90. [PMID: 27581129 DOI: 10.1007/s10549-016-3956-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/24/2016] [Indexed: 11/29/2022]
Abstract
PURPOSE Detection of predisposing copy number variants (CNV) in 330 families affected with hereditary breast and ovarian cancer (HBOC). METHODS In order to complement mutation detection with Illumina's TruSight Cancer panel, we designed a customized high-resolution 8 × 60k array for CGH (aCGH) that covers all 94 genes from the panel. RESULTS Copy number variants with immediate clinical relevance were detected in 12 families (3.6%). Besides 3 known CNVs in CHEK2, RAD51C, and BRCA1, we identified 3 novel pathogenic CNVs in BRCA1 (deletion of exons 4-13, deletion of exons 12-18) and ATM (deletion exons 57-63) plus an intragenic duplication of BRCA2 (exons 3-11) and an intronic BRCA1 variant with unknown pathogenicity. The precision of high-resolution aCGH enabled straight forward breakpoint amplification of a BRCA1 deletion which subsequently allowed for fast and economic CNV verification in family members of the index patient. Furthermore, we used our aCGH data to validate an algorithm that was able to detect all identified copy number changes from next-generation sequencing (NGS) data. CONCLUSIONS Copy number detection is a mandatory analysis in HBOC families at least if no predisposing mutations were found by sequencing. Currently, high-resolution array CGH is our first choice of method of analysis due to unmatched detection precision. Although it seems possible to detect CNV from sequencing data, there currently is no satisfying tool to do so in a routine diagnostic setting.
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Affiliation(s)
- Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany.
- German Cancer Consortium (DKTK), Dresden, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Dresden, Germany.
| | - Franziska Kuhlee
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Elitza Betcheva-Krajcir
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Anne-Karin Kahlert
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Luisa Mackenroth
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Barbara Klink
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Nataliya Di Donato
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Andreas Tzschach
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Karin Kast
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Klinik und Poliklinik fuer Gynäkologie und Geburtshilfe, Universitaetsklinikum Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Pauline Wimberger
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
- Klinik und Poliklinik fuer Gynäkologie und Geburtshilfe, Universitaetsklinikum Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Evelin Schrock
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Andreas Rump
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden, Fetscherstr. 74, 01307, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Dresden, Germany
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9
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Rump A, Benet-Pages A, Schubert S, Kuhlmann JD, Janavičius R, Macháčková E, Foretová L, Kleibl Z, Lhota F, Zemankova P, Betcheva-Krajcir E, Mackenroth L, Hackmann K, Lehmann J, Nissen A, DiDonato N, Opitz R, Thiele H, Kast K, Wimberger P, Holinski-Feder E, Emmert S, Schröck E, Klink B. Identification and Functional Testing of ERCC2 Mutations in a Multi-national Cohort of Patients with Familial Breast- and Ovarian Cancer. PLoS Genet 2016; 12:e1006248. [PMID: 27504877 PMCID: PMC4978395 DOI: 10.1371/journal.pgen.1006248] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
The increasing application of gene panels for familial cancer susceptibility disorders will probably lead to an increased proposal of susceptibility gene candidates. Using ERCC2 DNA repair gene as an example, we show that proof of a possible role in cancer susceptibility requires a detailed dissection and characterization of the underlying mutations for genes with diverse cellular functions (in this case mainly DNA repair and basic cellular transcription). In case of ERCC2, panel sequencing of 1345 index cases from 587 German, 405 Lithuanian and 353 Czech families with breast and ovarian cancer (BC/OC) predisposition revealed 25 mutations (3 frameshift, 2 splice-affecting, 20 missense), all absent or very rare in the ExAC database. While 16 mutations were unique, 9 mutations showed up repeatedly with population-specific appearance. Ten out of eleven mutations that were tested exemplarily in cell-based functional assays exert diminished excision repair efficiency and/or decreased transcriptional activation capability. In order to provide evidence for BC/OC predisposition, we performed familial segregation analyses and screened ethnically matching controls. However, unlike the recently published RECQL example, none of our recurrent ERCC2 mutations showed convincing co-segregation with BC/OC or significant overrepresentation in the BC/OC cohort. Interestingly, we detected that some deleterious founder mutations had an unexpectedly high frequency of > 1% in the corresponding populations, suggesting that either homozygous carriers are not clinically recognized or homozygosity for these mutations is embryonically lethal. In conclusion, we provide a useful resource on the mutational landscape of ERCC2 mutations in hereditary BC/OC patients and, as our key finding, we demonstrate the complexity of correct interpretation for the discovery of “bonafide” breast cancer susceptibility genes. Approximately 5–10% of breast/ovarian cancer (BC/OC) cases have inherited an increased risk of developing this malignancy. However, mutations in the two major breast cancer susceptibility genes BRCA1 