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Heshmatzad K, Naderi N, Maleki M, Abbasi S, Ghasemi S, Ashrafi N, Fazelifar AF, Mahdavi M, Kalayinia S. Role of non-coding variants in cardiovascular disease. J Cell Mol Med 2023; 27:1621-1636. [PMID: 37183561 PMCID: PMC10273088 DOI: 10.1111/jcmm.17762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/29/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023] Open
Abstract
Cardiovascular diseases (CVDs) constitute one of the significant causes of death worldwide. Different pathological states are linked to CVDs, which despite interventions and treatments, still have poor prognoses. The genetic component, as a beneficial tool in the risk stratification of CVD development, plays a role in the pathogenesis of this group of diseases. The emergence of genome-wide association studies (GWAS) have led to the identification of non-coding parts associated with cardiovascular traits and disorders. Variants located in functional non-coding regions, including promoters/enhancers, introns, miRNAs and 5'/3' UTRs, account for 90% of all identified single-nucleotide polymorphisms associated with CVDs. Here, for the first time, we conducted a comprehensive review on the reported non-coding variants for different CVDs, including hypercholesterolemia, cardiomyopathies, congenital heart diseases, thoracic aortic aneurysms/dissections and coronary artery diseases. Additionally, we present the most commonly reported genes involved in each CVD. In total, 1469 non-coding variants constitute most reports on familial hypercholesterolemia, hypertrophic cardiomyopathy and dilated cardiomyopathy. The application and identification of non-coding variants are beneficial for the genetic diagnosis and better therapeutic management of CVDs.
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Affiliation(s)
- Katayoun Heshmatzad
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Niloofar Naderi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Majid Maleki
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Shiva Abbasi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Serwa Ghasemi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Nooshin Ashrafi
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Amir Farjam Fazelifar
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Mohammad Mahdavi
- Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
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2
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SNP-Target Genes Interaction Perturbing the Cancer Risk in the Post-GWAS. Cancers (Basel) 2022; 14:cancers14225636. [PMID: 36428729 PMCID: PMC9688512 DOI: 10.3390/cancers14225636] [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: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
Cancer ranks as the second leading cause of death worldwide, and, being a genetic disease, it is highly heritable. Over the past few decades, genome-wide association studies (GWAS) have identified many risk-associated loci harboring hundreds of single nucleotide polymorphisms (SNPs). Some of these cancer-associated SNPs have been revealed as causal, and the functional characterization of the mechanisms underlying the cancer risk association has been illuminated in some instances. In this review, based on the different positions of SNPs and their modes of action, we discuss the mechanisms underlying how SNPs regulate the expression of target genes to consequently affect tumorigenesis and the development of cancer.
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Dottore GR, Lanzolla G, Comi S, Menconi F, Mencacci LC, Dallan I, Marcocci C, Marinò M. Insights into the role of DNA methylation and gene expression in Graves' orbitopathy. J Clin Endocrinol Metab 2022; 108:e160-e168. [PMID: 36334311 DOI: 10.1210/clinem/dgac645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2022]
Abstract
CONTEXT A role of DNA methylation in Graves' orbitopathy (GO) has been proposed. Design. To investigate DNA methylation and gene expression in orbital fibroblasts from control and GO patients, under basal conditions or following challenge with an anti-TSH receptor antibody (M22) or cytokines involved in GO; to investigate the relationship between DNA methylation and cell function (proliferation); to perform a methylome analysis. Setting. Referral Center. Materials. Orbital fibroblasts from six GO and six control patients. Intervention. None. Main Outcome Measure. Methylome analysis of the whole genome. Results. Global DNA methylation increased significantly both in control and GO fibroblasts upon incubation with M22. Expression of two selected genes (CYP19A1 and AIFM2) was variably affected by M22 and interleukin-6. M22 increased cell proliferation in control and GO fibroblasts, which correlated with global DNA methylation. Methylome analysis revealed 19,869 DNA regions differently methylated in GO fibroblasts, encompassing 3,957 genes and involving CpG islands, shores and shelves. One-hundred and nineteen gene families and subfamilies, 89 protein groups, 402 biological processes and seven pathways were involved. Three genes found to be differentially expressed were concordantly hyper- or hypomethylated. Among the differently methylated genes, insulin-like growth factor-1 receptor and several fibroblast growth factors and receptors were included. CONCLUSIONS We propose that, when exposed to an autoimmune environment, orbital fibroblasts undergo hyper- or hypomethylation of certain genes, involving CpG promoters, which results in differential gene expression, which may be responsible for functional alterations, in particular higher proliferation, and ultimately for the GO phenotype in vivo.
