651
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Coppola C, Oliva M, Saracino D, Pappatà S, Zampella E, Cimini S, Ricci M, Giaccone G, Di Iorio G, Rossi G. One novel GRN null mutation, two different aphasia phenotypes. Neurobiol Aging 2019; 87:141.e9-141.e14. [PMID: 31837909 DOI: 10.1016/j.neurobiolaging.2019.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/04/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
Progranulin gene (GRN) mutations are among the leading causes of frontotemporal lobar degeneration, a group of neurodegenerative diseases characterized by remarkable clinical heterogeneity. In this article, we report the new GRN 708+4A>T splicing mutation, identified in 2 siblings of a family with several members affected by cognitive, behavioral, and motor disorders. Plasma progranulin dosage and GRN expression analysis, together with in silico prediction studies, supported the pathogenicity of the mutation. Both the patients displayed a clinical syndrome in which language impairment was largely predominant. However, motor speech deficits were the major feature in one case, diagnosed as progressive nonfluent aphasia, whereas marked semantic alterations were present in the other, whose clinical phenotype was in favor of a mixed aphasia. The profile of neuroanatomical alterations from imaging studies was in line with the clinical phenotypes. Therefore, also this novel GRN mutation is associated with haploinsufficiency and phenotypic heterogeneity, which are both typical features of progranulinopathies.
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Affiliation(s)
- Cinzia Coppola
- Second Division of Neurology, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Mariano Oliva
- Second Division of Neurology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Dario Saracino
- Second Division of Neurology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sabina Pappatà
- Department of Biomedical Sciences, Institute of Biostructure and Bioimaging, National Council of Research, Naples, Italy
| | - Emilia Zampella
- Department of Advanced Biomedical Sciences, "Federico II" University, Naples, Italy
| | - Sara Cimini
- Division of Neurology V - Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Martina Ricci
- Division of Neurology V - Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giorgio Giaccone
- Division of Neurology V - Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Di Iorio
- Second Division of Neurology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giacomina Rossi
- Division of Neurology V - Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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652
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Evolutionary genomics analysis of human nucleus-encoded mitochondrial genes: implications for the roles of energy production and metabolic pathways in the pathogenesis and pathophysiology of demyelinating diseases. Neurosci Lett 2019; 715:134600. [PMID: 31726178 DOI: 10.1016/j.neulet.2019.134600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/19/2019] [Accepted: 10/28/2019] [Indexed: 02/02/2023]
Abstract
The myelin sheath is a plasma membrane extension that lines nerve fibers to protect, support and insulate neurons. The myelination of axons in vertebrates enables fast, saltatory impulse propagation, and this process relies on organelles, especially on mitochondria to supply energy. Approximately 99% of mitochondrial proteins are encoded in the nucleus. Since mitochondria play a central role in the energy production and metabolic pathways, which are essential for myelinogenesis, studying these nucleus-encoded genes (nMGs) may provide new insights into the roles of energy metabolism in demyelinating diseases. In this work, a multiomics-based approach was employed to 1) construct a 1,740 human nMG subset with mitochondrial localization evidence obtained from the Integrated Mitochondrial Protein Index (IMPI) and MitoCarta databases, 2) conduct an evolutionary genomics analysis across mouse, rat, monkey, chimp, and human models, 3) examine dysmyelination phenotype-related genes (nMG subset genes with oligodendrocyte- and myelin-related phenotypes, OMP-nMGs) in MGI mouse lines and human patients, 4) determine the expression discrepancy of OMP-nMGs in brain tissues of cuprizone-treated mice, multiple sclerosis patients, and normal controls, and 5) conduct literature data mining to explore OMP-nMG-associated disease impacts. By contrasting OMP-nMGs with other genes, OMP-nMGs were found to be more ubiquitously expressed (59.1% vs. 16.1%), disease-associated (67.3% vs. 20.2%), and evolutionarily conserved within the human populations. Our multiomics-based analysis identified 110 OMP-nMGs implicated in energy production and lipid and glycan biosynthesis in the pathogenesis and pathophysiology of demyelinating disorders. Future targeted characterization of OMP-nMGs in abnormal myelination conditions may allow the discovery of novel nMG mediated mechanisms underlying myelinogenesis and related diseases.
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653
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Zheng Y, Peng Y, Zhang S, Li L, Peng Y, Yin Q. Capillary Malformation-Arteriovenous Malformation Combined Alagille Syndrome in a Patient With Double Gene Variations of RASA1 and NOTCH2. Front Genet 2019; 10:1088. [PMID: 31749841 PMCID: PMC6848451 DOI: 10.3389/fgene.2019.01088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/09/2019] [Indexed: 11/24/2022] Open
Abstract
Background: Capillary malformation–arteriovenous malformation (CM-AVM) is an autosomal dominant disorder characterized by CMs, often in association with fast-flow vascular malformations. Alagille syndrome is an autosomal dominant multisystem disorder, usually involving hepatic, cardiac, ophthalmic, skeletal, or renal dysplasia. The combination of CM-AVM and Alagille syndrome in a patient presenting serious vascular malformations in the liver and heart has never been reported. Here, we report the case of a 20-month-old infant presenting these two diseases. Case presentation: The patient manifested port-wine stains, congenital heart disease, cholestasis with abnormal morphology, and vascular anomalies. Color Doppler (B-mode) ultrasonography, and radiological imaging including computed tomography (CT) with enhanced three-dimensional (3D) reconstruction and angiography, revealed a type II Abernethy malformation in the hepatic portal vein. The left hepatic lobe was enlarged showing dilation of the portal vein and the left artery. Whole exome sequencing (WES) identified a paternally inherited RASA1 heterozygous pathogenic variant p.(Ser219Ter) causing CM-AVM and a de novo NOTCH2 heterozygous variant p.(Met2042Thr) associated with Alagille syndrome. Conclusion: This is the first case of combined CM-AVM and Alagille syndrome presenting serious liver and heart abnormalities diagnosed using imaging technology and WES. The patient harbored variants in two genes: RASA1 and NOTCH2, which rarely contribute to aberrant vascular development. This report highlights the value of accurately diagnosing similar diseases and guiding therapy using genetic testing combined with careful clinical examinations.
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Affiliation(s)
- Yu Zheng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China.,Research Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Yuming Peng
- First Department of General Surgery, Hunan Children's Hospital, Changsha, China
| | - Shuju Zhang
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Liping Li
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Yu Peng
- Pediatrics Research Institute of Hunan Province, Hunan Children's Hospital, Changsha, China
| | - Qiang Yin
- First Department of General Surgery, Hunan Children's Hospital, Changsha, China
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654
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Wheway G, Lord J, Baralle D. Splicing in the pathogenesis, diagnosis and treatment of ciliopathies. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194433. [PMID: 31698098 DOI: 10.1016/j.bbagrm.2019.194433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022]
Abstract
Primary cilia are essential signalling organelles found on the apical surface of epithelial cells, where they coordinate chemosensation, mechanosensation and light sensation. Motile cilia play a central role in establishing fluid flow in the respiratory tract, reproductive tract, brain ventricles and ear. Genetic defects affecting the structure or function of cilia can lead to a broad range of developmental and degenerative diseases known as ciliopathies. Splicing contributes to the pathogenesis, diagnosis and treatment of ciliopathies. Tissue-specific alternative splicing contributes to the tissue-specific manifestation of ciliopathy phenotypes, for example the retinal-specific effects of some genetic defects, due to specific transcript expression in the highly specialised ciliated cells of the retina, the photoreceptor cells. Ciliopathies can arise both as a result of genetic variants in spliceosomal proteins, or as a result of variants affecting splicing of specific cilia genes. Here we discuss the opportunities and challenges in diagnosing ciliopathies using RNA sequence analysis and the potential for treating ciliopathies in a relatively mutation-neutral way by targeting splicing. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland
| | - Jenny Lord
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland
| | - Diana Baralle
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland.
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655
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Tang B, Li B, Gao LD, He N, Liu XR, Long YS, Zeng Y, Yi YH, Su T, Liao WP. Optimization of in silico tools for predicting genetic variants: individualizing for genes with molecular sub-regional stratification. Brief Bioinform 2019; 21:1776-1786. [PMID: 31686106 DOI: 10.1093/bib/bbz115] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/06/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Abstract
Genes are unique in functional role and differ in their sensitivities to genetic defects, but with difficulties in pathogenicity prediction. This study attempted to improve the performance of existing in silico algorithms and find a common solution based on individualization strategy. We initiated the individualization with the epilepsy-related SCN1A variants by sub-regional stratification. SCN1A missense variants related to epilepsy were retrieved from mutation databases, and benign missense variants were collected from ExAC database. Predictions were performed by using 10 traditional tools with stepwise optimizations. Model predictive ability was evaluated using the five-fold cross-validations on variants of SCN1A, SCN2A, and KCNQ2. Additional validation was performed in SCN1A variants of damage-confirmed/familial epilepsy. The performance of commonly used predictors was less satisfactory for SCN1A with accuracy less than 80% and varied dramatically by functional domains of Nav1.1. Multistep individualized optimizations, including cutoff resetting, domain-based stratification, and combination of predicting algorithms, significantly increased predictive performance. Similar improvements were obtained for variants in SCN2A and KCNQ2. The predictive performance of the recently developed ensemble tools, such as Mendelian clinically applicable pathogenicity, combined annotation-dependent depletion and Eigen, was also improved dramatically by application of the strategy with molecular sub-regional stratification. The prediction scores of SCN1A variants showed linear correlations with the degree of functional defects and the severity of clinical phenotypes. This study highlights the need of individualized optimization with molecular sub-regional stratification for each gene in practice.
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Affiliation(s)
- Bin Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Bin Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzo, China
| | - Liang-Di Gao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Na He
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzo, China
| | - Xiao-Rong Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Yue-Sheng Long
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Yang Zeng
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Yong-Hong Yi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzo, China
| | - Tao Su
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University
| | - Wei-Ping Liao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzo, China
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656
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Mai TL, Chuang TJ. A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations. Genome Res 2019; 29:1766-1776. [PMID: 31515285 PMCID: PMC6836733 DOI: 10.1101/gr.246033.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated with the deleteriousness of A-to-G genomic changes and positively correlated with that of G-to-A genomic changes within the population. We find a significantly negative correlation between nonsynonymous editing activities and allele frequency of A within the population. This negative editing-allele frequency correlation is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G-to-A changes increases with increasing deleterious effects of the changes. Moreover, the deleteriousness of G-to-A changes is significantly positively correlated with the percentage of editing enzyme binding motifs at the variants. Overall, we show that nonsynonymous editing is associated with the increased burden of G-to-A missense mutations in healthy individuals, expanding RNA editing in pathogenomics studies.