and BRCA2 explain only 15–20% of all familial BC/OC cases. With the emergence of the high throughput NGS-technology, the number of proposed novel candidate genes for breast cancer predisposition continuously increases. However, a “bonafide” proof of cancer susceptibility requires a detailed characterization of candidate mutations, which we addressed in the current study. Using the DNA repair gene ERCC2 as an example, we performed a comprehensive multi-center approach, analyzing ERCC2 mutations in 1000+ patients with hereditary BC/OC. We identified 25 potential candidate mutations for cancer breast cancer susceptibility, some of them affecting ERCC2 functional activity in appropriate cell-culture based assays. However, a more dissected analysis showed no convincing co-segregation with BC/OC and there was no longer a significant overrepresentation in BC/OC when compared to regionally matched controls instead of the global ExAc variant data base, pointing to the relevance of founder-mutations. In conclusion, we provide a useful resource on the mutational landscape of ERCC2 mutations in hereditary BC/OC patients and, as our key finding, we highlight the complexity of correct interpretation for the discovery of “bonafide” breast cancer susceptibility genes.
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Affiliation(s)
- Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Steffen Schubert
- Clinic for Dermatology Venerology and Allergology, Göttingen, Germany
| | - Jan Dominik Kuhlmann
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
- * E-mail:
| | - Ramūnas Janavičius
- Vilnius University Hospital Santariskiu Clinics, Hematology, Oncology and Transfusion Medicine Center, Vilnius, Lithuania
- State Research Institute Innovative Medicine Center, Vilnius, Lithuania
| | | | | | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Filip Lhota
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Elitza Betcheva-Krajcir
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luisa Mackenroth
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Janin Lehmann
- Clinic for Dermatology Venerology and Allergology, Göttingen, Germany
| | - Anke Nissen
- MGZ—Medical Genetics Center, Munich, Germany
| | - Nataliya DiDonato
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Romy Opitz
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | | | - Karin Kast
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Pauline Wimberger
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | | | - Steffen Emmert
- Clinic for Dermatology Venerology and Allergology, Göttingen, Germany
- Clinic of Dermatology, Rostock, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany
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10
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Mackenroth L, Hackmann K, Klink B, Weber JS, Mayer B, Schröck E, Tzschach A. Interstitial 1q23.3q24.1 deletion in a patient with renal malformation, congenital heart disease, and mild intellectual disability. Am J Med Genet A 2016; 170:2394-9. [PMID: 27255444 DOI: 10.1002/ajmg.a.37785] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/17/2016] [Indexed: 01/25/2023]
Abstract
Interstitial deletions including chromosome region 1q23.3q24.1 are rare. Only eight patients with molecularly characterized deletions have been reported to date. Their phenotype included intellectual disability/developmental delay, growth retardation, microcephaly, congenital heart disease, and renal malformations. We report on a female patient with mild developmental delay, congenital heart disease, and bilateral renal hypoplasia in whom an interstitial de novo deletion of approximately 2.7 Mb in 1q23.3q24.1 was detected by array CGH. This is the smallest deletion described in this region so far. Genotype-phenotype comparison with previously published patients allowed us to propose LMX1A and RXRG as potential candidate genes for intellectual disability, PBX1 as a probable candidate gene for renal malformation, and enabled us to narrow down a chromosome region associated with microcephaly. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Luisa Mackenroth
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Barbara Klink
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Julia Sara Weber
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Brigitte Mayer
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Evelin Schröck
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Andreas Tzschach
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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11
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Dehmel M, Brenner S, Suttorp M, Hahn G, Schützle H, Dinger J, Di Donato N, Mackenroth L, von der Hagen M. Novel Mutation in the DKC1 Gene: Neonatal Hoyeraal-Hreidarsson Syndrome As a Rare Differential Diagnosis in Pontocerebellar Hypoplasia, Primary Microcephaly, and Progressive Bone Marrow Failure. Neuropediatrics 2016; 47:182-6. [PMID: 26951492 DOI: 10.1055/s-0036-1578799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Primary microcephaly and severe developmental delay are complex but unspecific signs pointing to various genetic or acquired diseases. A concomitant finding of hematological failure may lead to the differential diagnosis of rare genetic diseases such as chromosome breakage disorders or diseases associated with telomere dysfunction. X-linked Hoyeraal-Hreidarsson syndrome (HHS) is a rare heterogenic disorder characterized by severe neurological impairment and progressive bone marrow failure. The latter represents the main cause of mortality, usually in early childhood. We report on the clinical course of an infant with HHS due to a novel mutation in the DKC1 gene and the particular finding of pontocerebellar hypoplasia.