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Affiliation(s)
- Giovanna Rotondo Dottore
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
| | - Giulia Lanzolla
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
| | - Simone Comi
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
| | - Francesca Menconi
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
| | - Lodovica Cristofani Mencacci
- Department of Surgical, Medical and Molecular Pathology, ENT Unit I, University of Pisa and University Hospital of Pisa, Italy, Via Paradisa 2, 56124, Pisa, Italy
| | - Iacopo Dallan
- Department of Surgical, Medical and Molecular Pathology, ENT Unit I, University of Pisa and University Hospital of Pisa, Italy, Via Paradisa 2, 56124, Pisa, Italy
| | - Claudio Marcocci
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
| | - Michele Marinò
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Via Paradisa 2, 56124, Pisa, Italy
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4
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A machine learning approach based on ACMG/AMP guidelines for genomic variant classification and prioritization. Sci Rep 2022; 12:2517. [PMID: 35169226 PMCID: PMC8847497 DOI: 10.1038/s41598-022-06547-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 01/07/2022] [Indexed: 01/19/2023] Open
Abstract
Genomic variant interpretation is a critical step of the diagnostic procedure, often supported by the application of tools that may predict the damaging impact of each variant or provide a guidelines-based classification. We propose the application of Machine Learning methodologies, in particular Penalized Logistic Regression, to support variant classification and prioritization. Our approach combines ACMG/AMP guidelines for germline variant interpretation as well as variant annotation features and provides a probabilistic score of pathogenicity, thus supporting the prioritization and classification of variants that would be interpreted as uncertain by the ACMG/AMP guidelines. We compared different approaches in terms of variant prioritization and classification on different datasets, showing that our data-driven approach is able to solve more variant of uncertain significance (VUS) cases in comparison with guidelines-based approaches and in silico prediction tools.
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Clinical, Genetic and Functional Characterization of a Novel AVPR2 Missense Mutation in a Woman with X-Linked Recessive Nephrogenic Diabetes Insipidus. J Pers Med 2022; 12:jpm12010118. [PMID: 35055433 PMCID: PMC8779739 DOI: 10.3390/jpm12010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
Nephrogenic diabetes insipidus (NDI) is a rare disorder characterized by renal unresponsiveness to the hormone vasopressin, leading to excretion of large volumes of diluted urine. Mutations in the arginine vasopressin receptor-2 (AVPR2) gene cause congenital NDI and have an X-linked recessive inheritance. The disorder affects almost exclusively male family members, but female carriers occasionally present partial phenotypes due to skewed inactivation of the X-chromosome. Here, we report a rare case of a woman affected with X-linked recessive NDI, presenting an average urinary output of 12 L/day. Clinical and biochemical studies showed incomplete responses to water deprivation and vasopressin stimulation tests. Genetic analyses revealed a novel heterozygous missense mutation (c.493G > C, p.Ala165Pro) in the AVPR2 gene. Using a combination of in-silico protein modeling with human cellular models and molecular phenotyping, we provide functional evidence for phenotypic effects. The mutation destabilizes the helical structure of the AVPR2 transmembrane domains and disrupts its plasma membrane localization and downstream intracellular signaling pathways upon activation with its agonist vasopressin. These defects lead to deficient aquaporin 2 (AQP2) membrane translocation, explaining the inability to concentrate urine in this patient.
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Song B, Buckler ES, Wang H, Wu Y, Rees E, Kellogg EA, Gates DJ, Khaipho-Burch M, Bradbury PJ, Ross-Ibarra J, Hufford MB, Romay MC. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Res 2021; 31:1245-1257. [PMID: 34045362 PMCID: PMC8256870 DOI: 10.1101/gr.266528.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/21/2021] [Indexed: 01/16/2023]
Abstract
Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.
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Affiliation(s)
- Baoxing Song
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA
| | - Hai Wang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yaoyao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Evan Rees
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | | | - Daniel J Gates
- Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
| | - Merritt Khaipho-Burch
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Peter J Bradbury
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
- Center for Population Biology and Genome Center, University of California Davis, Davis, California 95616, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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7
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Rotondo Dottore G, Bucci I, Lanzolla G, Dallan I, Sframeli A, Torregrossa L, Casini G, Basolo F, Figus M, Nardi M, Marcocci C, Marinò M. Genetic Profiling of Orbital Fibroblasts from Patients with Graves' Orbitopathy. J Clin Endocrinol Metab 2021; 106:e2176-e2190. [PMID: 33484567 DOI: 10.1210/clinem/dgab035] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Indexed: 02/04/2023]
Abstract
CONTEXT Graves' orbitopathy (GO) is an autoimmune disease that persists when immunosuppression is achieved. Orbital fibroblasts from GO patients display peculiar phenotypes even if not exposed to autoimmunity, possibly reflecting genetic or epigenetic mechanisms, which we investigated here. OBJECTIVE We aimed to explore potential genetic or epigenetic differences using primary cultures of orbital fibroblasts from GO and control patients. METHODS Cell proliferation, hyaluronic acid (HA) secretion, and HA synthases (HAS) were measured. Next-generation sequencing and gene expression analysis of the whole genome were performed, as well as real-time-PCR of selected genes and global DNA methylation assay on orbital fibroblasts from 6 patients with GO and 6 control patients from a referral center. RESULTS Cell proliferation was higher in GO than in control fibroblasts. Likewise, HA in the cell medium was higher in GO fibroblasts. HAS-1 and HAS-2 did not differ between GO and control fibroblasts, whereas HAS-3 was more expressed in GO fibroblasts. No relevant gene variants were detected by whole-genome sequencing. However, 58 genes were found to be differentially expressed in GO compared with control fibroblasts, and RT-PCR confirmed the findings in 10 selected genes. We postulated that the differential gene expression was related to an epigenetic mechanism, reflecting diverse DNA methylation, which we therefore measured. In support of our hypothesis, global DNA methylation was significantly higher in GO fibroblasts. CONCLUSIONS We propose that, following an autoimmune insult, DNA methylation elicits differential gene expression and sustains the maintenance of GO.
