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Niazi R, Gonzalez MA, Balciuniene J, Evans P, Sarmady M, Abou Tayoun AN. The Development and Validation of Clinical Exome-Based Panels Using ExomeSlicer: Considerations and Proof of Concept Using an Epilepsy Panel. J Mol Diagn 2018; 20:643-652. [PMID: 29936260 DOI: 10.1016/j.jmoldx.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/14/2018] [Accepted: 05/11/2018] [Indexed: 12/14/2022] Open
Abstract
Exome-based panels are becoming the preferred diagnostic strategy in clinical laboratories. This approach enables dynamic gene content update and, if needed, cost-effective reflex to whole-exome sequencing. Currently, no guidelines or appropriate resources are available to support the clinical implementation of exome-based panels. Here, we highlight principles and important considerations for the clinical development and validation of exome-based panels. In addition, we developed ExomeSlicer, a novel, web-based resource, which uses empirical exon-level next-generation sequencing quality metrics to predict and visualize technically challenging exome-wide regions in any gene or genes of interest. Exome sequencing data from 100 clinical epilepsy cases were used to illustrate the clinical utility of ExomeSlicer in predicting poor-quality regions and its impact on streamlining the ad hoc Sanger sequencing fill in burden. With the use of ExomeSlicer, >2100 low complexity and/or high-homology regions affecting >1615 genes across the exome were also characterized. These regions can be a source of false-positive or false-negative variant calls, which can lead to misdiagnoses in tested patients and/or inaccurate functional annotations. We provide important considerations and a novel resource for the clinical development of exome-based panels.
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Affiliation(s)
- Rojeen Niazi
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael A Gonzalez
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jorune Balciuniene
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Perry Evans
- Department of Biomedical and Health Informatics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Genetics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.
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102
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Townend GS, Ehrhart F, van Kranen HJ, Wilkinson M, Jacobsen A, Roos M, Willighagen EL, van Enckevort D, Evelo CT, Curfs LMG. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. Hum Mutat 2018; 39:914-924. [PMID: 29704307 PMCID: PMC6033003 DOI: 10.1002/humu.23542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022]
Abstract
Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data.
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Affiliation(s)
- Gillian S Townend
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Henk J van Kranen
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Institute for Public Health Genomics, Maastricht University, Maastricht, The Netherlands
| | - Mark Wilkinson
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid, Madrid, Spain
| | - Annika Jacobsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - David van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Chris T Evelo
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Leopold M G Curfs
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands
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103
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Kawakami H, Ogimoto A, Tokunaga N, Nishimura K, Kawakami H, Higashi H, Iio C, Kono T, Aono J, Uetani T, Nagai T, Inoue K, Suzuki J, Ikeda S, Okura T, Ohyagi Y, Tabara Y, Higaki J. A Novel Truncating LMNA Mutation in Patients with Cardiac Conduction Disorders and Dilated Cardiomyopathy. Int Heart J 2018; 59:531-541. [PMID: 29628476 DOI: 10.1536/ihj.17-377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cardiac phenotype of laminopathies is characterized by cardiac conduction disorders (CCDs) and dilated cardiomyopathy (DCM). Although laminopathies have been considered monogenic, they exhibit a remarkable degree of clinical variability. This case series aimed to detect the causal mutation and to investigate the causes of clinical variability in a Japanese family with inherited CCD and DCM.Of the five family members investigated, four had either CCD/DCM or CCD alone, while one subject had no cardiovascular disease and acted as a normal control. We performed targeted resequencing of 174 inherited cardiovascular disease-associated genes in this family and pathological mutations were confirmed using Sanger sequencing. The degree of clinical severity and variability were also evaluated using long-term medical records. We discovered a novel heterozygous truncating lamin A/C (LMNA) mutation (c.774delG) in all four subjects with CCD. Because this mutation was predicted to cause a frameshift mutation and premature termination (p.Gln258HisfsTer222) in LMNA, we believe that this LMNA mutation was the causal mutation in this family with CCD and laminopathies. In addition, gender-specific intra-familiar clinical variability was observed in this Japanese family where affected males exhibited an earlier onset of CCD and more severe DCM compared to affected females. Using targeted resequencing, we discovered a novel truncating LMNA mutation associated with CCD and DCM in this family characterized by gender differences in clinical severity in LMNA carriers. Our results suggest that in patients with laminopathy, clinical severity may be the result of multiple factors.
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Affiliation(s)
- Hiroshi Kawakami
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Akiyoshi Ogimoto
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Naohito Tokunaga
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Kazuhisa Nishimura
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Hideo Kawakami
- Department of Cardiology, Ehime Prefectural Imabari Hospital
| | - Haruhiko Higashi
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Chiharuko Iio
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Tamami Kono
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Jun Aono
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Teruyoshi Uetani
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Takayuki Nagai
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Katsuji Inoue
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Jun Suzuki
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Shuntaro Ikeda
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Takafumi Okura
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
| | - Yasumasa Ohyagi
- Department of Geriatric Medicine, Ehime University Graduate School of Medicine
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine
| | - Jitsuo Higaki
- Department of Cardiology, Pulmonology, Hypertension & Nephrology, Ehime University Graduate School of Medicine
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104
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Coene KLM, Kluijtmans LAJ, van der Heeft E, Engelke UFH, de Boer S, Hoegen B, Kwast HJT, van de Vorst M, Huigen MCDG, Keularts IMLW, Schreuder MF, van Karnebeek CDM, Wortmann SB, de Vries MC, Janssen MCH, Gilissen C, Engel J, Wevers RA. Next-generation metabolic screening: targeted and untargeted metabolomics for the diagnosis of inborn errors of metabolism in individual patients. J Inherit Metab Dis 2018; 41:337-353. [PMID: 29453510 PMCID: PMC5959972 DOI: 10.1007/s10545-017-0131-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/17/2017] [Accepted: 12/21/2017] [Indexed: 12/30/2022]
Abstract
The implementation of whole-exome sequencing in clinical diagnostics has generated a need for functional evaluation of genetic variants. In the field of inborn errors of metabolism (IEM), a diverse spectrum of targeted biochemical assays is employed to analyze a limited amount of metabolites. We now present a single-platform, high-resolution liquid chromatography quadrupole time of flight (LC-QTOF) method that can be applied for holistic metabolic profiling in plasma of individual IEM-suspected patients. This method, which we termed "next-generation metabolic screening" (NGMS), can detect >10,000 features in each sample. In the NGMS workflow, features identified in patient and control samples are aligned using the "various forms of chromatography mass spectrometry (XCMS)" software package. Subsequently, all features are annotated using the Human Metabolome Database, and statistical testing is performed to identify significantly perturbed metabolite concentrations in a patient sample compared with controls. We propose three main modalities to analyze complex, untargeted metabolomics data. First, a targeted evaluation can be done based on identified genetic variants of uncertain significance in metabolic pathways. Second, we developed a panel of IEM-related metabolites to filter untargeted metabolomics data. Based on this IEM-panel approach, we provided the correct diagnosis for 42 of 46 IEMs. As a last modality, metabolomics data can be analyzed in an untargeted setting, which we term "open the metabolome" analysis. This approach identifies potential novel biomarkers in known IEMs and leads to identification of biomarkers for as yet unknown IEMs. We are convinced that NGMS is the way forward in laboratory diagnostics of IEMs.
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Affiliation(s)
- Karlien L M Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands.
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Ed van der Heeft
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Siebolt de Boer
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Brechtje Hoegen
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Hanneke J T Kwast
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marleen C D G Huigen
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
| | - Irene M L W Keularts
- Department of Clinical Genetics, Laboratory of Biochemical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Michiel F Schreuder
- Department of Pediatric Nephrology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Clara D M van Karnebeek
- Department of Genetic Metabolic Disorders, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | - Saskia B Wortmann
- Department of Pediatrics, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg, Austria
| | - Maaike C de Vries
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirian C H Janssen
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jasper Engel
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML), Radboud University Medical Center, Geert Groote Plein Zuid 10, 6525, GA, Nijmegen, The Netherlands
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105
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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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106
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Brown R, Kichaev G, Mancuso N, Boocock J, Pasaniuc B. Enhanced methods to detect haplotypic effects on gene expression. Bioinformatics 2018; 33:2307-2313. [PMID: 28369161 DOI: 10.1093/bioinformatics/btx142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 03/20/2017] [Indexed: 12/26/2022] Open
Abstract
Motivation Expression quantitative trait loci (eQTLs), genetic variants associated with gene expression levels, are identified in eQTL mapping studies. Such studies typically test for an association between single nucleotide polymorphisms (SNPs) and expression under an additive model, which ignores interaction and haplotypic effects. Mismatches between the model tested and the underlying genetic architecture can lead to a loss of association power. Here we introduce a new haplotype-based test for eQTL studies that looks for haplotypic effects on expression levels. Our test is motivated by compound heterozygous architectures, a common disease model for recessive monogenic disorders, where two different alleles can have the same effect on a gene's function. Results When the underlying true causal architecture for a simulated gene is a compound heterozygote, our method is better able to capture the signal than the marginal SNP method. When the underlying model is a single SNP, there is no difference in the power of our method relative to the marginal SNP method. We apply our method to empirical gene expression data measured in 373 European individuals from the GEUVADIS study and find 29 more eGenes (genes with at least one association) than the standard marginal SNP method. Furthermore, in 974 of the 3529 total eGenes, our haplotype-based method results in a stronger association signal than the standard marginal SNP method. This demonstrates our method both increases power over the standard method and provides evidence of haplotypic architectures regulating gene expression. Availability and Implementation http://bogdan.bioinformatics.ucla.edu/software/. Contact rob.brown@ucla.edu or pasaniuc@ucla.edu.