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Affiliation(s)
- Te-Lun Mai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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657
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Weiss Y, Chen B, Yasuda M, Nazarenko I, Anderson KE, Desnick RJ. Porphyria cutanea tarda and hepatoerythropoietic porphyria: Identification of 19 novel uroporphyrinogen III decarboxylase mutations. Mol Genet Metab 2019; 128:363-366. [PMID: 30514647 PMCID: PMC8132452 DOI: 10.1016/j.ymgme.2018.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 11/19/2022]
Abstract
Porphyria Cutanea Tarda (PCT) is a cutaneous porphyria that results from the hepatic inhibition of the heme biosynthetic enzyme uroporphyrinogen decarboxylase (UROD), and can occur either in the absence or presence of an inherited heterozygous UROD mutation (PCT subtypes 1 and 2, respectively). A heterozygous UROD mutation causes half-normal levels of UROD activity systemically, which is a susceptibility factor but is not sufficient alone to cause type 2 PCT. In both Types 1 and 2 PCT, the cutaneous manifestations are precipitated by additional factors that lead to generation of an inhibitor that more profoundly reduces hepatic UROD activity. PCT is an iron-related disorder, and many of its known susceptibility factors, which include infections (e.g. hepatitis C virus, HIV), high alcohol consumption, smoking, estrogens, and genetic traits (e.g. hemochromatosis mutations) can increase hepatic iron accumulation. Hepatoerythropoietic Porphyria (HEP) is a rare autosomal recessive disease that results from homozygosity or compound heterozygosity for UROD mutations and often causes infantile or childhood onset of both erythropoietic and cutaneous manifestations. During the 11-year period from 01/01/2007 through 12/31/2017, the Mount Sinai Porphyrias Diagnostic Laboratory provided molecular diagnostic testing for 387 unrelated patients with PCT and four unrelated patients with HEP. Of the 387 unrelated individuals tested for Type 2 PCT, 79 (20%) were heterozygous for UROD mutations. Among 26 family members of mutation-positive PCT patients, eight (31%) had the respective family mutation. Additionally, of the four unrelated HEP patients referred for UROD mutation analyses, all had homozygosity or compound heterozygosity for UROD mutations, and all eight asymptomatic family members were heterozygotes for UROD mutations. Of the UROD mutations identified, 19 were novel, including nine missense, two nonsense, one consensus splice-site, and seven insertions and deletions. These results expand the molecular heterogeneity of PCT and HEP by adding a total of 19 novel UROD mutations. Moreover, the results document the usefulness of molecular testing to confirm a genetic susceptibility trait in Type 2 PCT, confirm a diagnosis in HEP, and identify heterozygous family members.
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Affiliation(s)
- Yedidyah Weiss
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA.
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA.
| | - Irina Nazarenko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA.
| | - Karl E Anderson
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, USA.
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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658
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Yasuda M, Chen B, Desnick RJ. Recent advances on porphyria genetics: Inheritance, penetrance & molecular heterogeneity, including new modifying/causative genes. Mol Genet Metab 2019; 128:320-331. [PMID: 30594473 PMCID: PMC6542720 DOI: 10.1016/j.ymgme.2018.11.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022]
Abstract
The inborn errors of heme biosynthesis, the Porphyrias, include eight major disorders resulting from loss-of-function (LOF) or gain-of-function (GOF) mutations in eight of the nine heme biosynthetic genes. The major sites of heme biosynthesis are the liver and erythron, and the underlying pathophysiology of each of these disorders depends on the unique biochemistry, cell biology, and genetic mechanisms in these tissues. The porphyrias are classified into three major categories: 1) the acute hepatic porphyrias (AHPs), including Acute Intermittent Porphyria (AIP), Hereditary Coproporphyria (HCP), Variegate Porphyria (VP), and 5-Aminolevlulinic Acid Dehydratase Deficient Porphyria (ADP); 2) a hepatic cutaneous porphyria, Porphyria Cutanea Tarda (PCT); and 3) the cutaneous erythropoietic porphyrias, Congenital Erythropoietic Porphyria (CEP), Erythropoietic Protoporphyria (EPP), and X-Linked Protoporphyria (XLP). Their modes of inheritance include autosomal dominant with markedly decreased penetrance (AIP, VP, and HCP), autosomal recessive (ADP, CEP, and EPP), or X-linked (XLP), as well as an acquired sporadic form (PCT). There are severe homozygous dominant forms of the three AHPs. For each porphyria, its phenotype, inheritance pattern, unique genetic principles, and molecular genetic heterogeneity are presented. To date, >1000 mutations in the heme biosynthetic genes causing their respective porphyrias have been reported, including low expression alleles and genotype/phenotype correlations that predict severity for certain porphyrias. The tissue-specific regulation of heme biosynthesis and the unique genetic mechanisms for each porphyria are highlighted.
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Affiliation(s)
- Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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659
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López G, Bernal LM, Gelvez N, Gómez LF, Nova A, Sánchez AI, Tamayo ML. Mutational analysis of the LDLR gene in a cohort of Colombian families with familial hypercholesterolemia. Atherosclerosis 2019; 277:434-439. [PMID: 30270082 DOI: 10.1016/j.atherosclerosis.2018.08.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia (FH) is characterized by elevated serum cholesterol levels due to high low-density lipoprotein (LDL) cholesterol levels. FH is an autosomal dominant genetic disorder and one of the most common dominant hereditary diseases in the world. However, the frequency of mutations in Colombia is unknown. The purpose of this preliminary study was to identify mutations in the LDL receptor (LDLR) gene in a Colombian population with FH. METHODS The study included 24 families with clinical diagnosis of sure/probable FH. The 18 exons of the LDLR were sequenced by Sanger method. RESULTS Among 18 variants identified, 3 were known pathogenic mutations and were identified in nine individuals in five unrelated families. Five affected individuals were heterozygous for one mutation each. They were the p.W4X in two, the p.D139G in two and the p.G396D in one. Two affected individuals were homozygous for p.G396D. The variant c.1187-1G > T, which has uncertain significance in FH pathogenesis, was present in all the individuals with the p.D139G mutation. CONCLUSIONS In total, 18 variants were identified, of which 14 correspond to known nonpathogenic variants. Three pathogenic variants were identified in the LDLR. No pathological mutations were identified in the LDLR in 79% of the study population.
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Affiliation(s)
- Greizy López
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luz M Bernal
- Escuela de Ciencias de la Salud, Universidad Nacional Abierta y a Distancia, Bogotá, Colombia
| | - Nancy Gelvez
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luisa F Gómez
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alejandra Nova
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Ana I Sánchez
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Martha L Tamayo
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia; Fundación Derecho a la Desventaja, FUNDALDE, Bogotá, Colombia.
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660
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Erwin AL, Desnick RJ. Congenital erythropoietic porphyria: Recent advances. Mol Genet Metab 2019; 128:288-297. [PMID: 30685241 PMCID: PMC6597325 DOI: 10.1016/j.ymgme.2018.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022]
Abstract
Congenital erythropoietic porphyria (CEP) is a rare autosomal recessive disorder characterized by photosensitivity and by hematologic abnormalities in affected individuals. CEP is caused by mutations in the uroporphyrinogen synthase (UROS) gene. In three reported cases, CEP has been associated with a specific X-linked GATA1 mutation. Disease-causing mutations in either gene result in absent or markedly reduced UROS enzymatic activity. This in turn leads to the accumulation of the non-physiologic and photoreactive porphyrinogens, uroporphyrinogen I and coproporphyrinogen I, which damage erythrocytes and elicit a phototoxic reaction upon light exposure. The clinical spectrum of CEP depends on the level of residual UROS activity, which is determined by the underlying pathogenic loss-of-function UROS mutations. Disease severity ranges from non-immune hydrops fetalis in utero to late-onset disease with only mild cutaneous involvement. The clinical characteristics of CEP include exquisite photosensitivity to visible light resulting in bullous vesicular lesions which, when infected lead to progressive photomutilation of sun-exposed areas such as the face and hands. In addition, patients have erythrodontia (brownish discoloration of teeth) and can develop corneal scarring. Chronic transfusion-dependent hemolytic anemia is common and leads to bone marrow hyperplasia, which further increases porphyrin production. Management of CEP consists of strict avoidance of exposure to visible light with sun-protective clothing, sunglasses, and car and home window filters. Adequate care of ruptured vesicles and use of topical antibiotics is indicated to prevent superinfections and osteolysis. In patients with symptomatic hemolytic anemia, frequent erythrocyte cell transfusions may be necessary to suppress hematopoiesis and decrease marrow production of the phototoxic porphyrins. In severe transfection-dependent cases, bone marrow or hematopoietic stem cell transplantation has been performed, which is curative. Therapeutic approaches including gene therapy, proteasome inhibition, and pharmacologic chaperones are under investigation.
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Affiliation(s)
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Address all Correspondence to: R. J. Desnick, PhD, MD, Dean for Genetic and Genomic Medicine Professor and Chairman Emeritus, Department of Genetic and Genomic Sciences Icahn School of Medicine at Mount Sinai New York, NY 10029, Phone: (212) 659-6700 Fax: (212) 360-1809
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661
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Petrulioniene Z, Gargalskaite U, Mikstiene V, Norvilas R, Skiauteryte E, Utkus A. Autosomal recessive hypercholesterolemia: Case report. J Clin Lipidol 2019; 13:887-893. [PMID: 31734096 DOI: 10.1016/j.jacl.2019.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Autosomal recessive hypercholesterolemia (ARH; OMIM #603813) is a very rare monogenic disorder affecting less than 1 in 1000,000 people and is characterized by very high levels of low-density lipoprotein cholesterol (LDL-C), leading to aggressive and premature atherosclerotic cardiovascular disease if left untreated. Lowering of LDL-C is the main target of the treatment. We report on a 29-year-old male patient born in nonconsanguineous Lithuanian family homo(hemi-)zygous for LDLRAP1 gene variant causing ARH. This variant is not present in population databases and, to our knowledge, has not been reported in scientific literature before. METHODS AND RESULTS The earliest clinical sign, noticed at the age of 5 years, was painful and enlarging nodules on Achilles tendons. At the age of 10 years, xanthomas of the metacarpal joint area on both hands emerged. The first lipid panel was performed at the age of 12 years. In accordance with Dutch Lipid Clinic Network diagnostic criteria for familial hypercholesterolemia (FH), definite FH (type IIA hyperlipoproteinemia) was diagnosed and the treatment with cholestyramine 4 grams per day was initiated. As the patient was 15 years old, direct adsorption of low-density lipoprotein apheresis was started and repeated monthly. At the age of 20 years, along with lipoprotein apheresis, 10 mg of rosuvastatin daily intake was prescribed. At the age of 28 years, the dose of rosuvastatin was increased to 40 mg per day, and 10 mg of ezetimibe daily intake was added. At the age of 28 years, homozygous LDLRAP1 gene variant NM_015627.2:c.488A>C, NP_056442.2:p.(Gln163Pro) causing autosomal recessive hypercholesterolemia was determined by genetic testing. CONCLUSIONS This case report implies that ARH, being an extremely rare disorder, is a severe disease. As there is limited routine testing, including genetic testing, patients suffering from both this disease and FH may remain undiagnosed. Cascade screening and genetic counseling differ for ARH as compared with FH, as the carrier of a pathogenic variant in the LDLRAP1 gene does not have marked total cholesterol and LDL-C elevations. However, genetic testing of the proband and their relatives is essential to evaluate the risk of development of FH and to provide prognosis as well as adequate, timely treatment. To improve the quality of life of patients with FH and prolong their life expectancy, national registries of FH and wider laboratory and genetic testing are undoubtedly necessary. A national FH screening program was set up in Lithuania, which helps to identify, monitor, and treat subjects with FH.