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Affiliation(s)
- Maria Dehmel
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Sebastian Brenner
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Meinolf Suttorp
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Gabriele Hahn
- Bereich Kinderradiologie, Institut und Poliklinik für Radiologische Diagnostik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Heike Schützle
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Jürgen Dinger
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Nataliya Di Donato
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Luisa Mackenroth
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
| | - Maja von der Hagen
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße, Dresden, Germany
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12
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Mackenroth L, Fischer-Zirnsak B, Egerer J, Hecht J, Kallinich T, Stenzel W, Spors B, von Moers A, Mundlos S, Kornak U, Gerhold K, Horn D. An overlapping phenotype of Osteogenesis imperfecta and Ehlers-Danlos syndrome due to a heterozygous mutation in COL1A1
and biallelic missense variants in TNXB
identified by whole exome sequencing. Am J Med Genet A 2016; 170A:1080-5. [DOI: 10.1002/ajmg.a.37547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 12/21/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Luisa Mackenroth
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
- Faculty of Medicine Carl Gustav Carus; Institute for Clinical Genetics; Dresden Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
- Max-Planck-Institut für Molekulare Genetik; Berlin Germany
| | - Johannes Egerer
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Jochen Hecht
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Tilmann Kallinich
- Department of Pediatric Pneumology and Immunology; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Werner Stenzel
- Institute for Neuropathology; Charité; Universitätsmedizin Berlin; Berlin Germany
| | - Birgit Spors
- Department of Radiology; Charité; Universitätsmedizin Berlin; Berlin Germany
| | | | - Stefan Mundlos
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
- Max-Planck-Institut für Molekulare Genetik; Berlin Germany
| | - Uwe Kornak
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
- Max-Planck-Institut für Molekulare Genetik; Berlin Germany
| | - Kerstin Gerhold
- Department of Pediatric Pneumology and Immunology; Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Denise Horn
- Institute of Medical and Human Genetics; Charité-Universitätsmedizin Berlin; Berlin Germany
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13
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Mackenroth L, Hackmann K, Beyer A, Schallner J, Novotna B, Klink B, Schröck E, Di Donato N. 6q22.33 microdeletion in a family with intellectual disability, variable major anomalies, and behavioral abnormalities. Am J Med Genet A 2015; 167A:2800-7. [PMID: 26334553 DOI: 10.1002/ajmg.a.37266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 07/13/2015] [Indexed: 01/23/2023]
Abstract
Interstitial deletions on the long arm of chromosome six have been described for several regions including 6q16, 6q22.1, and 6q21q22.1, and with variable phenotypes such as intellectual disability/developmental delay, growth retardation, major and minor facial anomalies. However, an isolated microdeletion of the sub-band 6q22.33 has not been reported so far and thus, no information about the specific phenotype associated with such a copy number variant is available. Here, we define the clinical picture of an isolated 6q22.33 microdeletion based on the phenotype of six members of one family with loss of approximately 1 Mb in this region. Main clinical features include mild intellectual disability and behavioral abnormalities as well as microcephaly, heart defect, and cleft lip and palate.
