1
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Zhang Y, Liu W, Duan J. On the core segmentation algorithms of copy number variation detection tools. Brief Bioinform 2024; 25:bbae022. [PMID: 38340093 PMCID: PMC10858679 DOI: 10.1093/bib/bbae022] [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: 07/17/2023] [Revised: 10/26/2023] [Indexed: 02/12/2024] Open
Abstract
Shotgun sequencing is a high-throughput method used to detect copy number variants (CNVs). Although there are numerous CNV detection tools based on shotgun sequencing, their quality varies significantly, leading to performance discrepancies. Therefore, we conducted a comprehensive analysis of next-generation sequencing-based CNV detection tools over the past decade. Our findings revealed that the majority of mainstream tools employ similar detection rationale: calculates the so-called read depth signal from aligned sequencing reads and then segments the signal by utilizing either circular binary segmentation (CBS) or hidden Markov model (HMM). Hence, we compared the performance of those two core segmentation algorithms in CNV detection, considering varying sequencing depths, segment lengths and complex types of CNVs. To ensure a fair comparison, we designed a parametrical model using mainstream statistical distributions, which allows for pre-excluding bias correction such as guanine-cytosine (GC) content during the preprocessing step. The results indicate the following key points: (1) Under ideal conditions, CBS demonstrates high precision, while HMM exhibits a high recall rate. (2) For practical conditions, HMM is advantageous at lower sequencing depths, while CBS is more competitive in detecting small variant segments compared to HMM. (3) In case involving complex CNVs resembling real sequencing, HMM demonstrates more robustness compared with CBS. (4) When facing large-scale sequencing data, HMM costs less time compared with the CBS, while their memory usage is approximately equal. This can provide an important guidance and reference for researchers to develop new tools for CNV detection.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Wenyu Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
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2
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Copy number variant analysis and expression profiling of the olfactory receptor-rich 11q11 region in obesity predisposition. Mol Genet Metab Rep 2020; 25:100656. [PMID: 33145169 PMCID: PMC7596328 DOI: 10.1016/j.ymgmr.2020.100656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 11/22/2022] Open
Abstract
Genome-wide copy number surveys associated chromosome 11q11 with obesity. As this is an olfactory receptor-rich region, we hypothesize that genetic variation in olfactory receptor genes might be implicated in the pathogenesis of obesity. Multiplex Amplicon Quantification analysis was applied to screen for copy number variants at chromosome 11q11 in 627 patients with obesity and 330 healthy-weight individuals. A ± 80 kb deletion with an internally 1.3 kb retained segment was identified, covering the three olfactory receptor genes OR4C11, OR4P4, and OR4S2. A significant increase in copy number loss(es) was perceived in our patient cohort (MAF = 27%; p = 0.02). Gene expression profiling in metabolic relevant tissues was performed to evaluate the functional impact of the obesity susceptible locus. All three 11q11 genes were present in visceral and subcutaneous adipose tissue while no expression was perceived in the liver. These results support the 'metabolic system' hypothesis and imply that gene disruption of OR4C11, OR4P4, and OR4S2 will negatively influence energy metabolism, ultimately leading to fat accumulation and obesity. Our study thus demonstrates a role for structural variation within olfactory receptor-rich regions in complex diseases and defines the 11q11 deletion as a risk factor for obesity.
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3
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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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5
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Scaglione GL, Concolino P, De Bonis M, De Paolis E, Minucci A, Ferrandina G, Scambia G, Capoluongo E. A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis. Int J Mol Sci 2018; 19:ijms19040961. [PMID: 29570666 PMCID: PMC5979302 DOI: 10.3390/ijms19040961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
BRCA1/2 screening in Hereditary Breast and Ovarian Syndrome (HBOC) is an essential step for effective patients’ management. Next-Generation Sequencing (NGS) can rapidly provide high throughput and reliable information about the qualitative and quantitative status of tumor-associated genes. Straightforwardly, bioinformatics methods play a key role in molecular diagnostics pipelines. BRCA1/2 genes were evaluated with our NGS workflow, coupled with Multiplex Amplicon Quantification (MAQ) and Multiplex Ligation-dependent Probe Amplification (MLPA) assays. Variant calling was performed on Amplicon Suite, while Copy Number Variant (CNV) prediction by in house and commercial CNV tools, before confirmatory MAQ/MLPA testing. The germline profile of BRCA genes revealed a unique HBOC pattern. Although variant calling analysis pinpointed heterozygote and homozygote polymorphisms on BRCA1 and BRCA2, respectively, the CNV predicted by our script suggested two conflicting interpretations: BRCA1 duplication and/or BRCA2 deletion. Our commercial software reported a BRCA1 duplication, in contrast with variant calling results. Finally, the MAQ/MLPA assays assessed a whole BRCA2 copy loss. In silico CNV analysis is a time and cost-saving procedure to powerfully identify possible Large Rearrangements using robust and efficient NGS pipelines. Our layout shows as bioinformatics algorithms alone cannot completely and correctly identify whole BRCA1/2 deletions/duplications. In particular, the complete deletion of an entire gene, like in our case, cannot be solved without alternative strategies as MLPA/MAQ. These findings support the crucial role of bioinformatics in deciphering pitfalls within NGS data analysis.