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Affiliation(s)
- Robert Brown
- Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA, USA
| | - Gleb Kichaev
- Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA, USA
| | | | - James Boocock
- Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics IDP, University of California Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine.,Department of Human Genetics, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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107
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Genetic analysis of early onset familial coronary artery diseases. ACTA ACUST UNITED AC 2018; 4:e1-e6. [PMID: 30863800 PMCID: PMC6412034 DOI: 10.5114/amsad.2019.83149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Abstract
Introduction Coronary artery diseases (CAD) are the most common causes of death. Myocardial infarction (MI) is a complex multifactorial and the most severe type of CAD. Early onset MI in a first-degree relative could be defined as an independent risk factor for CAD. This study was performed to investigate the genetic cause of early onset familial CAD. Material and methods In this study, the genetic cause of familial CAD was investigated in patients with a family history of CAD who underwent angiography before the age of 50 years. The patients did not have any diagnostic criteria for familial hypercholesterolemia, diabetes, or obesity, and also they were not opium or alcohol users. Whole exome sequencing in probands was performed and mutation was confirmed by PCR and Sanger sequencing. Results In our studied population, the c.501G>C (p.K167N) mutation in the OLR1 gene was identified in a family. Mutation was confirmed by PCR and Sanger sequencing in the homozygous state (GG) in patients. Healthy individuals in this family were heterozygous (GC) and homozygous (CC). Conclusions This finding suggests that the OLR1 gene could be a possible cause of early onset familial MI. Considering that parents of all affected individuals had a consanguineous marriage, it is important to perform carrier screening and genetic counseling in this family and their close relatives as a prevention strategy in populations at risk.
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108
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Abstract
Technologies such as next-generation sequencing and chromosomal microarray have advanced the understanding of the molecular pathogenesis of a variety of renal disorders. Genetic findings are increasingly used to inform the clinical management of many nephropathies, enabling targeted disease surveillance, choice of therapy, and family counselling. Genetic analysis has excellent diagnostic utility in paediatric nephrology, as illustrated by sequencing studies of patients with congenital anomalies of the kidney and urinary tract and steroid-resistant nephrotic syndrome. Although additional investigation is needed, pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients. Reaching a genetic diagnosis first involves choosing the appropriate testing modality, as guided by the clinical presentation of the patient and the number of potential genes associated with the suspected nephropathy. Genome-wide sequencing increases diagnostic sensitivity relative to targeted panels, but holds the challenges of identifying causal variants in the vast amount of data generated and interpreting secondary findings. In order to realize the promise of genomic medicine for kidney disease, many technical, logistical, and ethical questions that accompany the implementation of genetic testing in nephrology must be addressed. The creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
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109
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Ben-Salem S, Robbins SM, Sobreira NLM, Lyon A, Al-Shamsi AM, Islam BK, Akawi NA, John A, Thachillath P, Hamed SA, Valle D, Ali BR, Al-Gazali L. Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy. J Med Genet 2018; 55:122-130. [PMID: 29122926 PMCID: PMC8215682 DOI: 10.1136/jmedgenet-2017-104827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/19/2017] [Accepted: 10/06/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Bone dysplasias are a large group of disorders affecting the growth and structure of the skeletal system. METHODS In the present study, we report the clinical and molecular delineation of a new form of syndromic autosomal recessive spondylometaphyseal dysplasia (SMD) in two Emirati first cousins. They displayed postnatal growth deficiency causing profound limb shortening with proximal and distal segments involvement, narrow chest, radiological abnormalities involving the spine, pelvis and metaphyses, corneal clouding and intellectual disability. Whole genome homozygosity mapping localised the genetic cause to 11q12.1-q13.1, a region spanning 19.32 Mb with ~490 genes. Using whole exome sequencing, we identified four novel homozygous variants within the shared block of homozygosity. Pathogenic variants in genes involved in phospholipid metabolism, such as PLCB4 and PCYT1A, are known to cause bone dysplasia with or without eye anomalies, which led us to select PLCB3 as a strong candidate. This gene encodes phospholipase C β 3, an enzyme that converts phosphatidylinositol 4,5 bisphosphate (PIP2) to inositol 1,4,5 triphosphate (IP3) and diacylglycerol. RESULTS The identified variant (c.2632G>T) substitutes a serine for a highly conserved alanine within the Ha2' element of the proximal C-terminal domain. This disrupts binding of the Ha2' element to the catalytic core and destabilises PLCB3. Here we show that this hypomorphic variant leads to elevated levels of PIP2 in patient fibroblasts, causing disorganisation of the F-actin cytoskeleton. CONCLUSIONS Our results connect a homozygous loss of function variant in PLCB3 with a new SMD associated with corneal dystrophy and developmental delay (SMDCD).
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, University Al-Ain, Al Ain, AbuDhabi, United Arab Emirates
| | - Sarah M Robbins
- Human genetics and Molecular Biology, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nara LM Sobreira
- Human genetics and Molecular Biology, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angeline Lyon
- Chemistry and Biological Sciences, West Lafayette, USA
| | - Aisha M Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Barira K Islam
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Nadia A Akawi
- Division of Cardiovascular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Anne John
- Department of Pathology, College of Medicine and Heath Sciences, University Al-Ain, Al Ain, AbuDhabi, United Arab Emirates
| | - Pramathan Thachillath
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Sania Al Hamed
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - David Valle
- Human genetics and Molecular Biology, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Heath Sciences, University Al-Ain, Al Ain, AbuDhabi, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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110
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Katsanis SH, Minear MA, Sadeghpour A, Cope H, Perilla Y, Cook-Deegan R, Katsanis N, Davis EE, Angrist M. Participant-Partners in Genetic Research: An Exome Study with Families of Children with Unexplained Medical Conditions. J Particip Med 2018; 10:e2. [PMID: 33052113 PMCID: PMC7489233 DOI: 10.2196/jopm.8958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/08/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Unlike aggregate research on groups of participants with a particular disorder, genomic research on discrete families' rare conditions could result in data of use to families, their healthcare, as well as generating knowledge on the human genome. OBJECTIVE In a study of families seeking to rule in/out genetic causes for their children's medical conditions via exome sequencing, we solicited their views on the importance of genomic information. Our aim was to learn the interests of parents in seeking genomic research data and to gauge their responsiveness and engagement with the research team. METHODS At enrollment, we offered participants options in the consent form for receiving potentially clinically relevant research results. We also offered an option of being a "partner" versus a "traditional" participant; partners could be re-contacted for research and study activities. We invited adult partners to complete a pre-exome survey, attend annual family forums, and participate in other inter-family interaction opportunities. RESULTS Of the 385 adults enrolled, 79% opted for "partnership" with the research team. Nearly all (99.2%) participants opted to receive research results pertaining to their children's primary conditions. A majority indicated the desire to receive additional clinically relevant outside the scope of their children's conditions (92.7%) and an interest in non-clinically relevant genetic information (82.7%). CONCLUSIONS Most participants chose partnership, including its rights and potential burdens; however, active engagement in study activities remained the exception. Not surprisingly, the overwhelming majority of participants-both partners and traditional-expected to receive all genetic information resulting from the research study.
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Affiliation(s)
- Sara Huston Katsanis
- Duke Initiative for Science and Society, Duke University, Durham, NC, United States
| | - Mollie A Minear
- Duke Initiative for Science and Society, Duke University, Durham, NC, United States
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University, Durham, NC, United States
| | - Heidi Cope
- Center for Human Disease Modeling, Duke University, Durham, NC, United States
| | - Yezmin Perilla
- Center for Human Disease Modeling, Duke University, Durham, NC, United States
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ, United States
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- Duke University Medical Center, Durham, NC, United States
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC, United States
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC, United States
| | - Misha Angrist
- Duke Initiative for Science and Society, Duke University, Durham, NC, United States.,Social Science Research Institute, Duke University, Durham, NC, United States
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111
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Targeted next-generation sequencing analysis in couples at increased risk for autosomal recessive disorders. Orphanet J Rare Dis 2018; 13:23. [PMID: 29373990 PMCID: PMC5787287 DOI: 10.1186/s13023-018-0763-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Background Many of the genetic childhood disorders leading to death in the pre- or neonatal period or during early childhood follow autosomal recessive modes of inheritance and bear specific challenges for genetic counseling and prenatal diagnostics. Parents are carriers but clinically unaffected, and diseases are rare but have recurrence risks of 25% in the same family. Often, affected children (or fetuses) die before a genetic diagnosis can be established, post-mortem analysis and phenotypic descriptions are insufficient and DNA from affected fetuses or children is not available for later analysis. A genetic diagnosis showing biallelic causative mutations is, however, the requirement for targeted carrier testing in parents and prenatal and preimplantation genetic diagnosis in further pregnancies. Methods We undertook targeted next-generation sequencing (NGS) for carrier screening of autosomal recessive lethal disorders in 8 consanguineous and 5 non-consanguineous couples with one or more affected children. We searched for heterozygous variants (non-synonymous coding or splice variants) in parents’ DNA, using a set of 430 genes known to be causative for rare autosomal recessive diseases with poor prognosis, and then filtering for variants present in genes overlapping in both partners. Putative pathogenic variants were tested for cosegregation in affected fetuses or children where material was available. Results The diagnosis for the premature death in children was established in 5 of the 13 couples. Out of the 8 couples in which no causative diagnosis could be established 4 consented to undergo further analysis, in two of those a potentially causative variant in a novel candidate gene was identified. Conclusions For the families in whom causative variants could be identified, these may now be used for prenatal and preimplantation genetic diagnostics. Our data show that NGS based gene panel sequencing of selected genes involved in lethal autosomal recessive disorders is an effective tool for carrier screening in parents and for the identification of recessive gene defects and offers the possibility of prenatal and preimplantation genetic diagnosis in further pregnancies in families that have experienced deaths in early childhood and /or multiple abortions. Electronic supplementary material The online version of this article (10.1186/s13023-018-0763-0) contains supplementary material, which is available to authorized users.