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Affiliation(s)
- Giovanna Rotondo Dottore
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Ilaria Bucci
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Giulia Lanzolla
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Iacopo Dallan
- Department of Surgical, Medical and Molecular Pathology, ENT Unit I, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Angela Sframeli
- Department of Surgical, Medical and Molecular Pathology, Ophthalmopathy Unit I, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Liborio Torregrossa
- Department of Surgical, Medical and Molecular Pathology, Pathology Unit, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Giamberto Casini
- Department of Surgical, Medical and Molecular Pathology, Ophthalmopathy Unit I, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology, Pathology Unit, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Michele Figus
- Department of Surgical, Medical and Molecular Pathology, Ophthalmopathy Unit I, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Marco Nardi
- Department of Surgical, Medical and Molecular Pathology, Ophthalmopathy Unit I, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Claudio Marcocci
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
| | - Michele Marinò
- Department of Clinical and Experimental Medicine, Endocrinology Unit II, University of Pisa and University Hospital of Pisa, Pisa, Italy
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Lemos MC, Thakker RV. Hypoparathyroidism, deafness, and renal dysplasia syndrome: 20 Years after the identification of the first GATA3 mutations. Hum Mutat 2020; 41:1341-1350. [PMID: 32442337 DOI: 10.1002/humu.24052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/28/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022]
Abstract
The hypoparathyroidism, deafness, and renal dysplasia (HDR) syndrome is an autosomal dominant disorder caused by heterozygous mutations of the GATA3 gene. In the last 20 years, since the identification of the genetic cause of the HDR syndrome, GATA3 mutations have been reported in 124 families (177 patients). The clinical aspects and molecular genetics of the HDR syndrome are reviewed here together with the reported mutations and phenotypes. Reported mutations consist of 40% frameshift deletions or insertions, 23% missense mutations, 14% nonsense mutations, 6% splice-site mutations, 1% in-frame deletions or insertions, 15% whole-gene deletions, and 1% whole-gene duplication. Missense mutations were found to cluster in the regions encoding the two GATA3 zinc-finger domains. Patients showed great clinical variability and the penetrance of each HDR defect increased with age. The most frequently observed abnormality was deafness (93%), followed by hypoparathyroidism (87%) and renal defects (61%). The mean age of diagnosis of HDR was 15.3, 7.5, and 14.0 years, respectively. However, patients with whole-gene deletions and protein-truncating mutations were diagnosed earlier than patients with missense mutations.
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Affiliation(s)
- Manuel C Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Rajesh V Thakker
- Academic Endocrine Unit, Nuffield Department of Clinical Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), Churchill Hospital, University of Oxford, Oxford, UK
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9
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Pandurangan AP, Blundell TL. Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning. Protein Sci 2020; 29:247-257. [PMID: 31693276 PMCID: PMC6933854 DOI: 10.1002/pro.3774] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing methods have not only allowed an understanding of genome sequence variation during the evolution of organisms but have also provided invaluable information about genetic variants in inherited disease and the emergence of resistance to drugs in cancers and infectious disease. A challenge is to distinguish mutations that are drivers of disease or drug resistance, from passengers that are neutral or even selectively advantageous to the organism. This requires an understanding of impacts of missense mutations in gene expression and regulation, and on the disruption of protein function by modulating protein stability or disturbing interactions with proteins, nucleic acids, small molecule ligands, and other biological molecules. Experimental approaches to understanding differences between wild-type and mutant proteins are most accurate but are also time-consuming and costly. Computational tools used to predict the impacts of mutations can provide useful information more quickly. Here, we focus on two widely used structure-based approaches, originally developed in the Blundell lab: site-directed mutator (SDM), a statistical approach to analyze amino acid substitutions, and mutation cutoff scanning matrix (mCSM), which uses graph-based signatures to represent the wild-type structural environment and machine learning to predict the effect of mutations on protein stability. Here, we describe DUET that uses machine learning to combine the two approaches. We discuss briefly the development of mCSM for understanding the impacts of mutations on interfaces with other proteins, nucleic acids, and ligands, and we exemplify the wide application of these approaches to understand human genetic disorders and drug resistance mutations relevant to cancer and mycobacterial infections. STATEMENT FOR A BROADER AUDIENCE: Genetic or somatic changes in genes can lead to mutations in human proteins, which give rise to genetic disorders or cancer, or to genes of pathogens leading to drug resistance. Computer software described here, using statistical approaches or machine learning, uses the information from genome sequencing of humans and pathogens, together with experimental or modeled 3D structures of gene products, the proteins, to predict impacts of mutations in genetic disease, cancer and drug resistance.