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Affiliation(s)
- Zaneta Petrulioniene
- Vilnius University Faculty of Medicine, Vilnius, Lithuania; Clinic for Cardiovascular Disease, Center of Cardiology and Angiology, Vilnius, Lithuania
| | - Urte Gargalskaite
- Vilnius University Faculty of Medicine, Vilnius, Lithuania; Clinic for Cardiovascular Disease, Center of Cardiology and Angiology, Vilnius, Lithuania.
| | - Violeta Mikstiene
- Clinic for Cardiovascular Disease, Center of Cardiology and Angiology, Vilnius, Lithuania; Faculty of Medicine, Department of Human and Medical Genetics, Vilnius University, Institute of Biomedical Sciences, Vilnius, Lithuania
| | - Rimvydas Norvilas
- Clinic for Cardiovascular Disease, Center of Cardiology and Angiology, Vilnius, Lithuania; Faculty of Medicine, Department of Human and Medical Genetics, Vilnius University, Institute of Biomedical Sciences, Vilnius, Lithuania; Department of Experimental, Preventive, and Clinical Medicine, State Research Institute, Center for Innovative Medicine, Vilnius, Lithuania
| | - Egle Skiauteryte
- Clinic for Cardiovascular Disease, Center of Cardiology and Angiology, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Experimental, Preventive, and Clinical Medicine, State Research Institute, Center for Innovative Medicine, Vilnius, Lithuania
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662
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del Angel G, Hutchinson AT, Jain NK, Forbes CD, Reynders J. Large-scale functional LIPA variant characterization to improve birth prevalence estimates of lysosomal acid lipase deficiency. Hum Mutat 2019; 40:2007-2020. [PMID: 31180157 PMCID: PMC6852163 DOI: 10.1002/humu.23837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/11/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023]
Abstract
Lysosomal acid lipase (LAL) deficiency is an autosomal recessive disorder caused by LIPA gene mutations that disrupt LAL activity. We performed in vitro functional testing of 149 LIPA variants to increase the understanding of the variant effects on LAL deficiency and to improve disease prevalence estimates. Chosen variants had been reported in literature or population databases. Functional testing was done by plasmid transient transfection and LAL activity assessment. We assembled a set of 165 published LAL deficient patient genotypes to evaluate this assay's effectiveness to recapitulate genotype/phenotype relationships. Rapidly progressive LAL deficient patients showed negligible enzymatic activity (<1%), whereas patients with childhood/adult LAL deficiency typically have 1-7% average activity. We benchmarked six in silico variant effect prediction algorithms with these functional data. PolyPhen-2 was shown to have a superior area under the receiver operating curve performance. We used functional data along with Genome Aggregation Database (gnomAD) allele frequencies to estimate LAL deficiency birth prevalence, yielding a range of 3.45-5.97 cases per million births in European-ancestry populations. The low estimate only considers functionally assayed variants in gnomAD. The high estimate computes allele frequencies for variants absent in gnomAD, and uses in silico scores for unassayed variants. Prevalence estimates are lower than previously published, underscoring LAL deficiency's rarity.
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Affiliation(s)
- Guillermo del Angel
- Strategy, Program Management and Data Science DepartmentAlexion Pharmaceuticals Inc.BostonMassachusetts
| | | | - Nina K. Jain
- Research DepartmentAlexion Pharmaceuticals Inc.BostonMassachusetts
| | - Chris D. Forbes
- Research DepartmentAlexion Pharmaceuticals Inc.BostonMassachusetts
| | - John Reynders
- Strategy, Program Management and Data Science DepartmentAlexion Pharmaceuticals Inc.BostonMassachusetts
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663
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Lackie RE, Razzaq AR, Farhan SMK, Qiu LR, Moshitzky G, Beraldo FH, Lopes MH, Maciejewski A, Gros R, Fan J, Choy WY, Greenberg DS, Martins VR, Duennwald ML, Lerch JP, Soreq H, Prado VF, Prado MAM. Modulation of hippocampal neuronal resilience during aging by the Hsp70/Hsp90 co-chaperone STI1. J Neurochem 2019; 153:727-758. [PMID: 31562773 DOI: 10.1111/jnc.14882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/22/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
Abstract
Chaperone networks are dysregulated with aging, but whether compromised Hsp70/Hsp90 chaperone function disturbs neuronal resilience is unknown. Stress-inducible phosphoprotein 1 (STI1; STIP1; HOP) is a co-chaperone that simultaneously interacts with Hsp70 and Hsp90, but whose function in vivo remains poorly understood. We combined in-depth analysis of chaperone genes in human datasets, analysis of a neuronal cell line lacking STI1 and of a mouse line with a hypomorphic Stip1 allele to investigate the requirement for STI1 in aging. Our experiments revealed that dysfunctional STI1 activity compromised Hsp70/Hsp90 chaperone network and neuronal resilience. The levels of a set of Hsp90 co-chaperones and client proteins were selectively affected by reduced levels of STI1, suggesting that their stability depends on functional Hsp70/Hsp90 machinery. Analysis of human databases revealed a subset of co-chaperones, including STI1, whose loss of function is incompatible with life in mammals, albeit they are not essential in yeast. Importantly, mice expressing a hypomorphic STI1 allele presented spontaneous age-dependent hippocampal neurodegeneration and reduced hippocampal volume, with consequent spatial memory deficit. We suggest that impaired STI1 function compromises Hsp70/Hsp90 chaperone activity in mammals and can by itself cause age-dependent hippocampal neurodegeneration in mice. Cover Image for this issue: doi: 10.1111/jnc.14749.
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Affiliation(s)
- Rachel E Lackie
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada
| | - Abdul R Razzaq
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, and The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Lily R Qiu
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gilli Moshitzky
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Flavio H Beraldo
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Marilene H Lopes
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Laboratory of Neurobiology and Stem cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Andrzej Maciejewski
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Robert Gros
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jue Fan
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - David S Greenberg
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vilma R Martins
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Martin L Duennwald
- Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason P Lerch
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Hermona Soreq
- Department of Biological Chemistry, The Edmond and Lily Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vania F Prado
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marco A M Prado
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.,Program in Neuroscience, University of Western Ontario, London, Ontario, Canada.,Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.,Department of Anatomy & Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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Jaffey JA, Reading NS, Giger U, Abdulmalik O, Buckley RM, Johnstone S, Lyons LA. Clinical, metabolic, and genetic characterization of hereditary methemoglobinemia caused by cytochrome b 5 reductase deficiency in cats. J Vet Intern Med 2019; 33:2725-2731. [PMID: 31650629 PMCID: PMC6872605 DOI: 10.1111/jvim.15637] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/24/2019] [Indexed: 01/24/2023] Open
Abstract
Two non‐pedigreed male castrated cats had persistent cyanosis over a 3‐year observation period. Clinical cardiopulmonary evaluations did not reveal abnormalities, but the blood remained dark after exposure to air. Erythrocytic methemoglobin concentrations were high (~40% of hemoglobin) and cytochrome b5 reductase (CYB5R) activities in erythrocytes were low (≤15% of control). One cat remained intolerant of exertion, and the other cat developed anemia and died due to an unidentified comorbidity. Whole‐genome sequencing revealed a homozygous c.625G>A missense variant (B4:137967506) and a c.232‐1G>C splice acceptor variant (B4:137970815) in CYB5R3, respectively, which were absent in 193 unaffected additional cats. The p.Gly209Ser missense variant likely disrupts a nicotinamide adenine dinucleotide (NADH)‐binding domain, while the splicing error occurs at the acceptor site for exon 4, which likely affects downstream translation of the protein. The 2 novel CYB5R3 variants were associated with methemoglobinemia using clinical, biochemical, genomics, and in silico protein studies. The variant prevalence is unknown in the cat population.
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Affiliation(s)
- Jared A Jaffey
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Midwestern University, Glendale, Arizona
| | - N Scott Reading
- Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah.,Division of Hematology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Urs Giger
- Section of Medical Genetics (PennGen), School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Osheiza Abdulmalik
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ruben M Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri
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665
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Ali EZ, Yakob Y, Ngu LH. Identification of mutations in Malaysian patients with argininosuccinate lyase (ASL) deficiency. Mol Genet Metab Rep 2019; 21:100525. [PMID: 31709144 PMCID: PMC6831900 DOI: 10.1016/j.ymgmr.2019.100525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/16/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022] Open
Abstract
Argininosuccinate lyase (ASL) deficiency impairs the function of the urea cycle that detoxifies blood ammonia in the body. Mutation that occurs in the ASL gene is the cause of occurrence of ASL deficiency (ASLD). This deficiency causes hyperammonemia, hepatopathy and neurodevelopmental delay in patients. In this study, the clinical characteristics and molecular analysis of 10 ASLD patients were presented. 8 patients were associated with severe neonatal onset, while the other 2 were associated with late onset. Molecular analysis of ASL gene identified four new missense variants, which were c.778C>T, p.(Leu260Arg), c.1340G>C, p.(Ser447Thr), c.436C>G, p.(Arg146Gly) and c.595C>G, p.(Leu199Val) and four reported missense variants, which were c.638G>A, p.(Arg213Gln); c.556C>T, p.(Arg186Trp), c.578G>A, p.(Arg193Gln) and c.436C>G, p.(Arg146Trp). In silico servers predicted all new and reported variants as disease-causing. Structural examination exhibited that all pathogenic variants affected the stability of the tetrameric ASL structure by disturbing the bonding pattern with the neighboring residues. Conclusion This study revealed the genetic heterogeneity among Malaysian ASL patients. This study has also expanded the mutational spectrum of the ASL.
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Affiliation(s)
- Ernie Zuraida Ali
- Inborn Error of Metabolism and Genetic Unit, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Section U13 Setia Alam, 40170 Shah Alam, Selangor, Malaysia
- Corresponding authors.
| | - Yusnita Yakob
- Molecular Diagnostics and Protein Unit, Specialized Diagnostics Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Lock Hock Ngu
- Medical Genetics Department, Kuala Lumpur Hospital, Ministry of Health Malaysia, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
- Corresponding authors.
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666
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Schirwani S, Metcalfe K, Wagner B, Berry I, Sobey G, Jewell R. DSE associated musculocontractural EDS, a milder phenotype or phenotypic variability. Eur J Med Genet 2019; 63:103798. [PMID: 31655143 DOI: 10.1016/j.ejmg.2019.103798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 09/08/2019] [Accepted: 10/20/2019] [Indexed: 01/02/2023]
Abstract
Musculocontractural Ehlers-Danlos syndrome (mcEDS) is an autosomal recessive condition characterized by distinct craniofacial features, multisystem congenital malformations and progressive fragility of connective tissues. It is caused by pathogenic variants in CHST14 and DSE genes. There are three reports of pathogenic variants in DSE in four mcEDS patients. In this study we provide clinical and molecular presentation of two new patients with DSE related mcEDS. Analysing clinical exome data, a homozygous pathogenic DSE variant, c.1150_1157del p.(Pro384Trpfs*9), was identified in a 32 year old man with bilateral congenital talipes equinovarus, characteristic facial features, myopia, hyperextensible skin at the elbows, significant palmar wrinkling, bilateral inguinal hernias and chronic leg, back and joint pain. Electron microscopical examination of skin biopsy showed changes consistent with mild compensatory elastic fibre hypertrophy and mildly loose collagen bundles. The variant is predicted to result in a frameshift and introduction of a premature termination codon in the final exon of the DSE gene, anticipated to lead to the loss of approximately 60% of the normal reading frame. The second patient has a phenotype consistent with previously reported cases of DSE associated musculocontractural EDS. A novel homozygous missense DSE variant of uncertain clinical significance was detected. This case study further delineates the DSE associated mcEDS phenotype and illustrates absence of major cutaneous, cardiovascular, renal and respiratory features, which supports previous suggestions that patients with DSE associated mcEDS present with a milder phenotype compared to those with CHST14 mutations.
