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Aloi C, Salina A, Caroli F, Bocciardi R, Tappino B, Bassi M, Minuto N, d'Annunzio G, Maghnie M. Next Generation Sequencing (NGS) Target Approach for Undiagnosed Dysglycaemia. Life (Basel) 2023; 13:life13051080. [PMID: 37240725 DOI: 10.3390/life13051080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the field of genomics and created new opportunities for basic research. We described the strategy for the NGS validation of the "dysglycaemia panel" composed by 44 genes related to glucose metabolism disorders (MODY, Wolfram syndrome) and familial renal glycosuria using Ion AmpliSeq technology combined with Ion-PGM. Anonymized DNA of 32 previously genotyped cases with 33 different variants were used to optimize the methodology. Standard protocol was used to generate the primer design, library, template preparation, and sequencing. Ion Reporter tool was used for data analysis. In all the runs, the mean coverage was over 200×. Twenty-nine out of thirty three variants (96.5%) were detected; four frameshift variants were missed. All point mutations were detected with high sensitivity. We identified three further variants of unknown significance in addition to pathogenic mutations previously identified by Sanger sequencing. The NGS panel allowed us to identify pathogenic variants in multiple genes in a short time. This could help to identify several defects in children and young adults that have to receive the genetic diagnosis necessary for optimal treatment. In order not to lose any pathogenic variants, Sanger sequencing is included in our analytical protocol to avoid missing frameshift variants.
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Affiliation(s)
- Concetta Aloi
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Alessandro Salina
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Francesco Caroli
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Renata Bocciardi
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
| | - Barbara Tappino
- LABSIEM (Laboratory for the Study of Inborn Errors of Metabolism), IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Marta Bassi
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Nicola Minuto
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Giuseppe d'Annunzio
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Mohamad Maghnie
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16100 Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
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Bonnefond A, Semple RK. Achievements, prospects and challenges in precision care for monogenic insulin-deficient and insulin-resistant diabetes. Diabetologia 2022; 65:1782-1795. [PMID: 35618782 PMCID: PMC9522735 DOI: 10.1007/s00125-022-05720-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 01/19/2023]
Abstract
Integration of genomic and other data has begun to stratify type 2 diabetes in prognostically meaningful ways, but this has yet to impact on mainstream diabetes practice. The subgroup of diabetes caused by single gene defects thus provides the best example to date of the vision of 'precision diabetes'. Monogenic diabetes may be divided into primary pancreatic beta cell failure, and primary insulin resistance. In both groups, clear examples of genotype-selective responses to therapy have been advanced. The benign trajectory of diabetes due to pathogenic GCK mutations, and the sulfonylurea-hyperresponsiveness conferred by activating KCNJ11 or ABCC8 mutations, or loss-of-function HNF1A or HNF4A mutations, often decisively guide clinical management. In monogenic insulin-resistant diabetes, subcutaneous leptin therapy is beneficial in some severe lipodystrophy. Increasing evidence also supports use of 'obesity therapies' in lipodystrophic people even without obesity. In beta cell diabetes the main challenge is now implementation of the precision diabetes vision at scale. In monogenic insulin-resistant diabetes genotype-specific benefits are proven in far fewer patients to date, although further genotype-targeted therapies are being evaluated. The conceptual paradigm established by the insulin-resistant subgroup with 'adipose failure' may have a wider influence on precision therapy for common type 2 diabetes, however. For all forms of monogenic diabetes, population-wide genome sequencing is currently forcing reappraisal of the importance assigned to pathogenic mutations when gene sequencing is uncoupled from prior suspicion of monogenic diabetes.
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Affiliation(s)
- Amélie Bonnefond
- Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille University Hospital, Lille, France.
- Université de Lille, Lille, France.
- Department of Metabolism, Imperial College London, London, UK.
| | - Robert K Semple
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Abellan-Schneyder I, Schusser AJ, Neuhaus K. ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. BMC Microbiol 2021; 21:349. [PMID: 34922460 PMCID: PMC8684222 DOI: 10.1186/s12866-021-02391-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. RESULTS Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. CONCLUSION Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared.