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Affiliation(s)
- Arun Prasad Pandurangan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- MRC Laboratory of Molecular BiologyCambridgeUK
| | - Tom L. Blundell
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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Luo J, Zhou T, You X, Zi Y, Li X, Wu Y, Lan Z, Zhi Q, Yi D, Xu L, Li A, Zhong Z, Zhu M, Sun G, Zhu T, Rao J, Lin L, Sang J, Shi Y. Assessing concordance among human, in silico predictions and functional assays on genetic variant classification. Bioinformatics 2019; 35:5163-5170. [PMID: 31141141 DOI: 10.1093/bioinformatics/btz442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/14/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION A variety of in silico tools have been developed and frequently used to aid high-throughput rapid variant classification, but their performances vary, and their ability to classify variants of uncertain significance were not systemically assessed previously due to lack of validation data. This has been changed recently by advances of functional assays, where functional impact of genetic changes can be measured in single-nucleotide resolution using saturation genome editing (SGE) assay. RESULTS We demonstrated the neural network model AIVAR (Artificial Intelligent VARiant classifier) was highly comparable to human experts on multiple verified datasets. Although highly accurate on known variants, AIVAR together with CADD and PhyloP showed non-significant concordance with SGE function scores. Moreover, our results indicated that neural network model trained from functional assay data may not produce accurate prediction on known variants. AVAILABILITY AND IMPLEMENTATION All source code of AIVAR is deposited and freely available at https://github.com/TopGene/AIvar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiaqi Luo
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Tianliangwen Zhou
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Xiaobin You
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Yi Zi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Xiaoting Li
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Yangming Wu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Zhaoji Lan
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Qihuan Zhi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Dandan Yi
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Lei Xu
- Department of General Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ang Li
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Zaixuan Zhong
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Mei Zhu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Gang Sun
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Tao Zhu
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Jianmei Rao
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Luhua Lin
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
| | - Jianfeng Sang
- Department of General Surgery, Nanjing Drum Tower Hospital, Nanjing, Jiangsu, China
| | - Yujian Shi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd, Guangzhou, Guangdong, China
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11
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Coutinho E, Brandão CM, Lemos MC. Combined Pituitary Hormone Deficiency Caused by a Synonymous HESX1 Gene Mutation. J Clin Endocrinol Metab 2019; 104:2851-2854. [PMID: 30888394 DOI: 10.1210/jc.2019-00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/13/2019] [Indexed: 02/05/2023]
Abstract
CONTEXT Mutations in the HESX1 gene can give rise to complex phenotypes that involve variable pituitary hormone deficiencies and other developmental defects. CASE DESCRIPTION A 14-year-old boy presented with short stature and delayed puberty and received a diagnosis of GH deficiency, central hypothyroidism, hypogonadotropic hypogonadism, and secondary adrenal insufficiency. He had anterior pituitary hypoplasia, ectopic posterior pituitary, and an interrupted pituitary stalk. Genetic studies uncovered a heterozygous variant in exon 2 of the HESX1 gene (c.219C>T; p.Ser73Ser). This single base change was predicted to be synonymous at the translational level but was shown to cause skipping of exon 2 in the RNA transcript. CONCLUSIONS This study of a patient with combined pituitary hormone deficiency revealed an unusual synonymous mutation of the HESX1 gene leading to abnormal RNA processing and indicates the importance of investigating silent variants that at first glance appear to be benign.