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Affiliation(s)
- Giovanni Luca Scaglione
- Fondazione di Ricerca e Cura Giovanni Paolo II, Laboratorio di Oncologia Molecolare, Molipharma a spin-off of Fondazione di Ricerca e Cura Giovanni Paolo II, Contrada Tappino, 86100 Campobasso, Italy.
- Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico, Dipartimento di Diagnostica di Laboratorio e Biologia Molecolare Clinica, 00168 Roma, Italy.
| | - Paola Concolino
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, 00168 Rome, Italy.
| | - Maria De Bonis
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, 00168 Rome, Italy.
| | - Elisa De Paolis
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, 00168 Rome, Italy.
| | - Angelo Minucci
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze delle Immagini, di Laboratorio ed Infettivologiche, 00168 Rome, Italy.
| | - Gabriella Ferrandina
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze della Salute della Donna e del Bambino, 00168 Rome, Italy.
| | - Giovanni Scambia
- Fondazione di Ricerca e Cura Giovanni Paolo II, Laboratorio di Oncologia Molecolare, Molipharma a spin-off of Fondazione di Ricerca e Cura Giovanni Paolo II, Contrada Tappino, 86100 Campobasso, Italy.
- Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Polo Scienze della Salute della Donna e del Bambino, 00168 Rome, Italy.
| | - Ettore Capoluongo
- Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico, Dipartimento di Diagnostica di Laboratorio e Biologia Molecolare Clinica, 00168 Roma, Italy.
- Laboratory of Molecular Genomics XBiogem, Catholic University of Rome, 00168 Rome, Italy.
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6
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Aerts E, Geets E, Sorber L, Beckers S, Verrijken A, Massa G, Hoorenbeeck K, Verhulst SL, Gaal LF, Hul W. Evaluation of a Role for
NPY
and
NPY2R
in the Pathogenesis of Obesity by Mutation and Copy Number Variation Analysis in Obese Children and Adolescents. Ann Hum Genet 2017; 82:1-10. [DOI: 10.1111/ahg.12211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Evi Aerts
- Department of Medical Genetics University of Antwerp Antwerp Belgium
| | - Ellen Geets
- Department of Medical Genetics University of Antwerp Antwerp Belgium
| | - Laure Sorber
- Department of Medical Genetics University of Antwerp Antwerp Belgium
| | - Sigri Beckers
- Department of Medical Genetics University of Antwerp Antwerp Belgium
| | - An Verrijken
- Department of Endocrinology, Diabetology and Metabolic Diseases Antwerp University Hospital Antwerp Belgium
| | - Guy Massa
- Department of Pediatrics Jessa Hospital Hasselt Belgium
| | - Kim Hoorenbeeck
- Department of Pediatrics Antwerp University Hospital Antwerp Belgium
| | - Stijn L Verhulst
- Department of Pediatrics Antwerp University Hospital Antwerp Belgium
| | - Luc F Gaal
- Department of Endocrinology, Diabetology and Metabolic Diseases Antwerp University Hospital Antwerp Belgium
| | - Wim Hul
- Department of Medical Genetics University of Antwerp Antwerp Belgium
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7
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Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders. Genet Med 2016; 19:667-675. [PMID: 28574513 PMCID: PMC5460076 DOI: 10.1038/gim.2016.163] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/31/2016] [Indexed: 01/08/2023] Open
Abstract
Purpose: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10–20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. Methods: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. Results: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to –5.8% per disorder). Conclusions: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016
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8
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Pinto C, Bella MA, Capoluongo E, Carrera P, Clemente C, Colombo N, Cortesi L, De Rosa G, Fenizia F, Genuardi M, Gori S, Guarneri V, Marchetti A, Marchetti P, Normanno N, Pasini B, Pignata S, Radice P, Ricevuto E, Russo A, Tagliaferri P, Tassone P, Truini M, Varesco L. Recommendations for the implementation of BRCA testing in the care and treatment pathways of ovarian cancer patients. Future Oncol 2016; 12:2071-5. [DOI: 10.2217/fon-2016-0189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Carmine Pinto
- Medical Oncology S.Maria Nuova Hospital – IRCCS Reggio Emilia, Italy
| | | | - Ettore Capoluongo