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112
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Kamien B, Ronan A, Poke G, Sinnerbrink I, Baynam G, Ward M, Gibson WT, Dudding-Byth T, Scott RJ. A Clinical Review of Generalized Overgrowth Syndromes in the Era of Massively Parallel Sequencing. Mol Syndromol 2018; 9:70-82. [PMID: 29593474 DOI: 10.1159/000484532] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 12/22/2022] Open
Abstract
The overgrowth syndromes are important to diagnose, not just for accurate genetic counseling, but also for knowledge surrounding cancer surveillance and prognosis. There has been a recent expansion in the number of genes associated with a mendelian overgrowth phenotype, so this review updates previous classifications of overgrowth syndromes. We also describe a clinical and molecular approach to the investigation of individuals presenting with overgrowth. This review aims to assist the clinical diagnosis of generalized overgrowth syndromes by outlining the salient features of well-known overgrowth syndromes alongside the many syndromes that have been discovered and classified more recently. We provide key clinical "handles" to aid clinical diagnosis and a list of genes to aid with panel design when using next generation sequencing, which we believe is frequently needed due to the overlapping phenotypic features seen between overgrowth syndromes.
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Affiliation(s)
- Benjamin Kamien
- Hunter Genetics, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia.,School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW, Australia
| | - Anne Ronan
- Hunter Genetics, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia
| | - Gemma Poke
- Department of Clinical Genetics, Capital & Coast District Health Board, Wellington, New Zealand
| | - Ingrid Sinnerbrink
- Department of Clinical Genetics, Nepean Hospital, Perth, WA, Australia.,Nepean Clinical School, University of Sydney, Penrith, NSW, Australia
| | - Gareth Baynam
- Genetic Services of Western Australia, Newcastle, NSW, Australia.,Western Australian Register of Developmental Anomalies, Perth, WA, Australia.,Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia.,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Newcastle, NSW, Australia
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tracy Dudding-Byth
- Hunter Genetics, Perth, WA, Australia.,GrowUpWell Priority Research Center, Perth, WA, Australia.,School of Medicine and Public Health, The University of Newcastle, Perth, WA, Australia.,Hunter Medical Research Institute, Perth, WA, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW, Australia.,Molecular Pathology, Hunter Area Pathology Service, Perth, WA, Australia
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113
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Khalilipour N, Baranova A, Jebelli A, Heravi-Moussavi A, Bruskin S, Abbaszadegan MR. Familial Esophageal Squamous Cell Carcinoma with damaging rare/germline mutations in KCNJ12/KCNJ18 and GPRIN2 genes. Cancer Genet 2017; 221:46-52. [PMID: 29405996 DOI: 10.1016/j.cancergen.2017.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 11/12/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
In Iran, esophageal cancer is the fourth common cancers in women and sixth common cancers in men. Here we evaluated the importance of familial risk factors and the role of genetic predisposition in Esophageal Squamous Cell Carcinoma (ESCC) using Whole-Exome Sequencing (WES). Germline damaging mutations were identified in WES data from 9 probands of 9 unrelated ESCC pedigrees. Mutations were confirmed with Sanger sequencing and evaluated amplification-refractory mutation system-Polymerase Chain Reaction (ARMS-PCR) in 50 non-related ethnically matched samples and in complete genomics database. Sixteen candidate variants were detected in ESCC 9 probands. Four of these 16 variants were rare damaging mutations including novel mutations in KCNJ12/KCNJ18, and GPRIN2 genes. This WES study in Iranian patients with ESCC, provides insight into the identification of novel germline mutations in familial ESCC. Our data suggest an association between specific mutations and increased risk of ESCC.
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Affiliation(s)
- Narjes Khalilipour
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ancha Baranova
- Research Center for Medical Genetics RAMS, Moscow, Russia
| | - Amir Jebelli
- Stem Cell and Regenerative Medicine Research Department, Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch, Mashhad, Iran
| | | | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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114
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Jin ZB, Li Z, Liu Z, Jiang Y, Cai XB, Wu J. Identification of de novo germline mutations and causal genes for sporadic diseases using trio-based whole-exome/genome sequencing. Biol Rev Camb Philos Soc 2017; 93:1014-1031. [PMID: 29154454 DOI: 10.1111/brv.12383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome or whole-exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease-causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general-purpose discussion of important issues related to pathogenic gene identification based on trio-based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio-based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
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Affiliation(s)
- Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xue-Bi Cai
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
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115
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Albury CL, Gerring ZF, Griffiths LR, Nyholt DR, Rodriguez-Acevedo AJ. RE: Six novel rare non-synonymous mutations for migraine without aura identified by exome sequencing. J Neurogenet 2017; 31:320-321. [PMID: 29105529 DOI: 10.1080/01677063.2017.1382490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Cassie L Albury
- a Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , Australia
| | - Zachary F Gerring
- b Statistical and Genomic Epidemiology Laboratory , Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , Australia
| | - Lyn R Griffiths
- a Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , Australia
| | - Dale R Nyholt
- b Statistical and Genomic Epidemiology Laboratory , Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane , Australia
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116
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Knecht C, Mort M, Junge O, Cooper DN, Krawczak M, Caliebe A. IMHOTEP-a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants. Nucleic Acids Res 2017; 45:e13. [PMID: 28180317 PMCID: PMC5388428 DOI: 10.1093/nar/gkw886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 01/12/2023] Open
Abstract
The in silico prediction of the functional consequences of mutations is an important goal of human pathogenetics. However, bioinformatic tools that classify mutations according to their functionality employ different algorithms so that predictions may vary markedly between tools. We therefore integrated nine popular prediction tools (PolyPhen-2, SNPs&GO, MutPred, SIFT, MutationTaster2, Mutation Assessor and FATHMM as well as conservation-based Grantham Score and PhyloP) into a single predictor. The optimal combination of these tools was selected by means of a wide range of statistical modeling techniques, drawing upon 10 029 disease-causing single nucleotide variants (SNVs) from Human Gene Mutation Database and 10 002 putatively ‘benign’ non-synonymous SNVs from UCSC. Predictive performance was found to be markedly improved by model-based integration, whilst maximum predictive capability was obtained with either random forest, decision tree or logistic regression analysis. A combination of PolyPhen-2, SNPs&GO, MutPred, MutationTaster2 and FATHMM was found to perform as well as all tools combined. Comparison of our approach with other integrative approaches such as Condel, CoVEC, CAROL, CADD, MetaSVM and MetaLR using an independent validation dataset, revealed the superiority of our newly proposed integrative approach. An online implementation of this approach, IMHOTEP (‘Integrating Molecular Heuristics and Other Tools for Effect Prediction’), is provided at http://www.uni-kiel.de/medinfo/cgi-bin/predictor/.
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Affiliation(s)
- Carolin Knecht
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
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117
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Nestor JG, Groopman EE, Gharavi AG. Towards precision nephrology: the opportunities and challenges of genomic medicine. J Nephrol 2017; 31:47-60. [PMID: 29043570 DOI: 10.1007/s40620-017-0448-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/10/2017] [Indexed: 12/28/2022]
Abstract
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice. In addition, it will discuss some of the challenges associated with the expansion of genetic testing into the clinical setting, including clinical variant interpretation and return of genetic results.
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Affiliation(s)
- Jordan G Nestor
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Emily E Groopman
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Ave, Room 413, New York, NY, 10032, USA.
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118
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Quinodoz M, Royer-Bertrand B, Cisarova K, Di Gioia SA, Superti-Furga A, Rivolta C. DOMINO: Using Machine Learning to Predict Genes Associated with Dominant Disorders. Am J Hum Genet 2017; 101:623-629. [PMID: 28985496 DOI: 10.1016/j.ajhg.2017.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022] Open
Abstract
In contrast to recessive conditions with biallelic inheritance, identification of dominant (monoallelic) mutations for Mendelian disorders is more difficult, because of the abundance of benign heterozygous variants that act as massive background noise (typically, in a 400:1 excess ratio). To reduce this overflow of false positives in next-generation sequencing (NGS) screens, we developed DOMINO, a tool assessing the likelihood for a gene to harbor dominant changes. Unlike commonly-used predictors of pathogenicity, DOMINO takes into consideration features that are the properties of genes, rather than of variants. It uses a machine-learning approach to extract discriminant information from a broad array of features (N = 432), including: genomic data, intra-, and interspecies conservation, gene expression, protein-protein interactions, protein structure, etc. DOMINO's iterative architecture includes a training process on 985 genes with well-established inheritance patterns for Mendelian conditions, and repeated cross-validation that optimizes its discriminant power. When validated on 99 newly-discovered genes with pathogenic mutations, the algorithm displays an excellent final performance, with an area under the curve (AUC) of 0.92. Furthermore, unsupervised analysis by DOMINO of real sets of NGS data from individuals with intellectual disability or epilepsy correctly recognizes known genes and predicts 9 new candidates, with very high confidence. In summary, DOMINO is a robust and reliable tool that can infer dominance of candidate genes with high sensitivity and specificity, making it a useful complement to any NGS pipeline dealing with the analysis of the morbid human genome.