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Affiliation(s)
- Eduarda Coutinho
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | | | - Manuel Carlos Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
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12
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Nfonsam L, Ordorica S, Ghani M, Potter R, Schaffer A, Daoud H, Vasli N, Chisholm C, Sinclair-Bourque E, McGowan-Jordan J, Smith AC, Jarinova O, Bronicki L. Leveraging the power of new molecular technologies in the clinical setting requires unprecedented awareness of limitations and drawbacks: experience of one diagnostic laboratory. J Med Genet 2018; 56:408-412. [PMID: 30242101 DOI: 10.1136/jmedgenet-2018-105443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/27/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Advances in molecular technologies and in-silico variant prediction tools offer wide-ranging opportunities in diagnostic settings, yet they also present with significant limitations. OBJECTIVE Here, we contextualise the limitations of next-generation sequencing (NGS), multiplex ligation-dependent probe amplification (MLPA) and in-silico prediction tools routinely used by diagnostic laboratories by reviewing specific experiences from our diagnostic laboratory. METHODS We investigated discordant annotations and/or incorrect variant 'callings' in exons of 56 genes constituting our cardiomyopathy and connective tissue disorder NGS panels. Discordant variants and segmental duplications (SD) were queried using the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool and the University of California Santa Cruz genome browser, respectively, to identify regions of high homology. Discrepant variant analyses by in-silico models were re-evaluated using updated file entries. RESULTS We observed a 5% error rate in MYH7 variant 'calling' using MLPA, which resulted from >90% homology of the MYH7 probe-binding site to MYH6. SDs were detected in TTN, PKP2 and MYLK. SDs in MYLK presented the highest risk (15.7%) of incorrect variant 'calling'. The inaccurate 'callings' and discrepant in-silico predictions were resolved following detailed investigation into the source of error. CONCLUSION Recognising the limitations described here may help avoid incorrect diagnoses and leverage the power of new molecular technologies in diagnostic settings.
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Affiliation(s)
- Landry Nfonsam
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Shelley Ordorica
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Mahdi Ghani
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Ryan Potter
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Audrey Schaffer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Hussein Daoud
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nasim Vasli
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Caitlin Chisholm
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Jean McGowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda C Smith
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Lucas Bronicki
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Panoutsopoulou K, Wheeler E. Key Concepts in Genetic Epidemiology. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1793:7-24. [PMID: 29876888 DOI: 10.1007/978-1-4939-7868-7_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Genetic epidemiology is a discipline closely allied to traditional epidemiology that deals with the analysis of the familial distribution of traits. It emerged in the mid-1980s bringing together approaches and techniques developed in mathematical and quantitative genetics, medical and population genetics, statistics and epidemiology. The purpose of this chapter is to familiarize the reader with key concepts in genetic epidemiology as applied at present to unveil the familial and genetic determinants of disease and the joint effects of genes and environmental exposures.
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Affiliation(s)
- Kalliope Panoutsopoulou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, United Kingdom.
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, United Kingdom
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14
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Raraigh KS, Han ST, Davis E, Evans TA, Pellicore MJ, McCague AF, Joynt AT, Lu Z, Atalar M, Sharma N, Sheridan MB, Sosnay PR, Cutting GR. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. Am J Hum Genet 2018; 102:1062-1077. [PMID: 29805046 DOI: 10.1016/j.ajhg.2018.04.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/30/2018] [Indexed: 12/22/2022] Open
Abstract
Missense DNA variants have variable effects upon protein function. Consequently, interpreting their pathogenicity is challenging, especially when they are associated with disease variability. To determine the degree to which functional assays inform interpretation, we analyzed 48 CFTR missense variants associated with variable expressivity of cystic fibrosis (CF). We assessed function in a native isogenic context by evaluating CFTR mutants that were stably expressed in the genome of a human airway cell line devoid of endogenous CFTR expression. 21 of 29 variants associated with full expressivity of the CF phenotype generated <10% wild-type CFTR (WT-CFTR) function, a conservative threshold for the development of life-limiting CF lung disease, and five variants had moderately decreased function (10% to ∼25% WT-CFTR). The remaining three variants in this group unexpectedly had >25% WT-CFTR function; two were higher than 75% WT-CFTR. As expected, 14 of 19 variants associated with partial expressivity of CF had >25% WT-CFTR function; however, four had minimal to no effect on CFTR function (>75% WT-CFTR). Thus, 6 of 48 (13%) missense variants believed to be disease causing did not alter CFTR function. Functional studies substantially refined pathogenicity assignment with expert annotation and criteria from the American College of Medical Genetics and Genomics and Association for Molecular Pathology. However, four algorithms (CADD, REVEL, SIFT, and PolyPhen-2) could not differentiate between variants that caused severe, moderate, or minimal reduction in function. In the setting of variable expressivity, these results indicate that functional assays are essential for accurate interpretation of missense variants and that current prediction tools should be used with caution.
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15
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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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16
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Bean LJH, Hegde MR. Clinical implications and considerations for evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines. Genome Med 2017; 9:111. [PMID: 29254502 PMCID: PMC5733812 DOI: 10.1186/s13073-017-0508-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Clinical genetics laboratories have recently adopted guidelines for the interpretation of sequence variants set by the American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP). The use of in silico algorithms to predict whether amino acid substitutions result in human disease is inconsistent across clinical laboratories. The clinical genetics community must carefully consider how in silico predictions can be incorporated into variant interpretation in clinical practice. Please see related Research article: https://doi.org/10.1186/s13059-017-1353-5
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Affiliation(s)
- Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA. .,EGL Genetics, Tucker, GA, USA.