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Affiliation(s)
- Schaida Schirwani
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, UK
| | - Bart Wagner
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Histopathology Department, Sheffield, UK
| | - Ian Berry
- Leeds Genetics Laboratory, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Glenda Sobey
- EDS National Diagnostic Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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667
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Ponard D, Gaboriaud C, Charignon D, Ghannam A, Wagenaar-Bos IGA, Roem D, López-Lera A, López-Trascasa M, Tosi M, Drouet C. SERPING1 mutation update: Mutation spectrum and C1 Inhibitor phenotypes. Hum Mutat 2019; 41:38-57. [PMID: 31517426 DOI: 10.1002/humu.23917] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022]
Abstract
C1 inhibitor (C1Inh) deficiency is responsible for hereditary angioedema (C1-INH-HAE) and caused by variants of the SERPING1/C1INH/C1NH gene. C1Inh is the major control of kallikrein-kinin system. C1Inh deficiency leads to its uncontrolled activation, with subsequent generation of the vasoactive peptide bradykinin. This update documents 748 different SERPING1 variants, including published variants and additional 120 unpublished ones. They were identified as heterozygous variants (n = 729), as homozygous variants in 10 probands and as compound heterozygous variants (nine combinations). Six probands with heterozygous variants exhibited gonadal mosaicism. Probands with heterozygous (n = 72) and homozygous (n = 1) variants were identified as de novo cases. Overall, 58 variants were found at positions showing high residue conservation among serpins, and have been referred to as a mousetrap function of C1Inh: reactive center loop, gate, shutter, breach, and hinge. C1Inh phenotype analysis identified dysfunctional serpin variants with failed serpin-protease association and a residual 105-kDa species after incubation with target protease. Regarding this characteristic, in conditions with low antigenic C1Inh, 74 C1-INH-HAE probands presented with an additional so-called intermediate C1-INH-HAE phenotype. The present update addresses a comprehensive SERPING1 variant spectrum that facilitates genotype-phenotype correlations, highlighting residues of strategic importance for serpin function and for identification of C1Inh deficiency as serpinopathy.
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Affiliation(s)
- Denise Ponard
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,Laboratoire d'Immunologie, CHU Grenoble Alpes, Grenoble, France
| | | | - Delphine Charignon
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | - Arije Ghannam
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | | | - Dorina Roem
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Alberto López-Lera
- Biomedical Research Network on Rare Diseases (CIBERER)-U754, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | - Mario Tosi
- Inserm U1245, University of Rouen, Rouen, France
| | - Christian Drouet
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,Inserm U1016, CNRS UMR8104, Institut Cochin, Université Paris-Descartes, France
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668
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Lin L, Wang Y, Liu L, Ying W, Wang W, Sun B, Sun J, Wang X. Clinical phenotype of a Chinese patient with RIPK1 deficiency due to novel mutation. Genes Dis 2019; 7:122-127. [PMID: 32181283 PMCID: PMC7063410 DOI: 10.1016/j.gendis.2019.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence indicates that RIPK1 is associated with inflammation and apoptotic. RIPK1 deficiency leads to proinflammatory signaling impaired. However, only few patients with homozygous loss-of-function mutation in RIPK1 gene had been reported until now. Here, we report a Chinese combined immunodeficiency patient. He had recurrent infection, diarrhea after 3 months old. Immune function indicated that T, B and NK cells decreased significantly but immunoglobulins approximately remained normal. Whole-exome sequencing indicated that he had novel compound heterozygous mutations (c.998 C > A from his mother and c.1934 C > T from his father) in RIPK1 gene, which were confirmed by Sanger sequencing. Our study reports novel mutations in RIPK1 gene and new phenotype of patient with RIPK1 deficiency.
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Affiliation(s)
- Li Lin
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ying Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Luyao Liu
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Wenjing Ying
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Wenjie Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Bijun Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Jinqiao Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
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669
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Doubková M, Trizuljak J, Vrzalová Z, Hrazdirová A, Blaháková I, Radová L, Pospíšilová Š, Doubek M. Novel genetic variant of HPS1 gene in Hermansky-Pudlak syndrome with fulminant progression of pulmonary fibrosis: a case report. BMC Pulm Med 2019; 19:178. [PMID: 31619213 PMCID: PMC6794755 DOI: 10.1186/s12890-019-0941-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/16/2019] [Indexed: 01/22/2023] Open
Abstract
Background Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder that is associated with oculocutaneous albinism, bleeding diathesis, granulomatous colitis, and highly penetrant pulmonary fibrosis in some subtypes. Homozygous or compound heterozygous pathological variants in HPS1, HPS3, HPS4, and several other genes lead to clinical manifestation of the disease. Case presentation A 57-year-old female was admitted with congenital oculocutaneous albinism, thrombocytopathy and late-onset accelerated pulmonary fibrosis (first symptoms from age 50 onwards). Chest high-resolution computed tomography identified thickening of peribronchovascular interstitium, bronchiectasis, reticulations, honeycombing, ground glass opacities and lung parenchyma consolidations. HPS was clinically suspected. We performed whole exome sequencing (WES), a form of massive parallel sequencing, of proband-parents trio. Whole exome libraries were processed using KAPA Hyper Prep Kit, SeqCap EZ MedExome Enrichment Kit and HyperCap Bead Kit according to the SeqCap EZ HyperCap Workflow. The paired-end 2 × 75 bp sequencing was performed on the Illumina NextSeq 500 Sequencer (Illumina Inc., USA). Furthermore, obtained variants by WES were evaluated using a virtual panel of genes: HPS1, AP3B1, HPS3, HPS4, HPS5, HPS6, DTNBP1, BLOC1S3, and PLDN. We identified a compound heterozygous genotype in HPS1 gene in the proband. We identified a pathogenic frameshift variant c.1189delC; p.(Gln397Serfs*2), resulting in a premature stop codon. This variant has been previously associated with HPS. Furthermore, we characterized previously undescribed nonsense variant c.1507C > T; p.(Gln503*), resulting in a premature stop codon and mRNA degradation through nonsense-mediated decay. Sanger sequencing validated the presence of both variants and simultaneously confirmed the heterozygous carrier status of parents. Unfortunately, the patient died due to fulminant progression of pulmonary fibrosis 2 months after diagnostics. Conclusions Compound heterozygous mutations in HPS1 in the proband lead to disruption of HPS1 gene and clinical manifestation of HPS with severe pulmonary fibrosis. This case illustrates the need to consider HPS in differential diagnostics of pulmonary fibrosis. Pulmonary fibrosis is a common cause of death in HPS patients. Earlier diagnosis may enable better treatment for these patients.
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Affiliation(s)
- Martina Doubková
- Department of Pulmonary Diseases and Tuberculosis, Masaryk University, Faculty of Medicine and University Hospital, Brno, Czech Republic
| | - Jakub Trizuljak
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Vrzalová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Hrazdirová
- Department of Pulmonary Diseases and Tuberculosis, Masaryk University, Faculty of Medicine and University Hospital, Brno, Czech Republic
| | - Ivona Blaháková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Šárka Pospíšilová
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine, Hematology and Oncology, University Hospital and Faculty of Medicine, Jihlavská 20, 625 00, Brno, Czech Republic. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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670
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Bury L, Megy K, Stephens JC, Grassi L, Greene D, Gleadall N, Althaus K, Allsup D, Bariana TK, Bonduel M, Butta NV, Collins P, Curry N, Deevi SVV, Downes K, Duarte D, Elliott K, Falcinelli E, Furie B, Keeling D, Lambert MP, Linger R, Mangles S, Mapeta R, Millar CM, Penkett C, Perry DJ, Stirrups KE, Turro E, Westbury SK, Wu J, BioResource N, Gomez K, Freson K, Ouwehand WH, Gresele P, Simeoni I. Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants. Hum Mutat 2019; 41:277-290. [PMID: 31562665 PMCID: PMC6972977 DOI: 10.1002/humu.23927] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022]
Abstract
The heterogeneous manifestations of MYH9‐related disorder (MYH9‐RD), characterized by macrothrombocytopenia, Döhle‐like inclusion bodies in leukocytes, bleeding of variable severity with, in some cases, ear, eye, kidney, and liver involvement, make the diagnosis for these patients still challenging in clinical practice. We collected phenotypic data and analyzed the genetic variants in more than 3,000 patients with a bleeding or platelet disorder. Patients were enrolled in the BRIDGE‐BPD and ThromboGenomics Projects and their samples processed by high throughput sequencing (HTS). We identified 50 patients with a rare variant in MYH9. All patients had macrothrombocytes and all except two had thrombocytopenia. Some degree of bleeding diathesis was reported in 41 of the 50 patients. Eleven patients presented hearing impairment, three renal failure and two elevated liver enzymes. Among the 28 rare variants identified in MYH9, 12 were novel. HTS was instrumental in diagnosing 23 patients (46%). Our results confirm the clinical heterogeneity of MYH9‐RD and show that, in the presence of an unclassified platelet disorder with macrothrombocytes, MYH9‐RD should always be considered. A HTS‐based strategy is a reliable method to reach a conclusive diagnosis of MYH9‐RD in clinical practice.
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Affiliation(s)
- Loredana Bury
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Jonathan C Stephens
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Daniel Greene
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,Department of Haematology, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nick Gleadall
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Karina Althaus
- Institute for Immunology and Transfusion Medicine, Universitätsmedizin Greifswald Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany.,Transfusion Medicine, Medical Faculty Tübingen, Tübingen, Germany
| | - David Allsup
- Hull York Medical School, University of Hull, York, UK
| | - Tadbir K Bariana
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Mariana Bonduel
- Hematology/Oncology Department, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Nora V Butta
- Servicio de Hematología y Hemoterapia Hospital, Universitario La Paz-IDIPaz, Madrid, Spain
| | - Peter Collins
- Arthur Bloom Haemophilia Centre, Institute of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Nicola Curry
- Department of Clinical Haematology, Oxford Haemophilia and Thrombosis Centre, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford, UK
| | - Sri V V Deevi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Daniel Duarte
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Kim Elliott
- Oxford Haemophilia & Thrombosis Centre, Department of Haematology, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford and the NIHR BRC, Blood Theme, Oxford Centre for Haematology, Oxford, UK
| | - Emanuela Falcinelli
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Bruce Furie
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | | | - Michele P Lambert
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rachel Linger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Sarah Mangles
- Basingstoke and Hampshire Hospital, NHS Foundation Trust, UK
| | - Rutendo Mapeta
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Carolyn M Millar
- Hampshire Hospital NHS Foundation Trust, UK.,Centre for Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, UK
| | - Christopher Penkett
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - David J Perry
- Department of Haematology, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kathleen E Stirrups
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge, UK
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - John Wu
- British Columbia Children's Hospital, Vancouver, Canada
| | - Nihr BioResource
- NIHR BioResource, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Keith Gomez
- Transfusion Medicine, Medical Faculty Tübingen, Tübingen, Germany
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.,Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Paolo Gresele
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Ilenia Simeoni
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
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671
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Pugh J, Khan SG, Tamura D, Goldstein AM, Landi MT, DiGiovanna JJ, Kraemer KH. Use of Big Data to Estimate Prevalence of Defective DNA Repair Variants in the US Population. JAMA Dermatol 2019; 155:72-78. [PMID: 30516811 DOI: 10.1001/jamadermatol.2018.4473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance Wide use of genomic sequencing to diagnose disease has raised concern about the extent of genotype-phenotype correlations. Objective To correlate disease-associated allele frequencies with expected and reported prevalence of clinical disease. Design, Setting, and Participants Xeroderma pigmentosum (XP), a recessive, cancer-prone, neurocutaneous disorder, was used as a model for this study. From January 1, 2017, to May 4, 2018, the Human Gene Mutation Database and a cohort of patients at the National Institutes of Health were searched and screened to identify reported mutations associated with XP. The clinical phenotype of these patients was confirmed from reports in the literature and National Institutes of Health medical records. The genetically predicted prevalence of disease based on frequency of known pathogenic mutations was compared with the prevalence of patients clinically diagnosed with phenotypic XP. Exome sequencing of more than 200 000 alleles from the Genome Aggregation Database, the National Cancer Institute Division of Cancer Epidemiology and Genetics database of healthy controls, and an Inova Hospital Study database was used to investigate the frequencies of these mutations in the general population. Main Outcomes and Measures Listing of all reported mutations associated with XP, their frequencies in 3 large exome sequence databases, determination of the number of patients in the United States with XP using modeling equations, and comparison of the observed and reported numbers of patients with XP with specific mutations. Results A total of 156 pathogenic missense and nonsense mutations associated with XP were identified in the National Institutes of Health cohort and the Human Gene Mutation Database. The Genome Aggregation Database provided frequency data for 65 of these mutations, with a total allele frequency of 1.13%. The XPF (ERCC4) mutation, p.P379S, had an allele frequency of 0.4%, and the XPC mutation, p.P334H, had an allele frequency of 0.3%. With the Hardy-Weinberg equation, it was determined that there should be more than 8000 patients who are homozygous for these mutations in the United States. In contrast, only 3 patients with XP were reported as having the XPF mutation, and 1 patient was reported as having the XPC mutation. Conclusions and Relevance The findings from this study suggest that clinicians should approach large genomic databases with caution when trying to correlate the clinical implications of genetic variants with the prevalence of disease risk. Unsuspected mutations in known genes with a predisposition for skin cancer may be responsible for some of the high frequency of skin cancers in the general population.