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Affiliation(s)
- Luisa Mackenroth
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Karl Hackmann
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anke Beyer
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Jens Schallner
- Klinik und Poliklinik für Kinder-und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Barbara Novotna
- Klinik und Poliklinik für Kinder-und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Barbara Klink
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nataliya Di Donato
- Institut f, ü, r Klinische Genetik, Medizinische Fakult, ä, t Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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14
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Schrock E, Benet-Pagès A, Schubert S, Janavicius R, Hackmann K, Betcheva-Krajcir E, Mackenroth L, Lehmann J, Nissen AM, Altmueller J, Thiele H, Di Donato N, Klink B, Kuhlmann JD, Tzschach A, Kast K, Wimberger P, Holinski-Feder E, Meindl A, Emmert S, Rump A. Abstract LB-044: Germline mutations in patients with hereditary breast and ovarian cancer establish ERCC2 as a cancer susceptibility gene. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Breast and ovarian cancer (BC/OC) predisposition is associated with a number of high- and low-penetrance susceptibility genes. Despite comprehensive testing there is still a large portion of high risk cases without mutation in any of the known susceptibility loci. Therefore novel candidate genes need to be identified. Here we report on the results of testing 94 genes in 717 BC/OC patients from Germany and Lithuania.
Method: Inclusion criteria for the patients in this study were defined by the German Consortium for Breast and Ovarian Cancer. Next generation sequencing (NGS) was performed on an Illumina MiSeq sequencer, with 150 bp paired end sequencing chemistry and an average base coverage of 300 fold. Target enrichment was performed with the Illumina TruSight cancer panel, which includes 94 genes associated with both common (e.g., breast, colorectal) and rare cancers.
Results: In 19.7% of the patients, BRCA1 or BRCA2 variations have been found. These were either clearly pathogenic loss-of-function mutations (43%) or very rare, unclassified missense variations with high probability of a deleterious effect (57%). In 17.9% of the patients we found null-mutations and rare, unclassified missense variants in the acknowledged BC/OC susceptibility genes ATM, CDH1, CHEK2, NBN, PALB2, RAD51C/D and TP53. Analysis of the non-BC/OC genes on the NGS panel identified the “excision repair cross-complementing rodent repair deficiency, complementation group 2” gene (ERCC2 or XPD) as a promising BC/OC predisposition candidate: we found 3 frame-shift mutations and 1 splice-site mutation in four independent BC/OC families. Additionally we found 20 rare, unclassified sequence variations in ERCC2. These variants have a cumulative allele frequency of 2.9% in our BC/OC cohort, which is 14.5-fold overrepresentation compared to the “exome aggregation consortium” (ExAC) cohort (61486 exomes). In all affected families tested so far, the ERCC2 mutations co-segregate with the occurrence of BC and/or OC. Functional assays testing the ERCC2 variants have been initiated. First results show that at least some of the missense variants (e.g. NM_000400.3:p.Val536Met) have lost their DNA repair ability.
Conclusion: Deleterious mutations and probably pathogenic missense variations in ERCC2, which are significantly overrepresented in our BC/OC families and co-segregate with the affected individuals, define ERCC2 clearly as a susceptibility gene for BC/OC predisposition. Functional assays will be continued in order to identify missense variations that diminish the DNA-repair capacity of ERCC2. Affected individuals with excluded mutations in the known BC/OC predisposition genes should be tested for mutations in ERCC2.