| | - Madhuri R Hegde
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,PerkinElmer Genetics, Pittsburgh, PA, USA
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17
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Naik AS, Owsianka A, Palmer BA, O’Halloran CJ, Walsh N, Crosbie O, Kenny-Walsh E, Patel AH, Fanning LJ. Reverse epitope mapping of the E2 glycoprotein in antibody associated hepatitis C virus. PLoS One 2017; 12:e0175349. [PMID: 28558001 PMCID: PMC5448734 DOI: 10.1371/journal.pone.0175349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/24/2017] [Indexed: 12/20/2022] Open
Abstract
The humoral immune system responds to chronic hepatitis C virus (HCV) infection by producing neutralising antibodies (nAb). In this study we generated three HCV pseudoparticles in which E1E2 glycoprotein sequence was targeted by the host humoral immune system. We used patient derived virus free Fabs (VF-Fabs) obtained from HCV genotype 1a (n = 3), genotype 1b (n = 7) and genotype 3a (n = 1) for neutralisation of HCVpp produced in this study both individually and in combination. Based on the available anti-HCV monoclonal nAb mapping information we selected amino acid region 384-619 for conformational epitope mapping. Amongst our notable findings, we observed significant reduction in HCVpp infectivity (p<0.05) when challenged with a combination of inter genotype and subtype VF-Fabs. We also identified five binding motifs targeted by patient derived VF-Fab upon peptide mapping, of which two shared the residues with previously reported epitopes. One epitope lies within an immunodominant HVR1 and two were novel. In summary, we used a reverse epitope mapping strategy to identify preferred epitopes by the host humoral immune system. Additionally, we have combined different VF-Fabs to further reduce the HCVpp infectivity. Our data indicates that combining the antigen specificity of antibodies may be a useful strategy to reduce (in-vitro) infectivity.
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Affiliation(s)
- Amruta S. Naik
- Department of Medicine, University College Cork, Cork, Ireland
| | - Ania Owsianka
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Nicole Walsh
- Department of Medicine, University College Cork, Cork, Ireland
| | - Orla Crosbie
- Department of Hepatology, Cork University Hospital, Cork, Ireland
| | | | - Arvind H. Patel
- MRC—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Liam J. Fanning
- Department of Medicine, University College Cork, Cork, Ireland
- APC-Microbiome Institute, University College Cork, Cork, Ireland
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18
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Dalin MG, Engström PG, Ivarsson EG, Unneberg P, Light S, Schaufelberger M, Gilljam T, Andersson B, Bergo MO. Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy. Int J Cardiol 2017; 228:742-748. [DOI: 10.1016/j.ijcard.2016.11.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/05/2016] [Indexed: 01/13/2023]
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19
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Nishizaki SS, Boyle AP. Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms. Trends Genet 2016; 33:34-45. [PMID: 27939749 DOI: 10.1016/j.tig.2016.10.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/30/2016] [Accepted: 10/31/2016] [Indexed: 11/18/2022]
Abstract
One of the formative goals of genetics research is to understand how genetic variation leads to phenotypic differences and human disease. Genome-wide association studies (GWASs) bring us closer to this goal by linking variation with disease faster than ever before. Despite this, GWASs alone are unable to pinpoint disease-causing single nucleotide polymorphisms (SNPs). Noncoding SNPs, which represent the majority of GWAS SNPs, present a particular challenge. To address this challenge, an array of computational tools designed to prioritize and predict the function of noncoding GWAS SNPs have been developed. However, fewer than 40% of GWAS publications from 2015 utilized these tools. We discuss several leading methods for annotating noncoding variants and how they can be integrated into research pipelines in hopes that they will be broadly applied in future GWAS analyses.
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Affiliation(s)
- Sierra S Nishizaki
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
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20
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Kraker J, Viswanathan SK, Knöll R, Sadayappan S. Recent Advances in the Molecular Genetics of Familial Hypertrophic Cardiomyopathy in South Asian Descendants. Front Physiol 2016; 7:499. [PMID: 27840609 PMCID: PMC5083855 DOI: 10.3389/fphys.2016.00499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/12/2016] [Indexed: 12/14/2022] Open
Abstract
The South Asian population, numbered at 1.8 billion, is estimated to comprise around 20% of the global population and 1% of the American population, and has one of the highest rates of cardiovascular disease. While South Asians show increased classical risk factors for developing heart failure, the role of population-specific genetic risk factors has not yet been examined for this group. Hypertrophic cardiomyopathy (HCM) is one of the major cardiac genetic disorders among South Asians, leading to contractile dysfunction, heart failure, and sudden cardiac death. This disease displays autosomal dominant inheritance, and it is associated with a large number of variants in both sarcomeric and non-sarcomeric proteins. The South Asians, a population with large ethnic diversity, potentially carries region-specific polymorphisms. There is high variability in disease penetrance and phenotypic expression of variants associated with HCM. Thus, extensive studies are required to decipher pathogenicity and the physiological mechanisms of these variants, as well as the contribution of modifier genes and environmental factors to disease phenotypes. Conducting genotype-phenotype correlation studies will lead to improved understanding of HCM and, consequently, improved treatment options for this high-risk population. The objective of this review is to report the history of cardiovascular disease and HCM in South Asians, present previously published pathogenic variants, and introduce current efforts to study HCM using induced pluripotent stem cell-derived cardiomyocytes, next-generation sequencing, and gene editing technologies. The authors ultimately hope that this review will stimulate further research, drive novel discoveries, and contribute to the development of personalized medicine with the aim of expanding therapeutic strategies for HCM.