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Affiliation(s)
- Jennifer Pugh
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.,Academy Enrichment Program Scholar, Office of Intramural Training & Education, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Sikandar G Khan
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Deborah Tamura
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Alisa M Goldstein
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Maria Teresa Landi
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - John J DiGiovanna
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Kenneth H Kraemer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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672
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Oliynyk RT. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. Int J Mol Sci 2019; 20:E5013. [PMID: 31658652 PMCID: PMC6834143 DOI: 10.3390/ijms20205013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
With the accumulation of scientific knowledge of the genetic causes of common diseases and continuous advancement of gene-editing technologies, gene therapies to prevent polygenic diseases may soon become possible. This study endeavored to assess population genetics consequences of such therapies. Computer simulations were used to evaluate the heterogeneity in causal alleles for polygenic diseases that could exist among geographically distinct populations. The results show that although heterogeneity would not be easily detectable by epidemiological studies following population admixture, even significant heterogeneity would not impede the outcomes of preventive gene therapies. Preventive gene therapies designed to correct causal alleles to a naturally-occurring neutral state of nucleotides would lower the prevalence of polygenic early- to middle-age-onset diseases in proportion to the decreased population relative risk attributable to the edited alleles. The outcome would manifest differently for late-onset diseases, for which the therapies would result in a delayed disease onset and decreased lifetime risk; however, the lifetime risk would increase again with prolonging population life expectancy, which is a likely consequence of such therapies. If the preventive heritable gene therapies were to be applied on a large scale, the decreasing frequency of risk alleles in populations would reduce the disease risk or delay the age of onset, even with a fraction of the population receiving such therapies. With ongoing population admixture, all groups would benefit over generations.
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Affiliation(s)
- Roman Teo Oliynyk
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand.
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand.
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673
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Affiliation(s)
- Carlos G Vanoye
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.
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674
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Tey HJ, Ng CH. Computational analysis of functional SNPs in Alzheimer's disease-associated endocytosis genes. PeerJ 2019; 7:e7667. [PMID: 31592138 PMCID: PMC6776068 DOI: 10.7717/peerj.7667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Background From genome wide association studies on Alzheimer’s disease (AD), it has been shown that many single nucleotide polymorphisms (SNPs) of genes of different pathways affect the disease risk. One of the pathways is endocytosis, and variants in these genes may affect their functions in amyloid precursor protein (APP) trafficking, amyloid-beta (Aβ) production as well as its clearance in the brain. This study uses computational methods to predict the effect of novel SNPs, including untranslated region (UTR) variants, splice site variants, synonymous SNPs (sSNPs) and non-synonymous SNPs (nsSNPs) in three endocytosis genes associated with AD, namely PICALM, SYNJ1 and SH3KBP1. Materials and Methods All the variants’ information was retrieved from the Ensembl genome database, and then different variation prediction analyses were performed. UTRScan was used to predict UTR variants while MaxEntScan was used to predict splice site variants. Meta-analysis by PredictSNP2 was used to predict sSNPs. Parallel prediction analyses by five different software packages including SIFT, PolyPhen-2, Mutation Assessor, I-Mutant2.0 and SNPs&GO were used to predict the effects of nsSNPs. The level of evolutionary conservation of deleterious nsSNPs was further analyzed using ConSurf server. Mutant protein structures of deleterious nsSNPs were modelled and refined using SPARKS-X and ModRefiner for structural comparison. Results A total of 56 deleterious variants were identified in this study, including 12 UTR variants, 18 splice site variants, eight sSNPs and 18 nsSNPs. Among these 56 deleterious variants, seven variants were also identified in the Alzheimer’s Disease Sequencing Project (ADSP), Alzheimer’s Disease Neuroimaging Initiative (ADNI) and Mount Sinai Brain Bank (MSBB) studies. Discussion The 56 deleterious variants were predicted to affect the regulation of gene expression, or have functional impacts on these three endocytosis genes and their gene products. The deleterious variants in these genes are expected to affect their cellular function in endocytosis and may be implicated in the pathogenesis of AD as well. The biological consequences of these deleterious variants and their potential impacts on the disease risks could be further validated experimentally and may be useful for gene-disease association study.
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Affiliation(s)
- Han Jieh Tey
- Faculty of Information Science and Technology, Multimedia University, Ayer Keroh, Melaka, Malaysia
| | - Chong Han Ng
- Faculty of Information Science and Technology, Multimedia University, Ayer Keroh, Melaka, Malaysia
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675
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Disciglio V, Fasano C, Cariola F, Forte G, Grossi V, Sanese P, Lepore Signorile M, Resta N, Lotesoriere C, Stella A, Lolli I, Simone C. Gastric polyposis and desmoid tumours as a new familial adenomatous polyposis clinical variant associated with APC mutation at the extreme 3'-end. J Med Genet 2019; 57:356-360. [PMID: 31591141 PMCID: PMC7231465 DOI: 10.1136/jmedgenet-2019-106299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 01/23/2023]
Abstract
Germline mutations of the APC gene, which encodes a multidomain protein of 2843 amino acid residues, cause familial adenomatous polyposis (FAP). Three FAP clinical variants are correlated with the location of APC mutations: (1) classic FAP with profuse polyposis (>1000 adenomas), associated with mutations from codon 1250 to 1424; (2) attenuated FAP (<100 adenomas), associated with mutations at APC extremities (before codon 157 and after codon 1595); (3) classic FAP with intermediate colonic polyposis (100–1000 adenomas), associated with mutations located in the remaining part of APC. In an effort to decipher the clinical phenotype associated with APC C-terminal germline truncating mutations in patients with FAP, after screening APC mutations in one family whose members (n=4) developed gastric polyposis, colon oligo-polyposis and desmoid tumours, we performed a literature meta-analysis of clinically characterised patients (n=97) harbouring truncating mutations in APC C-terminus. The APC distal mutations identified in this study cluster with a phenotype characterised by colon oligo-polyposis, diffuse gastric polyposis and desmoid tumours. In conclusion, we describe a novel FAP clinical variant, which we propose to refer to as Gastric Polyposis and Desmoid FAP, that may require tailored management.
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Affiliation(s)
- Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Paola Sanese
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy.,Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Nicoletta Resta
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | - Claudio Lotesoriere
- Department of Oncology, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Alessandro Stella
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
| | - Ivan Lolli
- Department of Oncology, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy .,Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari "Aldo Moro", Bari, Italy
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676
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Zeng Z, Bromberg Y. Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives. Front Genet 2019; 10:914. [PMID: 31649718 PMCID: PMC6791167 DOI: 10.3389/fgene.2019.00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput experimentation have put the exploration of genome sequences at the forefront of precision medicine. In an effort to interpret the sequencing data, numerous computational methods have been developed for evaluating the effects of genome variants. Interestingly, despite the fact that every person has as many synonymous (sSNV) as non-synonymous single nucleotide variants, our ability to predict their effects is limited. The paucity of experimentally tested sSNV effects appears to be the limiting factor in development of such methods. Here, we summarize the details and evaluate the performance of nine existing computational methods capable of predicting sSNV effects. We used a set of observed and artificially generated variants to approximate large scale performance expectations of these tools. We note that the distribution of these variants across amino acid and codon types suggests purifying evolutionary selection retaining generated variants out of the observed set; i.e., we expect the generated set to be enriched for deleterious variants. Closer inspection of the relationship between the observed variant frequencies and the associated prediction scores identifies predictor-specific scoring thresholds of reliable effect predictions. Notably, across all predictors, the variants scoring above these thresholds were significantly more often generated than observed. which confirms our assumption that the generated set is enriched for deleterious variants. Finally, we find that while the methods differ in their ability to identify severe sSNV effects, no predictor appears capable of definitively recognizing subtle effects of such variants on a large scale.
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Affiliation(s)
- Zishuo Zeng
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, United States
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Genetics, Rutgers University, Human Genetics Institute, Piscataway, NJ, United States
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677
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Yamada M, Uehara T, Suzuki H, Takenouchi T, Fukushima H, Morisada N, Tominaga K, Onoda M, Kosaki K. IFT172 as the 19th gene causative of oral-facial-digital syndrome. Am J Med Genet A 2019; 179:2510-2513. [PMID: 31587445 DOI: 10.1002/ajmg.a.61373] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Fukushima
- Department of Pediatrics, Tokyo Dental College Ichikawa General Hospital, Chiba, Japan
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Kenta Tominaga
- Department of Cardiology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Motohiro Onoda
- Department of Plastic Surgery, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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678
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Ahmed Z, Zeeshan S, Xiong R, Liang BT. Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. Clin Transl Med 2019; 8:26. [PMID: 31586224 PMCID: PMC6778157 DOI: 10.1186/s40169-019-0243-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
Background The last decade has seen a dramatic increase in the availability of scientific data, where human-related biological databases have grown not only in count but also in volume, posing unprecedented challenges in data storage, processing, analysis, exchange, and curation. Next generation sequencing (NGS) advancements have facilitated and accelerated the process of identifying genetic variations. Adopting NGS with Whole-Genome and RNA sequencing in a diagnostic context has the potential to improve disease-risk detection in support of precision medicine and drug discovery. Several bioinformatics pipelines have been developed to strengthen variant interpretation by efficiently processing and analyzing sequence data, whereas many published results show how genomics data can be proactively incorporated into medical practices and improve utilization of clinical information. To utilize the wealth of genomics and health, there is a crucial need to generate appropriate gene-disease annotation repositories accessed through modern technology. Results Our focus here is to create a comprehensive database with mobile access to actionable genes and classified diseases, considered the foundation for clinical genomics and precision medicine. We present a publicly available iOS app, PAS-Gen, which invites global users to freely download it on iPhone and iPad devices, quickly adopt its easy to use interface, and search for genes and related diseases. PAS-Gen was developed using Swift, XCODE, and PHP scripting that uses Web and MySQL database servers, which includes over 59,000 protein-coding and non-coding genes, and over 90,000 classified gene-disease associations. PAS-Gen is founded on the clinical and scientific premise that easier healthcare and genomics data sharing will accelerate future medical discoveries. Conclusions We present a cutting-edge gene-disease database with a smart phone application, integrating information on classified diseases and related genes. The PAS-Gen app will assist researchers, medical practitioners, and pharmacists by providing a broad and view of genes that may be implicated in the likelihood of developing certain diseases. This tool with accelerate users’ abilities to understand the genetic basis of human complex diseases and by assimilating genomic and phenotypic data will support future work to identify gene-specific designer drugs, target precise molecular fingerprints for tumors, suggest appropriate drug therapies, predict individual susceptibility to disease, and diagnose and treat rare illnesses.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center (UConn Health), 263 Farmington Ave, Farmington, CT, 06032, USA. .,Institute for Systems Genomics, University of Connecticut, 263 Farmington Ave, Farmington, CT, 06032, USA.