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119
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Gambin T, Akdemir ZC, Yuan B, Gu S, Chiang T, Carvalho CMB, Shaw C, Jhangiani S, Boone PM, Eldomery MK, Karaca E, Bayram Y, Stray-Pedersen A, Muzny D, Charng WL, Bahrambeigi V, Belmont JW, Boerwinkle E, Beaudet AL, Gibbs RA, Lupski JR. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res 2017; 45:1633-1648. [PMID: 27980096 PMCID: PMC5389578 DOI: 10.1093/nar/gkw1237] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/29/2016] [Indexed: 11/14/2022] Open
Abstract
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, Norway
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
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120
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Wiel L, Venselaar H, Veltman JA, Vriend G, Gilissen C. Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics. Hum Mutat 2017; 38:1454-1463. [PMID: 28815929 PMCID: PMC5656839 DOI: 10.1002/humu.23313] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/03/2017] [Accepted: 08/08/2017] [Indexed: 12/11/2022]
Abstract
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population‐based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease‐causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 “meta‐domains.” These meta‐domains consist of 30,853 homologous Pfam protein domain instances that cover 36% of all human protein coding sequences. We find that genetic tolerance is consistent across protein domain homologues, and that patterns of genetic tolerance faithfully mimic patterns of evolutionary conservation. Furthermore, for a significant fraction (68%) of the meta‐domains high‐frequency population variation re‐occurs at the same positions across domain homologues more often than expected. In addition, we observe that the presence of pathogenic missense variants at an aligned homologous domain position is often paired with the absence of population variation and vice versa. The use of these meta‐domains can improve the interpretation of genetic variation.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands
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121
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Analysis of pathogenic variants from the ClinVar database in healthy people using next-generation sequencing. Genet Res (Camb) 2017; 99:e6. [PMID: 28851476 DOI: 10.1017/s0016672317000040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) became an effective approach for finding novel causative genomic variants of genetic disorders and is increasingly used for diagnostic purposes. Public variant databases that gather data of pathogenic variants are being relied upon as a source for clinical diagnosis. However, research of pathogenic variants using public databases data could be carried out not only in patients, but also in healthy people. This could provide insights into the most common recessive disorders in populations. The study aim was to use NGS and data from the ClinVar database for the identification of pathogenic variants in the exomes of healthy individuals from the Lithuanian population. To achieve this, 96 exomes were sequenced. An average of 42 139 single-nucleotide variants (SNVs) and 2306 short INDELs were found in each individual exome. Pooled data of study exomes provided a total of 243 192 unique SNVs and 31 623 unique short INDELs. Three hundred and twenty-one unique SNVs were classified as pathogenic. Comparison of the European data from the 1000 Genomes Project with our data revealed five pathogenic genomic variants that are inherited in an autosomal recessive pattern and that statistically significantly differ from the European population data.
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122
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Gupta S, Chatterjee S, Mukherjee A, Mutsuddi M. Whole exome sequencing: Uncovering causal genetic variants for ocular diseases. Exp Eye Res 2017; 164:139-150. [PMID: 28844620 DOI: 10.1016/j.exer.2017.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 01/23/2023]
Abstract
Identification of causal genetic defects for human diseases took a significant leap when the first generation DNA sequencing technologies enabled biologists extract sequence-based genetic information from living beings. However, these sequencing methods had unavoidable constraints of throughput, scalability, rapidity, and resolution. In this direction, next-generation sequencing (NGS) since the time of its advent has revolutionized the process of gene discovery for both monogenic and multifactorial genetic diseases. Among several variations of NGS, whole exome sequencing (WES) has emerged as a smart strategy that enables identification of disease causing variants present within the coding region of the human genome. The current review focuses primarily on the application of WES in identification of causal variants for ocular diseases. WES has successfully revealed pathogenic variants in a variety of ocular diseases such as retinal degenerations, refractive errors, lens diseases, corneal dystrophies, and developmental ocular defects. It has demonstrated immense potential for molecular diagnosis of genetic ocular diseases. WES has been extensively used in Mendelian and complex cases, familial and sporadic cases, simplex and multiplex cases, and syndromic and non-syndromic cases of ocular diseases. Although many such ocular diseases have been investigated using WES, reports indicate that it has been employed overwhelmingly for heterogeneous retinal degenerations. WES, within a short period of time, has proved to be a cost-effective and promising approach for understanding the genetic basis of ocular diseases.
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Affiliation(s)
- Shashank Gupta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Souradip Chatterjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Giacopuzzi E, Gennarelli M, Minelli A, Gardella R, Valsecchi P, Traversa M, Bonvicini C, Vita A, Sacchetti E, Magri C. Exome sequencing in schizophrenic patients with high levels of homozygosity identifies novel and extremely rare mutations in the GABA/glutamatergic pathways. PLoS One 2017; 12:e0182778. [PMID: 28787007 PMCID: PMC5546675 DOI: 10.1371/journal.pone.0182778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 07/24/2017] [Indexed: 11/18/2022] Open
Abstract
Inbreeding is a known risk factor for recessive Mendelian diseases and previous studies have suggested that it could also play a role in complex disorders, such as psychiatric diseases. Recent inbreeding results in the presence of long runs of homozygosity (ROHs) along the genome, which are also defined as autozygosity regions. Genetic variants in these regions have two alleles that are identical by descent, thus increasing the odds of bearing rare recessive deleterious mutations due to a homozygous state. A recent study showed a suggestive enrichment of long ROHs in schizophrenic patients, suggesting that recent inbreeding could play a role in the disease. To better understand the impact of autozygosity on schizophrenia risk, we selected, from a cohort of 180 Italian patients, seven subjects with extremely high numbers of large ROHs that were likely due to recent inbreeding and characterized the mutational landscape within their ROHs using Whole Exome Sequencing and, gene set enrichment analysis. We identified a significant overlap (17%; empirical p-value = 0.0171) between genes inside ROHs affected by low frequency functional homozygous variants (107 genes) and the group of most promising candidate genes mutated in schizophrenia. Moreover, in four patients, we identified novel and extremely rare damaging mutations in the genes involved in neurodevelopment (MEGF8) and in GABA/glutamatergic synaptic transmission (GAD1, FMN1, ANO2). These results provide insights into the contribution of rare recessive mutations and inbreeding as risk factors for schizophrenia. ROHs that are likely due to recent inbreeding harbor a combination of predisposing low-frequency variants and extremely rare variants that have a high impact on pivotal biological pathways implicated in the disease. In addition, this study confirms that focusing on patients with high levels of homozygosity could be a useful prioritization strategy for discovering new high-impact mutations in genetically complex disorders.
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Affiliation(s)
- Edoardo Giacopuzzi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetic Unit, IRCCS Centro S. Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Rita Gardella
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Paolo Valsecchi
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Michele Traversa
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Cristian Bonvicini
- Genetic Unit, IRCCS Centro S. Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Antonio Vita
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Emilio Sacchetti
- Department of Clinical and Experimental Sciences, Neuroscience Section, University of Brescia, Brescia, Italy
- Department of Mental Health, Spedali Civili Hospital, Brescia, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- * E-mail:
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Hoebel AK, Drichel D, van de Vorst M, Böhmer AC, Sivalingam S, Ishorst N, Klamt J, Gölz L, Alblas M, Maaser A, Keppler K, Zink AM, Dixon MJ, Dixon J, Hemprich A, Kruse T, Graf I, Dunsche A, Schmidt G, Daratsianos N, Nowak S, Aldhorae KA, Nöthen MM, Knapp M, Thiele H, Gilissen C, Reutter H, Hoischen A, Mangold E, Ludwig KU. Candidate Genes for Nonsyndromic Cleft Palate Detected by Exome Sequencing. J Dent Res 2017; 96:1314-1321. [PMID: 28767323 DOI: 10.1177/0022034517722761] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nonsyndromic cleft palate only (nsCPO) is a facial malformation that has a livebirth prevalence of 1 in 2,500. Research suggests that the etiology of nsCPO is multifactorial, with a clear genetic component. To date, genome-wide association studies have identified only 1 conclusive common variant for nsCPO, that is, a missense variant in the gene grainyhead-like-3 ( GRHL3). Thus, the underlying genetic causes of nsCPO remain largely unknown. The present study aimed at identifying rare variants that might contribute to nsCPO risk, via whole-exome sequencing (WES), in multiply affected Central European nsCPO pedigrees. WES was performed in 2 affected first-degree relatives from each family. Variants shared between both individuals were analyzed for their potential deleterious nature and a low frequency in the general population. Genes carrying promising variants were annotated for 1) reported associations with facial development, 2) multiple occurrence of variants, and 3) expression in mouse embryonic palatal shelves. This strategy resulted in the identification of a set of 26 candidate genes that were resequenced in 132 independent nsCPO cases and 623 independent controls of 2 different ethnicities, using molecular inversion probes. No rare loss-of-function mutation was identified in either WES or resequencing step. However, we identified 2 or more missense variants predicted to be deleterious in each of 3 genes ( ACACB, PTPRS, MIB1) in individuals from independent families. In addition, the analyses identified a novel variant in GRHL3 in 1 patient and a variant in CREBBP in 2 siblings. Both genes underlie different syndromic forms of CPO. A plausible hypothesis is that the apparently nonsyndromic clefts in these 3 patients might represent hypomorphic forms of the respective syndromes. In summary, the present study identified rare variants that might contribute to nsCPO risk and suggests candidate genes for further investigation.