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Affiliation(s)
- Jessica Kraker
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Shiv Kumar Viswanathan
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
| | - Ralph Knöll
- AstraZeneca R&D Mölndal, Innovative Medicines and Early Development, Cardiovascular and Metabolic Diseases iMedMölndal, Sweden; Integrated Cardio Metabolic Centre, Karolinska Institutet, Myocardial Genetics, Karolinska University Hospital in HuddingeHuddinge, Sweden
| | - Sakthivel Sadayappan
- Department of Internal Medicine, Heart, Lung and Vascular Institute, Division of Cardiovascular Health and Sciences, University of Cincinnati College of Medicine Cincinnati, OH, USA
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21
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Hu B, Yang YCT, Huang Y, Zhu Y, Lu ZJ. POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res 2016; 45:D104-D114. [PMID: 28053162 PMCID: PMC5210617 DOI: 10.1093/nar/gkw888] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 01/01/2023] Open
Abstract
We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e.g., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and gene expression and function. Moreover, POSTAR provides a friendly, multi-mode, integrated search interface, which helps users to connect multiple RBP binding sites with post-transcriptional regulatory events, phenotypes, and diseases. Based on our platform, we were able to obtain novel insights into post-transcriptional regulation, such as the putative association between CPSF6 binding, RNA structural domains, and Li-Fraumeni syndrome SNPs. In summary, POSTAR represents an early effort to systematically annotate post-transcriptional regulatory maps and explore the putative roles of RBPs in human diseases.
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Affiliation(s)
- Boqin Hu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu-Cheng T Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095-1554, USA
| | - Yiming Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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22
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Smedley D, Schubach M, Jacobsen J, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington N, McMurry J, Haendel M, Mungall C, Lewis S, Groza T, Valentini G, Robinson P. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet 2016; 99:595-606. [PMID: 27569544 DOI: 10.1016/j.ajhg.2016.07.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/01/2016] [Indexed: 12/17/2022] Open
Abstract
The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Overall, Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease.
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23
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Spielmann M, Mundlos S. Looking beyond the genes: the role of non-coding variants in human disease. Hum Mol Genet 2016; 25:R157-R165. [PMID: 27354350 DOI: 10.1093/hmg/ddw205] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Over the past decades the search for disease causing variants has been focusing exclusively on the coding genome. This highly selective approach has been extremely successful resulting in the identification of thousands of disease genes, but ignores the functional and therefore disease relevance of the rest of the genome. Dropping sequencing costs and new high-throughput technologies such as ChIP-seq and chromosome conformation capture have opened new possibilities for the systematic investigation of the non-coding genome. These data have revealed the importance of non-coding DNA in fundamental processes such as gene regulation and 3D chromatin folding. Research into the principles of chromatin folding has revealed a domain structure of the genome, called topologically associated domains that provide a scaffold for enhancer promoter contacts. Non-coding mutations that affect regulatory elements can affect gene regulation by a loss of function, resulting in reduced gene expression, or a gain of function resulting in gene mis- or overexpression. Structural variations such as deletions, inversions or duplications have the potential to disturb normal chromatin folding. This may lead to the repositioning or disruption of topological associating domains and the relocation of enhancer elements with consecutive gene misexpression. Several recent studies highlight this as important disease mechanisms in developmental disorders and cancer. Therefore, the regulatory landscape of the genome has to be taken into consideration when investigating the pathology of human disease. In this review, we will discuss the recent discoveries in the field of non-coding variation, gene regulation, 3D genome architecture, and their implications for human genetics.