| | - Saman Zeeshan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Ruoyun Xiong
- Department of Genetics and Genome Sciences, School of Medicine, University of Connecticut Health Center (UConn Health), 263 Farmington Ave, Farmington, CT, 06032, USA.,The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Bruce T Liang
- Pat and Jim Calhoun Cardiology Center, School of Medicine, UConn Health, 263 Farmington Ave, Farmington, CT, 06032, USA
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679
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Moisan S, Le Nabec A, Quillévéré A, Le Maréchal C, Férec C. Characterization of GJB2 cis-regulatory elements in the DFNB1 locus. Hum Genet 2019; 138:1275-1286. [PMID: 31586237 DOI: 10.1007/s00439-019-02068-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/29/2019] [Indexed: 11/28/2022]
Abstract
Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases, who present the most common hereditary type of nonsyndromic hearing loss (i.e., DFNB1), carry only one identified pathogenic allele. This strongly suggests the presence of uncharacterized distal cis-acting elements in the missing allele. Here within, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss phenotype, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus, we identify a novel set of cooperating GJB2 cis-acting elements and suggest a DFNB1 three-dimensional looping regulation model.
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Affiliation(s)
- Stéphanie Moisan
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
| | - Anaïs Le Nabec
- Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | | | - Cédric Le Maréchal
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France.,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHRU de Brest, Bretagne, Brest, France. .,Univ Brest, Inserm, EFS UMR 1078, GGB, 29200, Brest, France.
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680
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Chronic myelomonocytic leukemia with ETV6-ABL1 rearrangement and SMC1A mutation. Cancer Genet 2019; 238:31-36. [DOI: 10.1016/j.cancergen.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/18/2019] [Accepted: 07/06/2019] [Indexed: 12/16/2022]
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681
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Target discovery using biobanks and human genetics. Drug Discov Today 2019; 25:438-445. [PMID: 31562982 DOI: 10.1016/j.drudis.2019.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 08/18/2019] [Accepted: 09/18/2019] [Indexed: 11/22/2022]
Abstract
Large-scale biobanks can yield unprecedented insights into our health and provide discoveries of new and potentially targetable biomarkers. Several protective loss-of-function alleles have been identified, including variants that protect against cardiovascular disease, obesity, type 2 diabetes, and asthma and allergic diseases. These alleles serve as indicators of efficacy, mimicking the effects of drugs and suggesting that inhibiting these genes could provide therapeutic benefit, as has been observed for PCSK9. We provide a context for these findings through a multifaceted review covering the use of genetics in drug discovery efforts through genome-wide and phenome-wide association studies, linking deep mutation scanning data to molecular function and highlighting some additional tools that might help in the interpretation of newly discovered variants.
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682
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Ozdemir ES, Gursoy A, Keskin O. Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces. Bioinformatics 2019; 34:i795-i801. [PMID: 30423104 DOI: 10.1093/bioinformatics/bty569] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation Single amino acid variations (SAVs) in protein-protein interaction (PPI) sites play critical roles in diseases. PPI sites (interfaces) have a small subset of residues called hot spots that contribute significantly to the binding energy, and they may form clusters called hot regions. Singlet hot spots are the single amino acid hot spots outside of the hot regions. The distribution of SAVs on the interface residues may be related to their disease association. Results We performed statistical and structural analyses of SAVs with literature curated experimental thermodynamics data, and demonstrated that SAVs which destabilize PPIs are more likely to be found in singlet hot spots rather than hot regions and energetically less important interface residues. In contrast, non-hot spot residues are significantly enriched in neutral SAVs, which do not affect PPI stability. Surprisingly, we observed that singlet hot spots tend to be enriched in disease-causing SAVs, while benign SAVs significantly occur in non-hot spot residues. Our work demonstrates that SAVs in singlet hot spot residues have significant effect on protein stability and function. Availability and implementation The dataset used in this paper is available as Supplementary Material. The data can be found at http://prism.ccbb.ku.edu.tr/data/sav/ as well. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- E Sila Ozdemir
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul, Turkey.,Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.,Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul, Turkey
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683
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Vanoye CG, Desai RR, Fabre KL, Gallagher SL, Potet F, DeKeyser JM, Macaya D, Meiler J, Sanders CR, George AL. High-Throughput Functional Evaluation of KCNQ1 Decrypts Variants of Unknown Significance. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002345. [PMID: 30571187 DOI: 10.1161/circgen.118.002345] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The explosive growth in known human gene variation presents enormous challenges to current approaches for variant classification that have implications for diagnosis and treatment of many genetic diseases. For disorders caused by mutations in cardiac ion channels as in congenital arrhythmia syndromes, in vitro electrophysiological evidence has high value in discriminating pathogenic from benign variants, but these data are often lacking because assays are cost, time, and labor intensive. METHODS We implemented a strategy for performing high-throughput functional evaluations of ion channel variants that repurposed an automated electrophysiological recording platform developed previously for drug discovery. RESULTS We demonstrated the success of this approach by evaluating 78 variants in KCNQ1, a major gene involved in genetic disorders of cardiac arrhythmia susceptibility. We benchmarked our results with traditional electrophysiological approaches and observed a high level of concordance. This strategy also enabled studies of dominant-negative behavior of variants exhibiting severe loss-of-function. Overall, our results provided functional data useful for reclassifying >65% of the studied KCNQ1 variants. CONCLUSIONS Our results illustrate an efficient and high-throughput paradigm linking genotype to function for a human cardiac ion channel that will enable data-driven classification of large numbers of variants and create new opportunities for precision medicine.
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Affiliation(s)
- Carlos G Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Reshma R Desai
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Katarina L Fabre
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Shannon L Gallagher
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Franck Potet
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | - Jean-Marc DeKeyser
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University School of Medicine, Nashville, TN (J.M.).,the Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN (J.M.,C.R.S.)
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN (C.R.S.).,the Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN (J.M.,C.R.S.)
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (C.G.V., R.R.D., K.L.F., S.L.G., F.P., J.-M.D., A.L.G.)
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684
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Glöcklhofer CR, Steinfurt J, Franke G, Hoppmann A, Glantschnig T, Perez-Feliz S, Alter S, Fischer J, Brunner M, Rainer PP, Köttgen A, Bode C, Odening KE. A novel LMNA nonsense mutation causes two distinct phenotypes of cardiomyopathy with high risk of sudden cardiac death in a large five-generation family. Europace 2019; 20:2003-2013. [PMID: 29947763 DOI: 10.1093/europace/euy127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Aims Characterization of the cardiac phenotype associated with the novel LMNA nonsense mutation c.544C>T, p.Q182*, which we have identified in a large five-generation family. Methods and results A family tree was constructed. Clinical data [arrhythmia, syncope, sudden cardiac death (SCD), New York Heart Association (NYHA) class] were collected from living and deceased family members. DNA of 23 living family members was analysed for mutations in LMNA. Additionally, dilated cardiomyopathy multi-gene-panel testing and whole exome sequencing were performed in some family members to identify potential phenotype-modifiers. In this five-generation family (n = 65), 17 SCDs occurred at 49.3 ± 10.0 years. Furthermore, we identified eight additional mutation-carriers, seven symptomatic (44 ± 13 years), and one asymptomatic (44 years). First signs of disease [sinus bradycardia with atrioventricular (AV)-block I°] occurred at 36.5 ± 8.1 years. Paroxysmal atrial fibrillation (AF) (onset at 41.8 ± 5.7 years) rapidly progressed to permanent AF (46.2 ± 9.8 years). Subsequently, AV-conduction worsened, syncope, pacemaker-dependence, and non-sustained ventricular tachycardia (43.3 ± 8.2 years) followed. Ventricular arrhythmia caused SCD in patients without implantable cardioverter-defibrillator (ICD). Patients protected by ICD developed rapidly progressive heart failure (45.2 ± 10.6 years). A different phenotype was seen in a sub-family in three patients with early onset of rapidly decompensating heart failure and only minor prior arrhythmia-related symptoms. One patient received high-urgency heart transplantation (HTX) at 32 years, while two died prior to HTX. One of them developed lethal peripartum-associated heart failure. Possible disease-modifiers were identified in this 'heart failure sub-family'. Conclusion The novel LMNA nonsense mutation c.544C>T causes a severe arrhythmogenic phenotype manifesting with high incidence of SCD in most patients; and in one sub-family, a distinct phenotype with fast progressing heart failure, indicating the need for early consideration of ICD-implantation and listing for heart-transplantation.
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Affiliation(s)
- Christina R Glöcklhofer
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Steinfurt
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gerlind Franke
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anselm Hoppmann
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Genetic Epidemiology, Medical Center University of Freiburg, Freiburg, Germany.,Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Stefanie Perez-Feliz
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Svenja Alter
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Human Genetics, Medical Center University of Freiburg, Freiburg, Germany
| | - Judith Fischer
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Human Genetics, Medical Center University of Freiburg, Freiburg, Germany
| | - Michael Brunner
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter P Rainer
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Anna Köttgen
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Genetic Epidemiology, Medical Center University of Freiburg, Freiburg, Germany
| | - Christoph Bode
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katja E Odening
- Department of Cardiology and Angiology I, Heart Center University of Freiburg, Hugstetter Str. 55, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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685
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Wang Y, Zhu C, Du L, Li Q, Lin MF, Férec C, Cooper DN, Chen JM, Zhou Y. Compound Heterozygosity for Novel Truncating Variants in the LMOD3 Gene as the Cause of Polyhydramnios in Two Successive Fetuses. Front Genet 2019; 10:835. [PMID: 31572445 PMCID: PMC6753228 DOI: 10.3389/fgene.2019.00835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/13/2019] [Indexed: 01/03/2023] Open
Abstract
Polyhydramnios is sometimes associated with genetic defects. However, establishing an accurate diagnosis and pinpointing the precise genetic cause of polyhydramnios in any given case represents a major challenge because it is known to occur in association with over 200 different conditions. Whole exome sequencing (WES) is now a routine part of the clinical workup, particularly with diseases characterized by atypical manifestations and significant genetic heterogeneity. Here we describe the identification, by means of WES, of novel compound heterozygous truncating variants in the LMOD3 gene [i.e., c.1412delA (p.Lys471Serfs*18) and c.1283dupC (p.Gly429Trpfs*35)] in a Chinese family with two successive fetuses affected with polyhydramnios, thereby potentiating the prenatal diagnosis of nemaline myopathy (NM) in the proband. LMOD3 encodes leiomodin-3, which is localized to the pointed ends of thin filaments and acts as a catalyst of actin nucleation in skeletal and cardiac muscle. This is the first study to describe the prenatal and postnatal manifestations of LMOD3-related NM in the Chinese population. Of all the currently reported NM-causing LMOD3 nonsense and frameshifting variants, c.1412delA generates the shortest truncation at the C-terminal end of the protein, underscoring the critical role of the WH2 domain in LMOD3 structure and function. Survey of the prenatal phenotypes of all known LMOD3-related severe NM cases served to identify fetal edema as a novel presenting feature that may provide an early clue to facilitate prenatal diagnosis of the disease.