- Institute of Biochemistry & Clinical Biochemistry, Catholic University of the Sacred Heart, Rome, Italy
| | - Paola Carrera
- Unit of Genomics for Diagnosis of Human Pathologies, Division of Genetics & Cell Biology, & Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Claudio Clemente
- Pathology & Cytopathology Unit, Casa di Cura San Pio X & IRCCS Policlinico San Donato, Milano, Italy
| | | | - Laura Cortesi
- Department of Oncology, Hematology & Respiratory Diseases, University Hospital of Modena, Italy
| | - Gaetano De Rosa
- Department of Advanced Biomedical Sciences, Pathology Section, University of Naples Federico II, Naples, Italy
| | - Francesca Fenizia
- Pharmacogenomic Laboratory, Centro di Ricerche Oncologiche di Mercogliano (CROM), Istituto Nazionale per lo Studio e la Cura dei Tumori “Fondazione Giovanni Pascale” – IRCCS Naples, Italy
| | - Maurizio Genuardi
- Institute of Genomic Medicine, ‘A Gemelli’ School of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Stefania Gori
- Department of Oncology, Ospedale Sacro Cuore Don Calabria, Negrar-Verona, Italy
| | - Valentina Guarneri
- Department of Surgery, Oncology & Gastroenterology, University of Padova; Medical Oncology 2, Istituto Oncologico Veneto IRCCS, Padova, Italy
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Italy
| | - Paolo Marchetti
- Clinical & Molecular Medicine Department, Sapienza University, Rome, Italy
| | - Nicola Normanno
- Cell Biology & Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori ‘Fondazione Giovanni Pascale’ – IRCCS Naples, Italy
| | - Barbara Pasini
- Department of Medical Science, University of Turin, Turin, Italy
| | - Sandro Pignata
- Uro-Gynecological Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori ‘Fondazione Giovanni Pascale’ – IRCCS Naples, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk & Genetic Testing, Department of Preventive & Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Enrico Ricevuto
- Oncology Network ASL1 Abruzzo, Oncology Territorial Care Unit, Division of Medical Oncology, Department of Biotechnological & Applied Clinical Sciences, University of L'Aquila, Italy
| | - Antonio Russo
- Department of Surgical, Oncological & Oral Sciences, Section of Medical Oncology, University of Palermo, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental & Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Sbarro Institute for Cancer Research & Molecular Medicine, Center for Biotechnology, College of Science & Technology, Temple University, Philadelphia, PA, USA
| | - Mauro Truini
- Pathological Anatomy Histology & Cytogenetics, Niguarda Cancer Center, Niguarda Ca’ Granda Hospital, Milan, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancers, IRCCS AOU San Martino – IST, Genoa, Italy
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9
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Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, Boudewyns A, De Leenheer E, Janssens S, Claes K, Verstreken M, Strenzke N, Predöhl F, Wuyts W, Mortier G, Bitner-Glindzicz M, Moser T, Coucke P, Huentelman MJ, Van Camp G. DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System. Hum Mutat 2016; 37:812-9. [PMID: 27068579 DOI: 10.1002/humu.22999] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
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Affiliation(s)
- Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jenneke van den Ende
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Els De Leenheer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Margriet Verstreken
- University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium
| | - Nicola Strenzke
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Friederike Predöhl
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Maria Bitner-Glindzicz
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Tobias Moser
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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10
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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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11
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Vandeweyer G, Kooy RF. Detection and interpretation of genomic structural variation in health and disease. Expert Rev Mol Diagn 2014; 13:61-82. [DOI: 10.1586/erm.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Deshpande A, White PS. Multiplexed nucleic acid-based assays for molecular diagnostics of human disease. Expert Rev Mol Diagn 2014; 12:645-59. [DOI: 10.1586/erm.12.60] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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13