Citation Format: Evelin Schrock, Anna Benet-Pagès, Steffen Schubert, Ramūnas Janavicius, Karl Hackmann, Elitza Betcheva-Krajcir, Luisa Mackenroth, Janin Lehmann, AM Nissen, Janine Altmueller, Holger Thiele, Nataliya Di Donato, Barbara Klink, Jan D. Kuhlmann, Andreas Tzschach, Karin Kast, Pauline Wimberger, Elke Holinski-Feder, Alfons Meindl, Steffen Emmert, Andreas Rump. Germline mutations in patients with hereditary breast and ovarian cancer establish ERCC2 as a cancer susceptibility gene. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-044. doi:10.1158/1538-7445.AM2015-LB-044
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Affiliation(s)
- Evelin Schrock
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | | | - Steffen Schubert
- 3Clinic for Dermatology Venerology and Allergology, Goettingen, Germany
| | - Ramūnas Janavicius
- 4Vilnius University Hospital Santariskiu Clinics, Hematology, oncology and transfusion medicine center, Molecular medicine laboratory, Vilnius, Lithuania
| | - Karl Hackmann
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Elitza Betcheva-Krajcir
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Luisa Mackenroth
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Janin Lehmann
- 3Clinic for Dermatology Venerology and Allergology, Goettingen, Germany
| | - AM Nissen
- 2Medizinisch Genetisches Zentrum, Munich, Germany
| | | | | | - Nataliya Di Donato
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Barbara Klink
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Jan D. Kuhlmann
- 6Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Andreas Tzschach
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Karin Kast
- 6Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Pauline Wimberger
- 6Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | | | - Alfons Meindl
- 7Zentrum Familiärer Brust- und Eierstockkrebs, Frauenklinik und Poliklinik der Technischen Universität München, Munich, Germany
| | - Steffen Emmert
- 3Clinic for Dermatology Venerology and Allergology, Goettingen, Germany
| | - Andreas Rump
- 1Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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15
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Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med 2015; 6:252ra123. [PMID: 25186178 DOI: 10.1126/scitranslmed.3009262] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Less than half of patients with suspected genetic disease receive a molecular diagnosis. We have therefore integrated next-generation sequencing (NGS), bioinformatics, and clinical data into an effective diagnostic workflow. We used variants in the 2741 established Mendelian disease genes [the disease-associated genome (DAG)] to develop a targeted enrichment DAG panel (7.1 Mb), which achieves a coverage of 20-fold or better for 98% of bases. Furthermore, we established a computational method [Phenotypic Interpretation of eXomes (PhenIX)] that evaluated and ranked variants based on pathogenicity and semantic similarity of patients' phenotype described by Human Phenotype Ontology (HPO) terms to those of 3991 Mendelian diseases. In computer simulations, ranking genes based on the variant score put the true gene in first place less than 5% of the time; PhenIX placed the correct gene in first place more than 86% of the time. In a retrospective test of PhenIX on 52 patients with previously identified mutations and known diagnoses, the correct gene achieved a mean rank of 2.1. In a prospective study on 40 individuals without a diagnosis, PhenIX analysis enabled a diagnosis in 11 cases (28%, at a mean rank of 2.4). Thus, the NGS of the DAG followed by phenotype-driven bioinformatic analysis allows quick and effective differential diagnostics in medical genetics.
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Affiliation(s)
- Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland. Labor Berlin-Charité Vivantes GmbH, Humangenetik, Föhrer Straße 15, 13353 Berlin, Germany
| | - Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Luisa Mackenroth
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter Krawitz
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Luitgard Graul-Neumann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Sandra Doelken
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Nancy Christine Oien
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michal R Schweiger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Cologne Center for Genomics, University of Cologne, D-50931 Cologne, Germany
| | - Ulrike Krüger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Götz Frommer
- Agilent Technologies, Hewlett-Packard-Straße 8, 76337 Waldbronn, Germany
| | - Björn Fischer
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Ricarda Flöttmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Amin Ardeshirdavani
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Yves Moreau
- Department of Electrical Engineering, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, 3001 Leuven, Belgium
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa Haendel
- University Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Sciences University, Portland, OR 97327, USA
| | - Damian Smedley
- Mouse Informatics Group, Wellcome Trust Sanger Institute, CB10 1SA Hinxton, UK
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany. Berlin-Brandenburg Center for Regenerative Therapies, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany. Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.
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Hobbs J, Fardo DW, Cieply K, Dacic S, Hamilton RL, Horbinski C, Giannini C, Bernardo MC, Menke J, Radford JG, Hallemeier C, Boes CJ, Lewis M, Scheithauer BW, Kim SH, Change WS, Kim JP, Chang JH, Chen ZP, Chen YS, Mihalcik SA, Jentoft M, Giannini C, Scheithauer B, Laack N, Mori K, Fujita S, Tomogane Y, Izumoto S, Arita N, Pollo B, Maderna E, Calatozzolo C, Nunziata R, Silvani A, Eoli M, Salmaggi A, Finocchiaro G, Wesseling P, Boots-Sprenger S, Bleeker F, Sijben A, Rijntjes J, Gijtenbeek A, Jeuken J, Kirsch M, Mackenroth L, Geiger K, Schackert G, Steiner G, Engler J, Robinson A, Gupta N, James CD, Phillips JJ, Cole VR, Kennedy LD, Lesser G. PATHOLOGY. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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