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Affiliation(s)
- Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
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24
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Pons T, Vazquez M, Matey-Hernandez ML, Brunak S, Valencia A, Izarzugaza JM. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily. BMC Genomics 2016; 17 Suppl 2:396. [PMID: 27357839 PMCID: PMC4928150 DOI: 10.1186/s12864-016-2723-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background The association between aberrant signal processing by protein kinases and human diseases such as cancer was established long time ago. However, understanding the link between sequence variants in the protein kinase superfamily and the mechanistic complex traits at the molecular level remains challenging: cells tolerate most genomic alterations and only a minor fraction disrupt molecular function sufficiently and drive disease. Results KinMutRF is a novel random-forest method to automatically identify pathogenic variants in human kinases. Twenty six decision trees implemented as a random forest ponder a battery of features that characterize the variants: a) at the gene level, including membership to a Kinbase group and Gene Ontology terms; b) at the PFAM domain level; and c) at the residue level, the types of amino acids involved, changes in biochemical properties, functional annotations from UniProt, Phospho.ELM and FireDB. KinMutRF identifies disease-associated variants satisfactorily (Acc: 0.88, Prec:0.82, Rec:0.75, F-score:0.78, MCC:0.68) when trained and cross-validated with the 3689 human kinase variants from UniProt that have been annotated as neutral or pathogenic. All unclassified variants were excluded from the training set. Furthermore, KinMutRF is discussed with respect to two independent kinase-specific sets of mutations no included in the training and testing, Kin-Driver (643 variants) and Pon-BTK (1495 variants). Moreover, we provide predictions for the 848 protein kinase variants in UniProt that remained unclassified. A public implementation of KinMutRF, including documentation and examples, is available online (http://kinmut2.bioinfo.cnio.es). The source code for local installation is released under a GPL version 3 license, and can be downloaded from https://github.com/Rbbt-Workflows/KinMut2. Conclusions KinMutRF is capable of classifying kinase variation with good performance. Predictions by KinMutRF compare favorably in a benchmark with other state-of-the-art methods (i.e. SIFT, Polyphen-2, MutationAssesor, MutationTaster, LRT, CADD, FATHMM, and VEST). Kinase-specific features rank as the most elucidatory in terms of information gain and are likely the improvement in prediction performance. This advocates for the development of family-specific classifiers able to exploit the discriminatory power of features unique to individual protein families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2723-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tirso Pons
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Miguel Vazquez
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - María Luisa Matey-Hernandez
- Center for Biological Sequence Analysis (CBS), Systems Biology Department, Technical University of Denmark (DTU), Kemitorvet, Building 208, 2800 Kgs., Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis (CBS), Systems Biology Department, Technical University of Denmark (DTU), Kemitorvet, Building 208, 2800 Kgs., Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Jose Mg Izarzugaza
- Center for Biological Sequence Analysis (CBS), Systems Biology Department, Technical University of Denmark (DTU), Kemitorvet, Building 208, 2800 Kgs., Lyngby, Denmark.
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25
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Dalgleish R. LSDBs and How They Have Evolved. Hum Mutat 2016; 37:532-9. [DOI: 10.1002/humu.22979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/18/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Raymond Dalgleish
- Department of Genetics; University of Leicester; Leicester United Kingdom
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26
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Butkiewicz M, Bush WS. In Silico Functional Annotation of Genomic Variation. CURRENT PROTOCOLS IN HUMAN GENETICS 2016; 88:6.15.1-6.15.17. [PMID: 26724722 PMCID: PMC4722816 DOI: 10.1002/0471142905.hg0615s88] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This unit describes the concepts and practical techniques for annotating genomic variants in the human genome to estimate their functional significance. With the rapid increase of available whole exome and whole genome sequencing information for human studies, annotation techniques have become progressively more important for highlighting and prioritizing nucleotide variants and their potential impact on genes and other genetic constructs. Here, we present an overview of different types of variant annotation approaches and elaborate on their foundations, assumptions, and the downstream consequences of their use. Computational approaches and tools to assign annotations and to identify variants are reviewed. Further, the general philosophy of assigning potential function to a genetic change within the biological context of a disease is discussed.
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Affiliation(s)
- Mariusz Butkiewicz
- Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio
| | - William S Bush
- Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio
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Cunha MLR, Meijers JCM, Middeldorp S. Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism. Thromb Haemost 2015; 114:920-32. [PMID: 26446408 DOI: 10.1160/th15-05-0411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/26/2015] [Indexed: 12/13/2022]
Abstract
Despite knowledge of various inherited risk factors associated with venous thromboembolism (VTE), no definite cause can be found in about 50% of patients. The application of data-driven searches such as GWAS has not been able to identify genetic variants with implications for clinical care, and unexplained heritability remains. In the past years, the development of several so-called next generation sequencing (NGS) platforms is offering the possibility of generating fast, inexpensive and accurate genomic information. However, so far their application to VTE has been very limited. Here we review basic concepts of NGS data analysis and explore the application of NGS technology to VTE. We provide both computational and biological viewpoints to discuss potentials and challenges of NGS-based studies.
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Affiliation(s)
- Marisa L R Cunha
- Marisa L. R. Cunha, Department of Experimental Vascular Medicine, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands, Tel.: +31 20 5662824, Fax: +31 20 6968833, E-mail:
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Abstract
Heart failure is highly influenced by heritability, and nearly 100 genes link to familial cardiomyopathy. Despite the marked genetic diversity that underlies these complex cardiovascular phenotypes, several key genes and pathways have emerged. Hypertrophic cardiomyopathy is characterized by increased contractility and a greater energetic cost of cardiac output. Dilated cardiomyopathy is often triggered by mutations that disrupt the giant protein titin. The energetic consequences of these mutations offer molecular targets and opportunities for new drug development and gene correction therapies.
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Affiliation(s)
- Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - David Y Barefield
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA
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