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Multiplex amplicon quantification screening the ABCA13 gene for copy number variation in schizophrenia and bipolar disorder. Psychiatr Genet 2013; 22:269-70. [PMID: 22392056 DOI: 10.1097/ypg.0b013e32835185b3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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15
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van der Zee J, Gijselinck I, Dillen L, Van Langenhove T, Theuns J, Engelborghs S, Philtjens S, Vandenbulcke M, Sleegers K, Sieben A, Bäumer V, Maes G, Corsmit E, Borroni B, Padovani A, Archetti S, Perneczky R, Diehl-Schmid J, de Mendonça A, Miltenberger-Miltenyi G, Pereira S, Pimentel J, Nacmias B, Bagnoli S, Sorbi S, Graff C, Chiang HH, Westerlund M, Sanchez-Valle R, Llado A, Gelpi E, Santana I, Almeida MR, Santiago B, Frisoni G, Zanetti O, Bonvicini C, Synofzik M, Maetzler W, Vom Hagen JM, Schöls L, Heneka MT, Jessen F, Matej R, Parobkova E, Kovacs GG, Ströbel T, Sarafov S, Tournev I, Jordanova A, Danek A, Arzberger T, Fabrizi GM, Testi S, Salmon E, Santens P, Martin JJ, Cras P, Vandenberghe R, De Deyn PP, Cruts M, Van Broeckhoven C, van der Zee J, Gijselinck I, Dillen L, Van Langenhove T, Theuns J, Philtjens S, Sleegers K, Bäumer V, Maes G, Corsmit E, Cruts M, Van Broeckhoven C, van der Zee J, Gijselinck I, Dillen L, Van Langenhove T, Philtjens S, Theuns J, Sleegers K, Bäumer V, Maes G, Cruts M, Van Broeckhoven C, Engelborghs S, De Deyn PP, Cras P, Engelborghs S, De Deyn PP, Vandenbulcke M, Vandenbulcke M, Borroni B, Padovani A, Archetti S, Perneczky R, Diehl-Schmid J, Synofzik M, Maetzler W, Müller Vom Hagen J, Schöls L, Synofzik M, Maetzler W, Müller Vom Hagen J, Schöls L, Heneka MT, Jessen F, Ramirez A, Kurzwelly D, Sachtleben C, Mairer W, de Mendonça A, Miltenberger-Miltenyi G, Pereira S, Firmo C, Pimentel J, Sanchez-Valle R, Llado A, Antonell A, Molinuevo J, Gelpi E, Graff C, Chiang HH, Westerlund M, Graff C, Kinhult Ståhlbom A, Thonberg H, Nennesmo I, Börjesson-Hanson A, Nacmias B, Bagnoli S, Sorbi S, Bessi V, Piaceri I, Santana I, Santiago B, Santana I, Helena Ribeiro M, Rosário Almeida M, Oliveira C, Massano J, Garret C, Pires P, Frisoni G, Zanetti O, Bonvicini C, Sarafov S, Tournev I, Jordanova A, Tournev I, Kovacs GG, Ströbel T, Heneka MT, Jessen F, Ramirez A, Kurzwelly D, Sachtleben C, Mairer W, Jessen F, Matej R, Parobkova E, Danel A, Arzberger T, Maria Fabrizi G, Testi S, Ferrari S, Cavallaro T, Salmon E, Santens P, Cras P. A pan-European study of the C9orf72 repeat associated with FTLD: geographic prevalence, genomic instability, and intermediate repeats. Hum Mutat 2013; 34:363-73. [PMID: 23111906 PMCID: PMC3638346 DOI: 10.1002/humu.22244] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/09/2012] [Indexed: 12/12/2022]
Abstract
We assessed the geographical distribution of C9orf72 G(4) C(2) expansions in a pan-European frontotemporal lobar degeneration (FTLD) cohort (n = 1,205), ascertained by the European Early-Onset Dementia (EOD) consortium. Next, we performed a meta-analysis of our data and that of other European studies, together 2,668 patients from 15 Western European countries. The frequency of the C9orf72 expansions in Western Europe was 9.98% in overall FTLD, with 18.52% in familial, and 6.26% in sporadic FTLD patients. Outliers were Finland and Sweden with overall frequencies of respectively 29.33% and 20.73%, but also Spain with 25.49%. In contrast, prevalence in Germany was limited to 4.82%. In addition, we studied the role of intermediate repeats (7-24 repeat units), which are strongly correlated with the risk haplotype, on disease and C9orf72 expression. In vitro reporter gene expression studies demonstrated significantly decreased transcriptional activity of C9orf72 with increasing number of normal repeat units, indicating that intermediate repeats might act as predisposing alleles and in favor of the loss-of-function disease mechanism. Further, we observed a significantly increased frequency of short indels in the GC-rich low complexity sequence adjacent to the G(4) C(2) repeat in C9orf72 expansion carriers (P < 0.001) with the most common indel creating one long contiguous imperfect G(4) C(2) repeat, which is likely more prone to replication slippage and pathological expansion.