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Affiliation(s)
- Ye Wang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Caixia Zhu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Liu Du
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qiaoer Li
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, China
| | - Mei-Fang Lin
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Claude Férec
- EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France.,CHU Brest, Service de Génétique, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jian-Min Chen
- EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - Yi Zhou
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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686
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Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. Nat Commun 2019; 10:4141. [PMID: 31515488 PMCID: PMC6742646 DOI: 10.1038/s41467-019-11959-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual's genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.
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Affiliation(s)
- Robert Fragoza
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shayne D Wierbowski
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jin Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tina N Tran
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Siqi Liang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Juan F Beltran
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Christen A Rivera-Erick
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Kaixiong Ye
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Li Yao
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Xiaomu Wei
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alon Keinan
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - John C Schimenti
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew G Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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687
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Vandiedonck C. Genetic association of molecular traits: A help to identify causative variants in complex diseases. Clin Genet 2019; 93:520-532. [PMID: 29194587 DOI: 10.1111/cge.13187] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies. The genetic variants that modulate them are called expression quantitative trait loci. Their study has been extended to other molecular quantitative trait loci (molQTLs) that regulate gene expression at the various levels, from chromatin state to cellular responses. Altogether, these studies have generated a wealth of basic information on the genome-wide patterns of gene expression and their inter-individual variation. Most importantly, molQTLs have become an invaluable asset in the genetic study of complex diseases. Although the identification of the disease-causing variants on the basis of their overlap with molQTLs requires caution, molQTLs can help to prioritize the relevant candidate gene(s) in the disease-associated regions and bring a functional interpretation of the associated variants, therefore, bridging the gap between genotypes and clinical phenotypes.
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Affiliation(s)
- C Vandiedonck
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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688
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Flores MA, Lazar IM. XMAn v2-a database of Homo sapiens mutated peptides. Bioinformatics 2019; 36:1311-1313. [PMID: 31539018 PMCID: PMC8215914 DOI: 10.1093/bioinformatics/btz693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 09/03/2019] [Indexed: 01/31/2023] Open
Abstract
SUMMARY The 'Unknown Mutation Analysis (XMAn)' database is a compilation of Homo sapiens mutated peptides in FASTA format, that was constructed for facilitating the identification of protein sequence alterations by tandem mass spectrometry detection. The database comprises 2 539 031 non-redundant mutated entries from 17 599 proteins, of which 2 377 103 are missense and 161 928 are nonsense mutations. It can be used in conjunction with search engines that seek the identification of peptide amino acid sequences by matching experimental tandem mass spectrometry data to theoretical sequences from a database. AVAILABILITY AND IMPLEMENTATION XMAn v2 can be accessed from github.com/lazarlab/XMAnv2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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689
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Fokkema IFAC, van der Velde KJ, Slofstra MK, Ruivenkamp CAL, Vogel MJ, Pfundt R, Blok MJ, Lekanne Deprez RH, Waisfisz Q, Abbott KM, Sinke RJ, Rahman R, Nijman IJ, de Koning B, Thijs G, Wieskamp N, Moritz RJG, Charbon B, Saris JJ, den Dunnen JT, Laros JFJ, Swertz MA, van Gijn ME. Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data. Hum Mutat 2019; 40:2230-2238. [PMID: 31433103 PMCID: PMC6900155 DOI: 10.1002/humu.23896] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/05/2019] [Accepted: 08/14/2019] [Indexed: 11/06/2022]
Abstract
Each year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next-generation sequencing (NGS). This requires pathogenicity classification of millions of DNA variants on the standard 5-tier scale. To reduce time spent on data interpretation and increase data quality and reliability, the nine Dutch labs decided to publicly share their classifications. Variant classifications of nearly 100,000 unique variants were catalogued and compared in a centralized MOLGENIS database. Variants classified by more than one center were labeled as "consensus" when classifications agreed, and shared internationally with LOVD and ClinVar. When classifications opposed (LB/B vs. LP/P), they were labeled "conflicting", while other nonconsensus observations were labeled "no consensus". We assessed our classifications using the InterVar software to compare to ACMG 2015 guidelines, showing 99.7% overall consistency with only 0.3% discrepancies. Differences in classifications between Dutch labs or between Dutch labs and ACMG were mainly present in genes with low penetrance or for late onset disorders and highlight limitations of the current 5-tier classification system. The data sharing boosted the quality of DNA diagnostics in Dutch labs, an initiative we hope will be followed internationally. Recently, a positive match with a case from outside our consortium resulted in a more definite disease diagnosis.
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Affiliation(s)
- Ivo F A C Fokkema
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kasper J van der Velde
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Mariska K Slofstra
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ronald H Lekanne Deprez
- Department of Clinical Genetics, Academic Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rubayte Rahman
- Department of Research IT, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Isaäc J Nijman
- Medicine Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Gert Thijs
- DGG-Genomics Software Solutions, Agilent Technologies, Leuven, Belgium
| | - Nienke Wieskamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ruben J G Moritz
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bart Charbon
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center & Department of Genetics, University Medical Center, Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Medicine Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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690
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Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SC, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat 2019; 40:1330-1345. [PMID: 31144778 PMCID: PMC7341177 DOI: 10.1002/humu.23823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
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Affiliation(s)
- Marco Carraro
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | | | - Luigi Chiricosta
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Francesco Reggiani
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Information Engineering, University of Padua, Padua, Italy
| | | | - Mariagrazia Bellini
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Kymberleigh Pagel
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Yuxiang Jiang
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | | | - Gaia Andreoletti
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen J. Wilson
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Jingqi Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yaqiong Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carlo Ferrari
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Alessandra Murgia
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Silvio C.E. Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- CNR Institute of Neuroscience, Padua, Italy
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
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691
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Talbi S, Bonnet C, Boudjenah F, Mansouri MT, Petit C, Ammar Khodja F. The spectrum of GJB2 gene mutations in Algerian families with nonsyndromic hearing loss from Sahara and Kabylie regions. Int J Pediatr Otorhinolaryngol 2019; 124:157-160. [PMID: 31200317 DOI: 10.1016/j.ijporl.2019.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023]
Abstract
INTRODUCTION DFNB1, caused by mutations of GJB2 or GJB6, is the most prevalent genetic form of nonsyndromic (i.e., isolated) congenital deafness in countries located around the Mediterranean Sea. Because some mutations are restricted to specific ethnic-geographic groups, we studied the prevalence and spectrum of GJB2/GJB6 mutations in deaf patients originating from two different Algerian regions, Kabylie and Sahara. PATIENTS AND METHODS Among 91 reportedly unrelated Algerian patients affected by prelingual deafness, 80 patients (41 from Kabylie and 39 from Sahara) were diagnosed with isolated deafness. All had profound deafness, except one patient with mild deafness. They were screened for the presence of GJB2 mutations by direct sequencing of the single coding exon of GJB2. Patients without mutations were then screened for the presence of the most frequent two deletions of GJB6: del(GJB6-D13S1854) and del(GJB6-D13S1830). RESULTS Causative mutations were found in 13 and 8 patients from Kabylie and Sahara, respectively, accounting for more than a quarter of the cohort. The c.35delG, p.Gly12Valfs*2 mutation remains the most important mutation both in Kabylie (10 patients) and Sahara (7 patients). All detected patients were homozygous for this mutation. In addition, two other mutations (c.139G > T, p.Glu47* and c.167delT, p.Leu56Argfs*26) were found homozygous in one family each, and two patients were compound heterozygotes for (c.35delG p.Gly12Valfs*2/c.139G > T, p.Glu47*). No deletion of GJB6 was detected. CONCLUSION We confirm that mutations in GJB2, mainly c.35delG, are one of the most prevalent causes of nonsyndromic congenital deafness in Algeria, whereas the del (GJB6-D13S1854) and del (GJB6-D13S1830) deletions of GJB6 contribute little, if any. Further investigation is needed to identify the cause of deafness in other patients without diagnostic.
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Affiliation(s)
- Sonia Talbi
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene (USTHB), POB32 ElAlia, 16111, Bab Ezzouar, Alger, Algeria.
| | - Crystel Bonnet
- Inserm UMRS 1120, Institut de la Vision, Sorbonne Université, Paris, France
| | - Farid Boudjenah
- Service d'Otorhinolaryngologie (ORL), Hôpital de Frantz fanon, Bejaia, Algeria; Service d'Otorhinolaryngologie (ORL), Hôpital Sidi Belloua, Tizi-Ouzou, Algeria
| | | | - Christine Petit
- Inserm UMRS 1120, Institut de la Vision, Sorbonne Université, Paris, France; Institut Pasteur, Collège de France, Paris, France
| | - Fatima Ammar Khodja
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene (USTHB), POB32 ElAlia, 16111, Bab Ezzouar, Alger, Algeria
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692
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Deoxythymidylate kinase, DTYMK, is a novel gene for mitochondrial DNA depletion syndrome. Clin Chim Acta 2019; 496:93-99. [DOI: 10.1016/j.cca.2019.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/12/2022]
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693
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Hu Z, Yu C, Furutsuki M, Andreoletti G, Ly M, Hoskins R, Adhikari AN, Brenner SE. VIPdb, a genetic Variant Impact Predictor Database. Hum Mutat 2019; 40:1202-1214. [PMID: 31283070 PMCID: PMC7288905 DOI: 10.1002/humu.23858] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 12/30/2022]
Abstract
Genome sequencing identifies vast number of genetic variants. Predicting these variants' molecular and clinical effects is one of the preeminent challenges in human genetics. Accurate prediction of the impact of genetic variants improves our understanding of how genetic information is conveyed to molecular and cellular functions, and is an essential step towards precision medicine. Over one hundred tools/resources have been developed specifically for this purpose. We summarize these tools as well as their characteristics, in the genetic Variant Impact Predictor Database (VIPdb). This database will help researchers and clinicians explore appropriate tools, and inform the development of improved methods. VIPdb can be browsed and downloaded at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Changhua Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Mabel Furutsuki
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Melissa Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Data Sciences, University of California, Berkeley, California 94720, USA
| | - Roger Hoskins
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Aashish N. Adhikari
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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694
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Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, de la Cruz X, Díez O, Gutiérrez-Enríquez S, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Moles-Fernández A, Montalban G, Mooney SD, O’Conner R, Ootes L, Özkan S, Padilla N, Pagel KA, Pejaver V, Radivojac P, Riera C, Savojardo C, Shen Y, Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE. Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Hum Mutat 2019; 40:1546-1556. [PMID: 31294896 PMCID: PMC6744348 DOI: 10.1002/humu.23861] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022]
Abstract
Testing for variation in BRCA1 and BRCA2 (commonly referred to as BRCA1/2), has emerged as a standard clinical practice and is helping countless women better understand and manage their heritable risk of breast and ovarian cancer. Yet the increased rate of BRCA1/2 testing has led to an increasing number of Variants of Uncertain Significance (VUS), and the rate of VUS discovery currently outpaces the rate of clinical variant interpretation. Computational prediction is a key component of the variant interpretation pipeline. In the CAGI5 ENIGMA Challenge, six prediction teams submitted predictions on 326 newly-interpreted variants from the ENIGMA Consortium. By evaluating these predictions against the new interpretations, we have gained a number of insights on the state of the art of variant prediction and specific steps to further advance this state of the art.