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Affiliation(s)
- A K Hoebel
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - D Drichel
- 3 German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,4 Cologne Center for Genomics, Department of Statistical Genetics and Bioinformatics, University of Cologne, Cologne, Germany
| | - M van de Vorst
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A C Böhmer
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - S Sivalingam
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - N Ishorst
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - J Klamt
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - L Gölz
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - M Alblas
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A Maaser
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K Keppler
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - A M Zink
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - J Dixon
- 7 Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - A Hemprich
- 8 Department of Oral and Maxillo-Facial Surgery, University of Leipzig, Leipzig, Germany
| | - T Kruse
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - I Graf
- 9 Department of Orthodontics, University of Cologne, Cologne, Germany
| | - A Dunsche
- 10 Clinics Karlsruhe, Department of Oral and Maxillo-Facial Surgery, Karlsruhe, Germany
| | - G Schmidt
- 11 Department of Cleft Lip and Cleft Palate Surgery, Humboldt University of Berlin, Berlin, Germany
| | - N Daratsianos
- 6 Department of Orthodontics, University of Bonn, Bonn, Germany
| | - S Nowak
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K A Aldhorae
- 12 Department of Orthodontics, College of Dentistry, Dhamar University, Dhamar, Yemen
| | - M M Nöthen
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - M Knapp
- 13 Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - H Thiele
- 14 Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - C Gilissen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H Reutter
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,15 Department of Neonatology &Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - A Hoischen
- 5 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,16 Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,17 Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Mangold
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - K U Ludwig
- 1 Institute of Human Genetics, University of Bonn, Bonn, Germany.,2 Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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Gupta S, Chaurasia A, Pathak E, Mishra R, Chaudhry VN, Chaudhry P, Mukherjee A, Mutsuddi M. Whole exome sequencing unveils a frameshift mutation in CNGB3 for cone dystrophy: A case report of an Indian family. Medicine (Baltimore) 2017; 96:e7490. [PMID: 28746191 PMCID: PMC5627817 DOI: 10.1097/md.0000000000007490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RATIONALE Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES). PATIENT CONCERNS In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood. Fundus examination disclosed vascular attenuation and macular retinal pigment epithelium (RPE) changes in all the affected siblings, signifying degeneration of photoreceptor cells. DIAGNOSIS Complete clinical investigation and electroretinography studies led to the diagnosis of cone dystrophy in three siblings of the family. INTERVENTIONS Detailed ophthalmic examination, including family history, visual function testing, and retinal imaging, was performed. We captured and sequenced exomes of 2 affected siblings and their mother using SureSelect Human All Exon V5 Kit on Illumina HiSeq 2000/2500 platform with 100 bp paired-end sequencing method. Candidates after data analysis were screened by segregation analysis and Sanger sequencing. Considering recessive inheritance and consanguinity in the pedigree, we attempted to map large loci homozygous by descent in the genome of patients using exome sequencing variants. Extensive protein modeling was carried out to assess possible consequences of the identified variant on the 3-dimensional structure of the protein. OUTCOMES WES generated more than 65,000 variants for each individual. Assuming recessive inheritance, 13,026 variants were selected. Further filtering on the basis of their position in gene, class, and minor allele frequency constricted the huge list to 12 rare variants. Finally, we ascertained a single base deletion c.1148delC (p.Thr383fs) in the gene CNGB3 as the causal variant. This is a recurrent frameshift mutation resulting in truncated CNGB3 protein. We mapped a large 15-Mb stretch of homozygous markers spanning the causal variant in the proband. The gene CNGB3 encodes modulatory subunit of cyclic nucleotide-gated channels in cone photoreceptors. Protein modeling reveals loss of 2 transmembrane helices and conserved CAP_ED domain in truncated CNGB3, which eventually is predicted to form nonfunctional channels and hamper phototransduction. LESSONS We have identified a recurrent mutation c.1148delC (p.Thr383fs) in CNGB3 for autosomal recessive CD. The present report provides the first description of CNGB3 mutation from India. It is also the foremost investigation of familial CD in Indian patients; therefore, it presents the primary genetic etiology of CD in India.
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Affiliation(s)
- Shashank Gupta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh
| | | | - Ekta Pathak
- Department of Bioinformatics, Mahila Maha Vidyalaya, Banaras Hindu University
| | - Rajeev Mishra
- Department of Bioinformatics, Mahila Maha Vidyalaya, Banaras Hindu University
| | - Vidya Nair Chaudhry
- R. K. Netralaya Eye Hospital and Research Centre, Varanasi, Uttar Pradesh, India
| | - Prashaant Chaudhry
- R. K. Netralaya Eye Hospital and Research Centre, Varanasi, Uttar Pradesh, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh
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Didonna A, Opal P. Advances in Sequencing Technologies for Understanding Hereditary Ataxias: A Review. JAMA Neurol 2017; 73:1485-1490. [PMID: 27749953 DOI: 10.1001/jamaneurol.2016.3097] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Importance The hereditary progressive ataxias comprise genetic disorders that affect the cerebellum and its connections. Even though these diseases historically have been among the first familial disorders of the nervous system to have been recognized, progress in the field has been challenging because of the large number of ataxic genetic syndromes, many of which overlap in their clinical features. Observations We have taken a historical approach to demonstrate how our knowledge of the genetic basis of ataxic disorders has come about by novel techniques in gene sequencing and bioinformatics. Furthermore, we show that the genes implicated in ataxia, although seemingly unrelated, appear to encode for proteins that interact with each other in connected functional modules. Conclusions and Relevance It has taken approximately 150 years for neurologists to comprehensively unravel the genetic diversity of ataxias. There has been an explosion in our understanding of their molecular basis with the arrival of next-generation sequencing and computer-driven bioinformatics; this in turn has made hereditary ataxias an especially well-developed model group of diseases for gaining insights at a systems level into genes and cellular pathways that result in neurodegeneration.
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Affiliation(s)
| | - Puneet Opal
- Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois3Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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127
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Marano LA, Marcorin L, Castelli EDC, Mendes-Junior CT. Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project. Genet Mol Biol 2017; 40:530-539. [PMID: 28486572 PMCID: PMC5488459 DOI: 10.1590/1678-4685-gmb-2016-0180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/23/2016] [Indexed: 02/06/2023] Open
Abstract
The advent of next-generation sequencing allows simultaneous processing of several
genomic regions/individuals, increasing the availability and accuracy of whole-genome
data. However, these new approaches may present some errors and bias due to
alignment, genotype calling, and imputation methods. Despite these flaws, data
obtained by next-generation sequencing can be valuable for population and
evolutionary studies of specific genes, such as genes related to how pigmentation
evolved among populations, one of the main topics in human evolutionary biology.
Melanocortin-1 receptor (MC1R) is one of the most studied genes
involved in pigmentation variation. As MC1R has already been
suggested to affect melanogenesis and increase risk of developing melanoma, it
constitutes one of the best models to understand how natural selection acts on
pigmentation. Here we employed a locally developed pipeline to obtain genotype and
haplotype data for MC1R from the raw sequencing data provided by the
1000 Genomes FTP site. We also compared such genotype data to Phase
3 VCF to evaluate its quality and discover any polymorphic sites that may have been
overlooked. In conclusion, either the VCF file or one of the presently described
pipelines could be used to obtain reliable and accurate genotype calling from the
1000 Genomes Phase 3 data.
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Affiliation(s)
- Leonardo Arduino Marano
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Letícia Marcorin
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Erick da Cruz Castelli
- Departamento de Patologia, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista "Júlio de Mesquita Filho,"(UNESP) Botucatu, SP, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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128
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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129
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Wang Q, Shashikant CS, Jensen M, Altman NS, Girirajan S. Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity. Sci Rep 2017; 7:885. [PMID: 28408746 PMCID: PMC5429826 DOI: 10.1038/s41598-017-01005-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 03/24/2017] [Indexed: 12/24/2022] Open
Abstract
Whole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (UE) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms. This non-uniformity of coverage is both local (coverage of a given exon across different platforms) and global (coverage of all exons across the genome in the given platform). The low coverage regions encompassing functionally important genes were often associated with high GC content, repeat elements and segmental duplications. While a majority of the problems associated with WES are due to the limitations of the capture methods, further refinements in WES technologies have the potential to enhance its clinical applications.