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Genetic association of CR1 with Alzheimer's disease: A tentative disease mechanism. Neurobiol Aging 2012; 33:2949.e5-2949.e12. [DOI: 10.1016/j.neurobiolaging.2012.07.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/29/2012] [Accepted: 07/01/2012] [Indexed: 01/27/2023]
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Van Den Bossche MJ, Johnstone M, Strazisar M, Pickard BS, Goossens D, Lenaerts AS, De Zutter S, Nordin A, Norrback KF, Mendlewicz J, Souery D, De Rijk P, Sabbe BG, Adolfsson R, Blackwood D, Del-Favero J. Rare copy number variants in neuropsychiatric disorders: Specific phenotype or not? Am J Med Genet B Neuropsychiatr Genet 2012; 159B:812-22. [PMID: 22911887 DOI: 10.1002/ajmg.b.32088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/11/2012] [Indexed: 12/31/2022]
Abstract
From a number of genome-wide association studies it was shown that de novo and/or rare copy number variants (CNVs) are found at an increased frequency in neuropsychiatric diseases. In this study we examined the prevalence of CNVs in six genomic regions (1q21.1, 2p16.3, 3q29, 15q11.2, 15q13.3, and 16p11.2) previously implicated in neuropsychiatric diseases. Hereto, a cohort of four neuropsychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, and intellectual disability) and control individuals from three different populations was used in combination with Multilpex Amplicon Quantifiaction (MAQ) assays, capable of high resolution (kb range) and custom-tailored CNV detection. Our results confirm the etiological candidacy of the six selected CNV regions for neuropsychiatric diseases. It is possible that CNVs in these regions can result in disturbed brain development and in this way lead to an increased susceptibility for different neuropsychiatric disorders, dependent on additional genetic and environmental factors. Our results also suggest that the neurodevelopmental component is larger in the etiology of schizophrenia and intellectual disability than in mood disorders. Finally, our data suggest that deletions are in general more pathogenic than duplications. Given the high frequency of the examined CNVs (1-2%) in patients of different neuropsychiatric disorders, screening of large cohorts with an affordable and feasible method like the MAQ assays used in this study is likely to result in important progress in unraveling the genetic factors leading to an increased susceptibility for several psychiatric disorders.
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Garcia-Linares C, Mercadé J, Gel B, Biayna J, Terribas E, Lázaro C, Serra E. Applying microsatellite multiplex PCR analysis (MMPA) for determining allele copy-number status and percentage of normal cells within tumors. PLoS One 2012; 7:e42682. [PMID: 22916147 PMCID: PMC3419736 DOI: 10.1371/journal.pone.0042682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 07/11/2012] [Indexed: 11/18/2022] Open
Abstract
The study of somatic genetic alterations in tumors contributes to the understanding and management of cancer. Genetic alterations, such us copy number or copy neutral changes, generate allelic imbalances (AIs) that can be determined using polymorphic markers. Here we report the development of a simple set of calculations for analyzing microsatellite multiplex PCR data from control-tumor pairs that allows us to obtain accurate information not only regarding the AI status of tumors, but also the percentage of tumor-infiltrating normal cells, the locus copy-number status and the mechanism involved in AI. We validated this new approach by re-analyzing a set of Neurofibromatosis type 1-associated dermal neurofibromas and comparing newly generated data with results obtained for the same tumors in a previous study using MLPA, Paralog Ratio Analysis and SNP-array techniques.Microsatellite multiplex PCR analysis (MMPA) should be particularly useful for analyzing specific regions of the genome containing tumor suppressor genes and also for determining the percentage of infiltrating normal cells within tumors allowing them to be sorted before they are analyzed by more expensive techniques.