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Affiliation(s)
| | - Giulia Babbi
- Biocomputing Group, FaBiT Department, University of
Bologna, Bologna, Italy
| | - Sandra Bonache
- Oncogenetics Group, Vall d’Hebron Institute of
Oncology (VHIO), Barcelona, Spain
| | - Yue Cao
- Texas A&M University, College Station, TX, USA
| | - Rita Casadio
- Biocomputing Group, FaBiT Department, University of
Bologna, Bologna, Italy
| | - Xavier de la Cruz
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis
Avançats (ICREA), Barcelona, Spain
| | - Orland Díez
- Oncogenetics Group, Vall d’Hebron Institute of
Oncology (VHIO), Barcelona, Spain
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | | | | | - Carmen Lai
- Department of Biochemistry & Molecular Biology, Baylor
College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Medical and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Department of Biochemistry & Molecular Biology, Baylor
College of Medicine, Houston, TX, USA
- Department of Pharmacology, Baylor College of Medicine,
Houston, TX, USA
- Computational and Integrative Biomedical Research
Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Alejandro Moles-Fernández
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Gemma Montalban
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | | | | | - Lars Ootes
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Selen Özkan
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | - Natalia Padilla
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | | | | | - Predrag Radivojac
- Indiana University, Bloomington, IN, USA
- Northeastern University, Boston, MA, USA
| | - Casandra Riera
- Clinical and Translational Bioinformatics Research Unit,
Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de
Barcelona, Barcelona, Spain
| | | | - Yang Shen
- Texas A&M University, College Station, TX, USA
| | - Yuanfei Sun
- Texas A&M University, College Station, TX, USA
| | | | | | | | - David E. Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake
City, UT, USA
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695
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Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLoS Genet 2019; 15:e1007860. [PMID: 31469829 PMCID: PMC6742416 DOI: 10.1371/journal.pgen.1007860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 09/12/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
There has been much effort to prioritize genomic variants with respect to their impact on "function". However, function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions, it reflects a molecular effect on transcription or epigenetics. Here, we coupled multiple genomic predictors to build GRAM, a GeneRAlized Model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant on its associated gene, in a transferable, cell-specific manner. Firstly, we performed feature engineering: using LASSO, a regularized linear model, we found transcription factor (TF) binding most predictive, especially for TFs that are hubs in the regulatory network; in contrast, evolutionary conservation, a popular feature in many other variant-impact predictors, has almost no contribution. Moreover, TF binding inferred from in vitro SELEX is as effective as that from in vivo ChIP-Seq. Second, we implemented GRAM integrating only SELEX features and expression profiles; thus, the program combines a universal regulatory score with an easily obtainable modifier reflecting the particular cell type. We benchmarked GRAM on large-scale MPRA datasets, achieving AUROC scores of 0.72 in GM12878 and 0.66 in a multi-cell line dataset. We then evaluated the performance of GRAM on targeted regions using luciferase assays in the MCF7 and K562 cell lines. We noted that changing the insertion position of the construct relative to the reporter gene gave very different results, highlighting the importance of carefully defining the exact prediction target of the model. Finally, we illustrated the utility of GRAM in fine-mapping causal variants and developed a practical software pipeline to carry this out. In particular, we demonstrated in specific examples how the pipeline could pinpoint variants that directly modulate gene expression within a larger linkage-disequilibrium block associated with a phenotype of interest (e.g., for an eQTL).
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Affiliation(s)
- Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Kellie A Cotter
- Department for BioMedical Research, University of Bern, CH, Bern, Switzerland
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jin Liang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Hussein Mohsen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.,Program in the History of Science and Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Sandra Cohen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, New York, United States of America
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America.,Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, CH, Bern, Switzerland.,Weill Cornell Medicine, New York, United States of America
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
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696
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Boussaroque A, Bergougnoux A, Raynal C, Audrézet M, Sasorith S, Férec C, Bienvenu T, Girodon E. Pitfalls in the interpretation of
CFTR
variants in the context of incidental findings. Hum Mutat 2019; 40:2239-2246. [DOI: 10.1002/humu.23884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Agathe Boussaroque
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
| | - Anne Bergougnoux
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | - Caroline Raynal
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | | | - Souphatta Sasorith
- Laboratoire de Génétique MoléculaireCHU de Montpellier Montpellier France
| | - Claude Férec
- Laboratoire de Génétique MoléculaireCHU de Brest Brest France
| | - Thierry Bienvenu
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
| | - Emmanuelle Girodon
- Laboratoire de Génétique et Biologie Moléculaires, AP‐HP, Hôpital CochinHUPC Paris France
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697
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Jiang P, Hu Y, Wang Y, Zhang J, Zhu Q, Bai L, Tong Q, Li T, Zhao L. Efficient Mining of Variants From Trios for Ventricular Septal Defect Association Study. Front Genet 2019; 10:670. [PMID: 31440271 PMCID: PMC6694746 DOI: 10.3389/fgene.2019.00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 06/27/2019] [Indexed: 11/28/2022] Open
Abstract
Ventricular septal defect (VSD) is a fatal congenital heart disease showing severe consequence in affected infants. Early diagnosis plays an important role, particularly through genetic variants. Existing panel-based approaches of variants mining suffer from shortage of large panels, costly sequencing, and missing rare variants. Although a trio-based method alleviates these limitations to some extent, it is agnostic to novel mutations and computational intensive. Considering these limitations, we are studying a novel variants mining algorithm from trio-based sequencing data and apply it on a VSD trio to identify associated mutations. Our approach starts with irrelevant k-mer filtering from sequences of a trio via a newly conceived coupled Bloom Filter, then corrects sequencing errors by using a statistical approach and extends kept k-mers into long sequences. These extended sequences are used as input for variants needed. Later, the obtained variants are comprehensively analyzed against existing databases to mine VSD-related mutations. Experiments show that our trio-based algorithm narrows down candidate coding genes and lncRNAs by about 10- and 5-folds comparing with single sequence-based approaches, respectively. Meanwhile, our algorithm is 10 times faster and 2 magnitudes memory-frugal compared with existing state-of-the-art approach. By applying our approach to a VSD trio, we fish out an unreported gene—CD80, a combination of two genes—MYBPC3 and TRDN and a lncRNA—NONHSAT096266.2, which are highly likely to be VSD-related.
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Affiliation(s)
- Peng Jiang
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yaofei Hu
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yiqi Wang
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jin Zhang
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qinghong Zhu
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Lin Bai
- School of Computing and Electronic Information, Guangxi University, Nanning, China
| | - Qiang Tong
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tao Li
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,School of Computing and Electronic Information, Guangxi University, Nanning, China
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698
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Zhang D, Sun B, Zhang X, Li H, Lin Y, Qin L, Chen L, Zhang L, Ru K, Yang R. A novel SERPINC1 frameshift mutation in two antithrombin deficiency families. Int J Lab Hematol 2019; 42:e48-e51. [PMID: 31441586 DOI: 10.1111/ijlh.13097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Donglei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Sino-US Diagnostics Co., Ltd, Tianjin, China
| | - Boyang Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xian Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,The hematology department of Zhongnan hospital of Wuhan University, Wuhan, China
| | - Huiyuan Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yani Lin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Sino-US Diagnostics Co., Ltd, Tianjin, China
| | - Li Qin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Sino-US Diagnostics Co., Ltd, Tianjin, China
| | - Long Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Sino-US Diagnostics Co., Ltd, Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Laboratory of Blood Disease Gene Therapy, Tianjin, China
| | - Kun Ru
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Tianjin Sino-US Diagnostics Co., Ltd, Tianjin, China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological disorders, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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699
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Wang Z, Li L, Sun L, Mi Z, Fu F, Yu G, Fu X, Liu H, Zhang F. Review of 52 cases with Hailey-Hailey disease identified 25 novel mutations in Chinese Han population. J Dermatol 2019; 46:1024-1026. [PMID: 31435946 DOI: 10.1111/1346-8138.15055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022]
Abstract
Hailey-Hailey disease (HHD) is a rare autosomal dominant inherited keratosis caused by mutations in ATP2C1. The aim of our study was to identify and analyze the features of the mutations in HHD. We examined 52 Chinese Han cases which were diagnosed as HHD based on their clinical and histological findings. Genomic DNA polymerase chain reaction and direct sequencing of ATP2C1 were performed from peripheral blood samples of the patients and 100 unrelated healthy controls. Twenty-five novel mutations and 14 recurrent mutations were identified, including 11 (28.2%) missense mutations, nine (23.1%) frame-shift deletion mutations, eight (20.5%) nonsense mutations, seven (17.9%) splicing mutations and four (10.3%) frame-shift insertion mutations. Together with ours, all 209 mutations showed a uniform distribution without hotspots or clusters. In addition, there is no specific genotype-phenotype correlation in HHD. Our findings update the spectrum of mutations in ATP2C1.
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Affiliation(s)
- Zhe Wang
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, China.,Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Lulu Li
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Lele Sun
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Mi
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Fanghui Fu
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, China
| | - Gongqi Yu
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xian Fu
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, China.,Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, China.,Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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700
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Ye JZ, Delmar M, Lundby A, Olesen MS. Reevaluation of genetic variants previously associated with arrhythmogenic right ventricular cardiomyopathy integrating population-based cohorts and proteomics data. Clin Genet 2019; 96:506-514. [PMID: 31402444 DOI: 10.1111/cge.13621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/30/2019] [Indexed: 11/27/2022]
Abstract
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is one of the most common causes of sudden cardiac death in young people. Patients diagnosed with ARVC may experience increased likelihood of development of anxiety and depression, emphasizing the need for accurate diagnosis. To assist future genetic diagnosis and avoidance of misdiagnosis, we evaluated the reported monogenic disease-causing variants in ARVD/C Genetic Variants Database, Human Gene Mutation Database, and ClinVar. Within the aforementioned databases, 630 monogenic disease-causing variants from 18 genes were identified. In the genome Aggregation Database, 226 of these were identified; 68 of which were found at greater than expected prevalence. Furthermore, 37/226 genetic variants were identified amongst the 409 000 UK biobank participants, 23 were not associated with ARVC. Among the 14 remaining variants, 13 were previously found with greater than expected prevalence for a monogenic variant. Nevertheless, they were associated with serious cardiac phenotypes, suggesting that these 13 variants may be disease-modifiers of ARVC, rather than monogenic disease-causing. In summary, more than 10% of variants previously reported to cause ARVC were found unlikely to be associated with highly penetrant monogenic forms of ARVC. Notably, all variants in OBSCN and MYBPC3 were found, making these unlikely to be monogenic causes of ARVC.
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Affiliation(s)
- Johan Z Ye
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, DTU, Kgs. Lyngby, Denmark
| | - Mario Delmar
- The Leon H. Charney Division of Cardiology, New York University School of Medicine, New York, New York
| | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Morten S Olesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.,Laboratory of Molecular Cardiology, Department of Cardiology, Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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