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Affiliation(s)
- Qingyu Wang
- Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Cooduvalli S Shashikant
- Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew Jensen
- Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Naomi S Altman
- Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Santhosh Girirajan
- Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
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Mutated PET117 causes complex IV deficiency and is associated with neurodevelopmental regression and medulla oblongata lesions. Hum Genet 2017; 136:759-769. [PMID: 28386624 PMCID: PMC5429353 DOI: 10.1007/s00439-017-1794-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/31/2017] [Indexed: 10/30/2022]
Abstract
The genetic basis of the many progressive, multi systemic, mitochondrial diseases that cause a lack of cellular ATP production is heterogeneous, with defects found both in the mitochondrial genome as well as in the nuclear genome. Many different mutations have been found in the genes encoding subunits of the enzyme complexes of the oxidative phosphorylation system. In addition, mutations in genes encoding proteins involved in the assembly of these complexes are known to cause mitochondrial disorders. Here we describe two sisters with a mitochondrial disease characterized by lesions in the medulla oblongata, as demonstrated by brain magnetic resonance imaging, and an isolated complex IV deficiency and reduced levels of individual complex IV subunits. Whole exome sequencing revealed a homozygous nonsense mutation resulting in a premature stop codon in the gene encoding Pet117, a small protein that has previously been predicted to be a complex IV assembly factor. PET117 has not been identified as a mitochondrial disease gene before. Lentiviral complementation of patient fibroblasts with wild-type PET117 restored the complex IV deficiency, proving that the gene defect is responsible for the complex IV deficiency in the patients, and indicating a pivotal role of this protein in the proper functioning of complex IV. Although previous studies had suggested a possible role of this protein in the insertion of copper into complex IV, studies in patient fibroblasts could not confirm this. This case presentation thus implicates mutations in PET117 as a novel cause of mitochondrial disease.
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131
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Lacoste C, Fabre A, Pécheux C, Lévy N, Krahn M, Malzac P, Bonello-Palot N, Badens C, Bourgeois P. Le séquençage d’ADN à haut débit en pratique clinique. Arch Pediatr 2017; 24:373-383. [DOI: 10.1016/j.arcped.2017.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 01/03/2017] [Accepted: 01/03/2017] [Indexed: 12/22/2022]
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132
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Iqbal Z, Rydning SL, Wedding IM, Koht J, Pihlstrøm L, Rengmark AH, Henriksen SP, Tallaksen CME, Toft M. Targeted high throughput sequencing in hereditary ataxia and spastic paraplegia. PLoS One 2017; 12:e0174667. [PMID: 28362824 PMCID: PMC5375131 DOI: 10.1371/journal.pone.0174667] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/13/2017] [Indexed: 12/24/2022] Open
Abstract
Hereditary ataxia and spastic paraplegia are heterogeneous monogenic neurodegenerative disorders. To date, a large number of individuals with such disorders remain undiagnosed. Here, we have assessed molecular diagnosis by gene panel sequencing in 105 early and late-onset hereditary ataxia and spastic paraplegia probands, in whom extensive previous investigations had failed to identify the genetic cause of disease. Pathogenic and likely-pathogenic variants were identified in 20 probands (19%) and variants of uncertain significance in ten probands (10%). Together these accounted for 30 probands (29%) and involved 18 different genes. Among several interesting findings, dominantly inherited KIF1A variants, p.(Val8Met) and p.(Ile27Thr) segregated in two independent families, both presenting with a pure spastic paraplegia phenotype. Two homozygous missense variants, p.(Gly4230Ser) and p.(Leu4221Val) were found in SACS in one consanguineous family, presenting with spastic ataxia and isolated cerebellar atrophy. The average disease duration in probands with pathogenic and likely-pathogenic variants was 31 years, ranging from 4 to 51 years. In conclusion, this study confirmed and expanded the clinical phenotypes associated with known disease genes. The results demonstrate that gene panel sequencing and similar sequencing approaches can serve as efficient diagnostic tools for different heterogeneous disorders. Early use of such strategies may help to reduce both costs and time of the diagnostic process.
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Affiliation(s)
- Zafar Iqbal
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- * E-mail:
| | - Siri L. Rydning
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Iselin M. Wedding
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jeanette Koht
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Neurology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - Chantal M. E. Tallaksen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
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133
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Insights from early experience of a Rare Disease Genomic Medicine Multidisciplinary Team: a qualitative study. Eur J Hum Genet 2017; 25:680-686. [PMID: 28327571 PMCID: PMC5427178 DOI: 10.1038/ejhg.2017.37] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 11/08/2022] Open
Abstract
Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought. Allied to this is the need for an effective education programme for all members of clinical teams involved in care of patients with rare disease, as well as to maintain public confidence in the use of these technologies. We established a Genomic Medicine Multidisciplinary Team (GM-MDT) in 2014 to build on the experiences of earlier successful research-based WES/WGS studies, to address these needs and to review results including pertinent and secondary findings. Here we report on a qualitative study of decision-making in the GM-MDT combined with analysis of semi-structured interviews with GM-MDT members. Study findings show that members appreciate the clinical and scientific diversity of the GM-MDT and value it for education and oversight. To date, discussions have focussed on case selection including the extent and interpretation of clinical and family history information required to establish likely monogenic aetiology and inheritance model. Achieving a balance between effective use of WES/WGS - prioritising cases in a diverse and highly complex patient population where WES/WGS will be tractable - and meeting the recruitment targets of a large project is considered challenging.
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134
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Lohmann K, Masuho I, Patil DN, Baumann H, Hebert E, Steinrücke S, Trujillano D, Skamangas NK, Dobricic V, Hüning I, Gillessen-Kaesbach G, Westenberger A, Savic-Pavicevic D, Münchau A, Oprea G, Klein C, Rolfs A, Martemyanov KA. Novel GNB1 mutations disrupt assembly and function of G protein heterotrimers and cause global developmental delay in humans. Hum Mol Genet 2017; 26:1078-1086. [PMID: 28087732 PMCID: PMC6075543 DOI: 10.1093/hmg/ddx018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/22/2016] [Accepted: 12/30/2016] [Indexed: 12/31/2022] Open
Abstract
Global developmental delay (GDD), often accompanied by intellectual disability, seizures and other features is a severe, clinically and genetically highly heterogeneous childhood-onset disorder. In cases where genetic causes have been identified, de novo mutations in neuronally expressed genes are a common scenario. These mutations can be best identified by exome sequencing of parent-offspring trios. De novo mutations in the guanine nucleotide-binding protein, beta 1 (GNB1) gene, encoding the Gβ1 subunit of heterotrimeric G proteins, have recently been identified as a novel genetic cause of GDD. Using exome sequencing, we identified 14 different novel variants (2 splice site, 2 frameshift and 10 missense changes) in GNB1 in 16 pediatric patients. One mutation (R96L) was recurrently found in three ethnically diverse families with an autosomal dominant mode of inheritance. Ten variants occurred de novo in the patients. Missense changes were functionally tested for their pathogenicity by assaying the impact on complex formation with Gγ and resultant mutant Gβγ with Gα. Signaling properties of G protein complexes carrying mutant Gβ1 subunits were further analyzed by their ability to couple to dopamine D1R receptors by real-time bioluminescence resonance energy transfer (BRET) assays. These studies revealed altered functionality of the missense mutations R52G, G64V, A92T, P94S, P96L, A106T and D118G but not for L30F, H91R and K337Q. In conclusion, we demonstrate a pathogenic role of de novo and autosomal dominant mutations in GNB1 as a cause of GDD and provide insights how perturbation in heterotrimeric G protein function contributes to the disease.
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Affiliation(s)
- Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | - Ikuo Masuho
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Dipak N. Patil
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hauke Baumann
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | - Eva Hebert
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | - Sofia Steinrücke
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | | | | | | | - Irina Hüning
- Institut fur Humangenetik, Universität zu Lübeck, 23538 Lübeck, Germany
| | | | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | | | - Alexander Münchau
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | | | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538 Lübeck, Germany
| | - Arndt Rolfs
- Centogene AG, 18057 Rostock, Germany
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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135
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Poloni G, De Bortoli M, Calore M, Rampazzo A, Lorenzon A. Arrhythmogenic right-ventricular cardiomyopathy: molecular genetics into clinical practice in the era of next generation sequencing. J Cardiovasc Med (Hagerstown) 2017; 17:399-407. [PMID: 26990921 DOI: 10.2459/jcm.0000000000000385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sudden death, ventricular arrhythmia and heart failure are common features in arrhythmogenic right-ventricular cardiomyopathy (ARVC), an inheritable heart muscle disease, characterized by clinical and genetic heterogeneity. So far, 13 disease genes have been identified, responsible for around 60% of all ARVC cases. In this review, we summarize the main clinical and pathological aspects of ARVC, focusing on the importance of the genetic testing and the application of the new sequencing techniques referred to next generation sequencing technology.
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Affiliation(s)
- Giulia Poloni
- aDepartment of Biology, University of Padua, Padua, Italy bDepartment of Cardiology, School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
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136
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Ergun MA, Unal A, Ergun SG, Percin E. A new method for analysis of whole exome sequencing data (SELIM) depending on variant prioritization. INFORMATICS IN MEDICINE UNLOCKED 2017. [DOI: 10.1016/j.imu.2017.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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137
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The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands. Eur J Hum Genet 2016; 25:308-314. [PMID: 28000701 DOI: 10.1038/ejhg.2016.182] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 10/19/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.