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Affiliation(s)
- Carles Garcia-Linares
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Jaume Mercadé
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Bernat Gel
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Josep Biayna
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Ernest Terribas
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Conxi Lázaro
- Programa de Diagnòstic Molecular de Càncer Hereditari, Laboratori de Recerca Translacional, Institut Català d'Oncologia (ICO) – IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduard Serra
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
- * E-mail:
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Brouwers N, Van Cauwenberghe C, Engelborghs S, Lambert JC, Bettens K, Le Bastard N, Pasquier F, Montoya AG, Peeters K, Mattheijssens M, Vandenberghe R, De Deyn PP, Cruts M, Amouyel P, Sleegers K, Van Broeckhoven C. Alzheimer risk associated with a copy number variation in the complement receptor 1 increasing C3b/C4b binding sites. Mol Psychiatry 2012; 17:223-33. [PMID: 21403675 PMCID: PMC3265835 DOI: 10.1038/mp.2011.24] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two multicentre genome-wide association (GWA) studies provided substantial evidence, implicating the complement receptor 1 gene (CR1) in Alzheimer disease (AD) genetic etiology. CR1 encodes a large transmembrane receptor with a crucial role in the immune complement cascade. We performed a genetic follow-up of the GWA CR1 association in a Flanders-Belgian cohort (n=1883), and investigated the effect of single-nucleotide polymorphisms (SNPs) located in the CR1 locus on AD risk and cerebrospinal fluid (CSF) biomarker levels. We obtained significant association (P(adj)<0.03; odds ratio (OR)=1.24 (95% confidence interval (CI): 1.02-1.51)) for one CR1 risk haplotype, and haplotype association was strongest in individuals carrying apolipoprotein E (APOE) ɛ4 alleles (P(adj)<0.006; OR=1.50 (95% CI: 1.08-2.09)). Also, four SNPs correlated with increased CSF amyloid Aβ₁₋₄₂ levels, suggesting a role for the CR1 protein in Aβ metabolism. Moreover, we quantified a low-copy repeat (LCR)-associated copy number variation (CNV) in CR1, producing different CR1 isoforms, CR1-F and CR1-S, and obtained significant association in carriers of CR1-S. We replicated the CR1 CNV association finding in a French cohort (n=2003) and calculated in the combined cohorts, an OR of 1.32; 95% CI: 1.10-1.59 (P=0.0025). Our data showed that the common AD risk association may well be explained by the presence of CR1-S increasing the number of C3b/C4b and cofactor activity sites and AD risk with 30% in CR1-S carriers. How precisely the different functional role of CR1-S in the immune complement cascade contributes to AD pathogenesis will need additional functional studies.
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Affiliation(s)
- N Brouwers
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - C Van Cauwenberghe
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - S Engelborghs
- Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium,Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerpen, Belgium
| | - J-C Lambert
- INSERM U744, Lille, France,Institut Pasteur de Lille, Lille, France,Université de Lille Nord de France, Lille, France
| | - K Bettens
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - N Le Bastard
- Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - F Pasquier
- Université de Lille Nord de France, Lille, France,CHR&U de Lille, Lille, France
| | - A Gil Montoya
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - K Peeters
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - M Mattheijssens
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - R Vandenberghe
- Department of Neurology, University Hospitals Leuven and University of Leuven (KUL), Leuven, Belgium
| | - P P De Deyn
- Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium,Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, Antwerpen, Belgium
| | - M Cruts
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - P Amouyel
- INSERM U744, Lille, France,Institut Pasteur de Lille, Lille, France,Université de Lille Nord de France, Lille, France,CHR&U de Lille, Lille, France
| | - K Sleegers
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - C Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium,Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium,Neurodegenerative Brain Diseases Group, VIB Department of Molecular Genetics, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerpen, Belgium. E-mail:
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No evidence for GNAS copy number variants in patients with features of Albright's hereditary osteodystrophy and abnormal platelet Gs activity. J Hum Genet 2012; 57:277-9. [PMID: 22277900 DOI: 10.1038/jhg.2012.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Albright's hereditary osteodystrophy (AHO) is characterized by short stature, round face, calcifications, obesity, brachydactyly and intellectual disability. AHO without hormone resistance is called pseudopseudohypoparathyroidism (PPHP), a rare clinical condition difficult to diagnose with highly variable features. PPHP is caused by paternally inherited loss-of-function mutations in the GNAS. Patients with 2q37 microdeletions or HDAC4 mutations are also defined as having an AHO-like phenotype with normal stimulatory G (Gs) function. We have studied 256 patients with AHO features but no other diagnosis. Their platelet Gs activity was determined via the aggregation-inhibition test showing Gs hypo- or hyperfuncton in 24% and 15% of the patients, respectively. Before initiating with detailed (epi)genetic GNAS studies, we here wanted to excluded copy number variants (CNVs) in GNAS as cause of AHO with a novel large-scale screening technique. Multiplex amplicon quantification (MAQ) for CNVs screening was developed for the 20q13.3 region including GNAS and potential long-range imprinting control elements such as STX16. This is the first large-scale GNAS CNV study in patients with common AHO features but no CNVs were detected. In conclusion, CNVs in the GNAS region are not likely to cause an AHO-like phenotype with or without abnormal platelet Gs activity. Future studies will be undertaken to find out whether these AHO patients with abnormal Gs function are characterized by GNAS coding or methylation defects.
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Meeus B, Verstraeten A, Crosiers D, Engelborghs S, Van den Broeck M, Mattheijssens M, Peeters K, Corsmit E, Elinck E, Pickut B, Vandenberghe R, Cras P, De Deyn PP, Van Broeckhoven C, Theuns J. DLB and PDD: a role for mutations in dementia and Parkinson disease genes? Neurobiol Aging 2011; 33:629.e5-629.e18. [PMID: 22118943 DOI: 10.1016/j.neurobiolaging.2011.10.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 09/05/2011] [Accepted: 10/15/2011] [Indexed: 10/14/2022]
Abstract
Based on the substantial overlap in clinical and pathological characteristics of dementia with Lewy bodies (DLB) and Parkinson disease with dementia (PDD) with Alzheimer disease (AD) and Parkinson disease (PD) we hypothesized that these disorders might share underlying genetic factors. The contribution of both sequence and copy number variants (CNVs) in known AD and PD genes to the genetic etiology of DLB and PDD however is currently unclear. Therefore, we performed a gene-based mutation analysis of all major AD and PD genes in 99 DLB and 75 PDD patients, including familial and sporadic forms, from Flanders, Belgium. Also, copy number variants in APP, SNCA, and PARK2 were determined. In the AD genes we detected proven pathogenic missense mutations in PSEN1 and PSEN2, and 2 novel missense variants in PSEN2 and MAPT. In the PD genes we identified 1 SNCA duplication, the LRRK2 R1441C founder mutation and 4 novel heterozygous missense variants with unknown pathogenicity. Our results suggest a contribution of established AD and PD genes to the genetic etiology of DLB and PDD though to a limited extent. They do support the hypothesis of a genetic overlap between members of the Lewy body disease spectrum, but additional genes still have to exist.
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Affiliation(s)
- Bram Meeus
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerpen, Belgium
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Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet 2011; 12:363-76. [PMID: 21358748 DOI: 10.1038/nrg2958] [Citation(s) in RCA: 955] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comparisons of human genomes show that more base pairs are altered as a result of structural variation - including copy number variation - than as a result of point mutations. Here we review advances and challenges in the discovery and genotyping of structural variation. The recent application of massively parallel sequencing methods has complemented microarray-based methods and has led to an exponential increase in the discovery of smaller structural-variation events. Some global discovery biases remain, but the integration of experimental and computational approaches is proving fruitful for accurate characterization of the copy, content and structure of variable regions. We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation.
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Affiliation(s)
- Can Alkan
- Department of Genome Sciences, University of Washington School of Medicine, Foege S413C, 3720 15th Ave NE, Seattle, Washington, USA
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The Quassinoid Derivative NBT-272 Targets Both the AKT and ERK Signaling Pathways in Embryonal Tumors. Mol Cancer Ther 2010; 9:3145-57. [DOI: 10.1158/1535-7163.mct-10-0539] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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