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138
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Spier I, Kerick M, Drichel D, Horpaopan S, Altmüller J, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Holinski-Feder E, Perner S, Thiele H, Nöthen MM, Hoffmann P, Timmermann B, Schweiger MR, Aretz S. Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis. Fam Cancer 2016; 15:281-8. [PMID: 26780541 DOI: 10.1007/s10689-016-9870-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In up to 30% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, and POLE or POLD1, causing Polymerase-Proofreading-associated polyposis can be identified, although a hereditary etiology is likely. To uncover new causative genes, exome sequencing was performed using DNA from leukocytes and a total of 12 colorectal adenomas from seven unrelated patients with unexplained sporadic adenomatous polyposis. For data analysis and variant filtering, an established bioinformatics pipeline including in-house tools was applied. Variants were filtered for rare truncating point mutations and copy-number variants assuming a dominant, recessive, or tumor suppressor model of inheritance. Subsequently, targeted sequence analysis of the most promising candidate genes was performed in a validation cohort of 191 unrelated patients. All relevant variants were validated by Sanger sequencing. The analysis of exome sequencing data resulted in the identification of rare loss-of-function germline mutations in three promising candidate genes (DSC2, PIEZO1, ZSWIM7). In the validation cohort, further variants predicted to be pathogenic were identified in DSC2 and PIEZO1. According to the somatic mutation spectra, the adenomas in this patient cohort follow the classical pathways of colorectal tumorigenesis. The present study identified three candidate genes which might represent rare causes for a predisposition to colorectal adenoma formation. Especially PIEZO1 (FAM38A) and ZSWIM7 (SWS1) warrant further exploration. To evaluate the clinical relevance of these genes, investigation of larger patient cohorts and functional studies are required.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany. .,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany.
| | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Dmitriy Drichel
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Ronja Adam
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Bixiao Zhao
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Tim Becker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Richard P Lifton
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Sven Perner
- Section for Prostate Cancer Research, Center for Integrated Oncology Cologne/Bonn, Institute of Pathology, University Hospital of Bonn, Bonn, Germany.,Pathology Network of the University Hospital of Luebeck and Leibniz Research Center Borstel, Borstel, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R Schweiger
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
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139
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A Novel Sample Selection Strategy for Imbalanced Data of Biomedical Event Extraction with Joint Scoring Mechanism. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016; 2016:7536494. [PMID: 28096894 PMCID: PMC5206857 DOI: 10.1155/2016/7536494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/04/2016] [Accepted: 10/31/2016] [Indexed: 11/24/2022]
Abstract
Biomedical event extraction is an important and difficult task in bioinformatics. With the rapid growth of biomedical literature, the extraction of complex events from unstructured text has attracted more attention. However, the annotated biomedical corpus is highly imbalanced, which affects the performance of the classification algorithms. In this study, a sample selection algorithm based on sequential pattern is proposed to filter negative samples in the training phase. Considering the joint information between the trigger and argument of multiargument events, we extract triplets of multiargument events directly using a support vector machine classifier. A joint scoring mechanism, which is based on sentence similarity and importance of trigger in the training data, is used to correct the predicted results. Experimental results indicate that the proposed method can extract events efficiently.
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140
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Hahn MM, de Voer RM, Hoogerbrugge N, Ligtenberg MJL, Kuiper RP, van Kessel AG. The genetic heterogeneity of colorectal cancer predisposition - guidelines for gene discovery. Cell Oncol (Dordr) 2016; 39:491-510. [PMID: 27279102 PMCID: PMC5121185 DOI: 10.1007/s13402-016-0284-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a cumulative term applied to a clinically and genetically heterogeneous group of neoplasms that occur in the bowel. Based on twin studies, up to 45 % of the CRC cases may involve a heritable component. Yet, only in 5-10 % of these cases high-penetrant germline mutations are found (e.g. mutations in APC and DNA mismatch repair genes) that result in a familial aggregation and/or an early onset of the disease. Genome-wide association studies have revealed that another ~5 % of the CRC cases may be explained by a cumulative effect of low-penetrant risk factors. Recent attempts to identify novel genetic factors using whole exome and whole genome sequencing has proven to be difficult since the remaining, yet to be discovered, high penetrant CRC predisposing genes appear to be rare. In addition, most of the moderately penetrant candidate genes identified so far have not been confirmed in independent cohorts. Based on literature examples, we here discuss how careful patient and cohort selection, candidate gene and variant selection, and corroborative evidence may be employed to facilitate the discovery of novel CRC predisposing genes. CONCLUSIONS The picture emerges that the genetic predisposition to CRC is heterogeneous, involving complex interplays between common and rare (inter)genic variants with different penetrances. It is anticipated, however, that the use of large clinically well-defined patient and control datasets, together with improved functional and technical possibilities, will yield enough power to unravel this complex interplay and to generate accurate individualized estimates for the risk to develop CRC.
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Affiliation(s)
- M M Hahn
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R M de Voer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - M J L Ligtenberg
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R P Kuiper
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
| | - A Geurts van Kessel
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
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141
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Sermon K. Novel technologies emerging for preimplantation genetic diagnosis and preimplantation genetic testing for aneuploidy. Expert Rev Mol Diagn 2016; 17:71-82. [PMID: 27855520 DOI: 10.1080/14737159.2017.1262261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Preimplantation genetic diagnosis (PGD) was introduced as an alternative to prenatal diagnosis: embryos cultured in vitro were analysed for a monogenic disease and only disease-free embryos were transferred to the mother, to avoid the termination of pregnancy with an affected foetus. It soon transpired that human embryos show a great deal of acquired chromosomal abnormalities, thought to explain the low success rate of IVF - hence preimplantation genetic testing for aneuploidy (PGT-A) was developed to select euploid embryos for transfer. Areas covered: PGD has followed the tremendous evolution in genetic analysis, with only a slight delay due to adaptations for diagnosis on small samples. Currently, next generation sequencing combining chromosome with single-base pair analysis is on the verge of becoming the golden standard in PGD and PGT-A. Papers highlighting the different steps in the evolution of PGD/PGT-A were selected. Expert commentary: Different methodologies used in PGD/PGT-A with their pros and cons are discussed.
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Affiliation(s)
- Karen Sermon
- a Research Group Reproduction and Genetics , Vrije Universiteit Brussel , Brussels , Belgium
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142
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Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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143
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Muntean I, Togănel R, Benedek T. Genetics of Congenital Heart Disease: Past and Present. Biochem Genet 2016; 55:105-123. [PMID: 27807680 DOI: 10.1007/s10528-016-9780-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022]
Abstract
Congenital heart disease is the most common congenital anomaly, representing an important cause of infant morbidity and mortality. Congenital heart disease represents a group of heart anomalies that include septal defects, valve defects, and outflow tract anomalies. The exact genetic, epigenetic, or environmental basis of congenital heart disease remains poorly understood, although the exact mechanism is likely multifactorial. However, the development of new technologies including copy number variants, single-nucleotide polymorphism, next-generation sequencing are accelerating the detection of genetic causes of heart anomalies. Recent studies suggest a role of small non-coding RNAs, micro RNA, in congenital heart disease. The recently described epigenetic factors have also been found to contribute to cardiac morphogenesis. In this review, we present past and recent genetic discoveries in congenital heart disease.
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Affiliation(s)
- Iolanda Muntean
- Institute of Cardiovascular Diseases and Transplantation, Clinic of Pediatric Cardiology, University of Medicine and Pharmacy Tîrgu Mureş, 50 Gh Marinescu St, 540136, Tirgu Mures, Romania
| | - Rodica Togănel
- Institute of Cardiovascular Diseases and Transplantation, Clinic of Pediatric Cardiology, University of Medicine and Pharmacy Tîrgu Mureş, 50 Gh Marinescu St, 540136, Tirgu Mures, Romania.
| | - Theodora Benedek
- Clinic of Cardiology, University of Medicine and Pharmacy Tîrgu Mureş, Tirgu Mures, Romania
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144
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Abstract
Historically, sequencing has been the key technology to assess variation in the genetic code, and has been widely accepted in clinical diagnostics of genetic disease. The advent of next-generation sequencing (NGS) methods increased the size of the analyzed target by several orders of magnitude, while at the same time drastically reducing the cost of sequencing. Current research allows sequencing of germline and tumor whole genomes. However, with the arrival of cutting-edge technology to the clinical diagnostic field, strict regulatory oversight is required to use the advances of the latest research when applied to routine clinical practice. We discuss the differences between sequencing in a research setting and sequencing in a clinical diagnostics setting, as applied to next-generation technology.
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145
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Masumura K, Toyoda-Hokaiwado N, Ukai A, Gondo Y, Honma M, Nohmi T. Dose-dependent de novo germline mutations detected by whole-exome sequencing in progeny of ENU-treated male gpt delta mice. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 810:30-39. [DOI: 10.1016/j.mrgentox.2016.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 01/06/2023]
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Amiri-Yekta A, Coutton C, Kherraf ZE, Karaouzène T, Le Tanno P, Sanati MH, Sabbaghian M, Almadani N, Sadighi Gilani MA, Hosseini SH, Bahrami S, Daneshipour A, Bini M, Arnoult C, Colombo R, Gourabi H, Ray PF. Whole-exome sequencing of familial cases of multiple morphological abnormalities of the sperm flagella (MMAF) reveals new DNAH1 mutations. Hum Reprod 2016; 31:2872-2880. [PMID: 27798045 DOI: 10.1093/humrep/dew262] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION Can whole-exome sequencing (WES) of patients with multiple morphological abnormalities of the sperm flagella (MMAF) identify causal mutations in new genes or mutations in the previously identified dynein axonemal heavy chain 1 (DNAH1) gene? SUMMARY ANSWER WES for six families with men affected by MMAF syndrome allowed the identification of DNAH1 mutations in four affected men distributed in two out of the six families but no new candidate genes were identified. WHAT IS KNOWN ALREADY Mutations in DNAH1, an axonemal inner dynein arm heavy chain gene, have been shown to be responsible for male infertility due to a characteristic form of asthenozoospermia called MMAF, defined by the presence in the ejaculate of spermatozoa with a mosaic of flagellar abnormalities including absent, coiled, bent, angulated, irregular and short flagella. STUDY DESIGN, SIZE, DURATION This was a retrospective genetics study of patients presenting a MMAF phenotype. Patients were recruited in Iran and Italy between 2008 and 2015. PARTICIPANTS/MATERIALS, SETTING, METHODS WES was performed for a total of 10 subjects. All identified variants were confirmed by Sanger sequencing. Two additional affected family members were analyzed by direct Sanger sequencing. To establish the prevalence of the DNAH1 mutation identified in an Iranian family, we carried out targeted sequencing on 38 additional MMAF patients of the same geographical origin. RT-PCR and immunochemistry were performed on sperm samples to assess the effect of the identified mutation on RNA and protein. MAIN RESULTS AND THE ROLE OF CHANCE WES in six families identified a causal mutations in two families. Two additional affected family members were confirmed to hold the same homozygous mutation as their sibling. In total, DNAH1 mutations were identified in 5 out of 12 analyzed subjects (41.7%). If we only include index cases, we detected two mutated subjects out of six (33%) tested MMAF individuals. Furthermore we sequenced one DNAH1 exon found to be mutated (c.8626-1G > A) in an Iranian family in an additional 38 MMAF patients from Iran. One of these patients carried the variant confirming that this variant is relatively frequent in the Iranian population. The effect of the c.8626-1G > A variant was confirmed by RT-PCR and immunochemistry as no RNA or protein could be observed in sperm from the affected men. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION WES allows the amplification of 80-90% of all coding exons. It is possible that some DNAH1 exons may not have been sequenced and that we may have missed some additional mutations. Also, WES cannot identify deep intronic mutations and it is not efficient for detection of large genomic events (deletions, insertions, inversions). We did not identify any causal mutations in DNAH1 or in other candidate genes in four out of the six tested families. This indicates that the technique and/or the analysis of our data can be improved to increase the diagnosis efficiency. WIDER IMPLICATIONS OF THE FINDINGS Our findings confirm that DNAH1 is one of the main genes involved in MMAF syndrome. It is a large gene with 78 exons making it challenging and expensive to sequence using the traditional Sanger sequencing methods. We show that WES sequencing is good alternative to Sanger sequencing to reach a genetic diagnosis in patients with severe male infertility phenotypes. STUDY FUNDING/COMPETING INTERESTS This work was supported by following grants: the 'MAS-Flagella' project financed by the French ANR and the DGOS for the program PRTS 2014 and the 'Whole genome sequencing of patients with Flagellar Growth Defects (FGD)' project financed by the Fondation Maladies Rares for the program Séquençage à haut débit 2012. The authors have no conflict of interest.
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Affiliation(s)
- Amir Amiri-Yekta
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran.,Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France
| | - Charles Coutton
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France.,CHU de Grenoble, UF de Génétique Chromosomique, Grenoble F-38000, France
| | - Zine-Eddine Kherraf
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France.,CHU de Grenoble, UF de Biochimie Génétique et Moléculaire, Grenoble F-38000, France
| | - Thomas Karaouzène
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France.,CHU de Grenoble, UF de Biochimie Génétique et Moléculaire, Grenoble F-38000, France
| | - Pauline Le Tanno
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France.,CHU de Grenoble, UF de Génétique Chromosomique, Grenoble F-38000, France
| | - Mohammad Hossein Sanati
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran.,Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Marjan Sabbaghian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Mohammad Ali Sadighi Gilani
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Seyedeh Hanieh Hosseini
- Center for the Study and Treatment of Fertility Disorders, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Salahadin Bahrami
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Abbas Daneshipour
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Maurizio Bini
- Center for the Study and Treatment of Fertility Disorders, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Christophe Arnoult
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France
| | - Roberto Colombo
- Faculty of Medicine, Institute of Clinical Biochemistry, Catholic University, Rome, Italy.,Center for the Study of Rare Hereditary Diseases, Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, PO Box 16635-148, Tehran, Iran
| | - Pierre F Ray
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, INSERM 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble F38000, France .,CHU de Grenoble, UF de Biochimie Génétique et Moléculaire, Grenoble F-38000, France
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147
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Li Z, Liu Z, Jiang Y, Chen D, Ran X, Sun ZS, Wu J. mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications. Hum Mutat 2016; 38:25-33. [PMID: 27676360 DOI: 10.1002/humu.23125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/19/2016] [Accepted: 09/16/2016] [Indexed: 12/12/2022]
Abstract
Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/.
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Affiliation(s)
- Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Denghui Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
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148
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Salgado D, Bellgard MI, Desvignes JP, Béroud C. How to Identify Pathogenic Mutations among All Those Variations: Variant Annotation and Filtration in the Genome Sequencing Era. Hum Mutat 2016; 37:1272-1282. [DOI: 10.1002/humu.23110] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/24/2016] [Accepted: 08/31/2016] [Indexed: 01/01/2023]
Affiliation(s)
- David Salgado
- Aix Marseille University; INSERM; GMGF; Marseille France
| | - Matthew I. Bellgard
- Centre for Comparative Genomics; Murdoch University; Perth Western Australia Australia
- Western Australian Neuroscience Research Institute; Perth Western Australia Australia
| | | | - Christophe Béroud
- Aix Marseille University; INSERM; GMGF; Marseille France
- APHM, Hôpital TIMONE Enfants; Laboratoire de Génétique Moléculaire; Marseille France
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149
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Dong HY, Zeng H, Hu YQ, Xie L, Wang J, Wang XY, Yang YF, Tan ZP. 19p13.2 Microdeletion including NFIX associated with overgrowth and intellectual disability suggestive of Malan syndrome. Mol Cytogenet 2016; 9:71. [PMID: 27688808 PMCID: PMC5034553 DOI: 10.1186/s13039-016-0282-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/13/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Overgrowth syndromes represent clinically and genetically heterogeneous conditions characterized by a wide spectrum of malformations, tall stature, intellectual disability and/or macrocephaly. RESULTS In a cohort of four clinically characterized patients with overgrowth syndrome without known causative gene mutation, we performed an Illumina SNP-array analysis to identify the pathogenic copy number variations. We identified two rare copy number variations harboring overgrowth syndrome related genes. Patient 1 was Malan syndrome with a 1.4 Mb 19p13.2-13.13 microdeletion including NFIX, and Patient 2 was identified as Sotos syndrome with a 1.6 Mb 5q35.2 microdeletion encompassing NSD1. CONCLUSIONS We identified two patients associated with Manlan syndrome and Sotos syndrome respectively. We also discuss the use of the microarrays-based candidate gene strategy in Mendelian disease-gene identification.
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Affiliation(s)
- Hai-Yun Dong
- Intensive Care Unit, Central South University, Changsha, Hunan Province 410011 China
| | - Hui Zeng
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital of Central South University, 139# Renmin Road, Changsha, Hunan 410011 China ; Department of Cardiothoracic Surgery, Central South University, Changsha, Hunan Province 410011 China
| | - Yi-Qiao Hu
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan Province 410011 China
| | - Li Xie
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital of Central South University, 139# Renmin Road, Changsha, Hunan 410011 China ; Department of Cardiothoracic Surgery, Central South University, Changsha, Hunan Province 410011 China
| | - Jian Wang
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital of Central South University, 139# Renmin Road, Changsha, Hunan 410011 China ; Department of Cardiothoracic Surgery, Central South University, Changsha, Hunan Province 410011 China
| | - Xiu-Ying Wang
- Department of Pediatrics, the Second Xiangya Hospital, Central South University, Changsha, Hunan Province 410011 China
| | - Yi-Feng Yang
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital of Central South University, 139# Renmin Road, Changsha, Hunan 410011 China ; Department of Cardiothoracic Surgery, Central South University, Changsha, Hunan Province 410011 China
| | - Zhi-Ping Tan
- Clinical Center for Gene Diagnosis and Therapy of State Key Laboratory of Medical Genetics, The Second Xiangya Hospital of Central South University, 139# Renmin Road, Changsha, Hunan 410011 China ; Department of Cardiothoracic Surgery, Central South University, Changsha, Hunan Province 410011 China
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150
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Gazdagh G, Tobias ES, Ahmed SF, McGowan R. Novel Genetic Associations and Range of Phenotypes in Children with Disorders of Sex Development and Neurodevelopment: Insights from the Deciphering Developmental Disorders Study. Sex Dev 2016; 10:130-5. [PMID: 27598577 PMCID: PMC5079067 DOI: 10.1159/000447958] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 11/30/2022] Open
Abstract
A range of phenotypes that are associated with disorders of sex development (DSD) may also be encountered in patients with neurodevelopmental delay. In this study we have undertaken a collaborative retrospective review of anonymised phenotypic and genotypic data from the UK-wide Deciphering Developmental Disorders (DDD) study. Our objectives were to determine the frequency and range of DSD phenotypes observed in participants in the DDD study and to identify novel genetic associations. We found that of 7,439 DDD participants, 603 (8%) had at least one genital abnormality. In addition, we found that DSD occurs in 5% of patients with learning difficulties. Causative mutations were found in 13 developmental genes, of which, crucially, 6 had no previous reported association with DSD. Our findings indicate that recognition of these associations should not be overlooked in the management of patients with complex conditions and that exomic sequencing through projects like DDD increases diagnostic yield.
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Affiliation(s)
- Gabriella Gazdagh
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
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