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Affiliation(s)
- Isabel Abellan-Schneyder
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Andrea Janina Schusser
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.
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Ding Y, Li N, Lou D, Zhang Q, Chang G, Li J, Li X, Li Q, Huang X, Wang J, Jiang F, Wang X. Clinical and genetic analysis in a Chinese cohort of children and adolescents with diabetes/persistent hyperglycemia. J Diabetes Investig 2020; 12:48-62. [PMID: 32531870 PMCID: PMC7779271 DOI: 10.1111/jdi.13322] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022] Open
Abstract
Aims/Introduction To investigate the genetic etiology and evaluate the diagnostic application of next‐generation sequencing for diabetes/persistent hyperglycemia in children and adolescents. Materials and Methods Patients with diabetes/persistent hyperglycemia, presenting with at least one other clinical manifestation (other than diabetes) or with a family history of diabetes, were recruited. The clinical and laboratory characteristics of the patients were recorded. Next‐generation sequencing was carried out, and candidate variants were verified by Sanger sequencing. Variant pathogenicity was further evaluated according to the American College of Medical Genetics and Genomics guidelines. Results This study included 101 potential probands, 36 of whom were identified as positive by genetic testing. A further 51.2 and 20.9% of variants were determined to be pathogenic or likely pathogenic, respectively. Variants associated with the disease were primarily identified in 21 genes and three regions of copy number variants. Among the 39 variants in 21 genes, 61.5% (24/39) were novel. The genetic diagnosis of 23 patients was confirmed based on genetic evidence and associated clinical manifestations. We reported GCK variants (21.7%, 5/23) as the most common etiology in our cohort. Different clinical manifestations were observed in one family with WFS1 variants. Conclusions Our findings support the use of next‐generation sequencing as a standard method in patients with diabetes/persistent hyperglycemia and provide insights into the etiologies of these conditions.
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Affiliation(s)
- Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dan Lou
- Department of Pediatrics, the First Affiliated Hospital of Henan University of Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qianwen Zhang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guoying Chang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xin Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qun Li
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaodong Huang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fan Jiang
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Vaxillaire M, Froguel P, Bonnefond A. How Recent Advances in Genomics Improve Precision Diagnosis and Personalized Care of Maturity-Onset Diabetes of the Young. Curr Diab Rep 2019; 19:79. [PMID: 31385057 DOI: 10.1007/s11892-019-1202-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Non-autoimmune monogenic diabetes (MD) in young people shows a broad spectrum of clinical presentations, which is largely explained by multiple genetic etiologies. This review discusses how the application of state-of-the-art genomics research to precision diagnosis of MD, particularly the various subtypes of maturity-onset diabetes of the young (MODY), has increasingly informed diabetes precision medicine and patient care throughout life. RECENT FINDINGS Due to extended genetic and clinical heterogeneity of MODY, diagnosis approaches based on next-generation sequencing have been worthwhile to better ascribe a specific subtype to each patient with young-onset diabetes. This guides the best appropriate treatment and clinical follow-up. Early etiological diagnosis of MD and individualized treatment are essential for achieving metabolic targets and avoiding long-term diabetes complications, as well as for drastically decreasing the financial and societal burden of diabetes-related healthcare. Genomic medicine-based practices help to optimize long-term clinical follow-up and patient care management.
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Affiliation(s)
- Martine Vaxillaire
- Univ. Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - European Genomic Institute for Diabetes (EGID), University Lille, F-59000, Lille, France.
- Faculty of Medicine, CNRS UMR 8199, 1 Place de Verdun, F-59045, Lille, France.
| | - Philippe Froguel
- Univ. Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - European Genomic Institute for Diabetes (EGID), University Lille, F-59000, Lille, France
- Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, UK
| | - Amélie Bonnefond
- Univ. Lille, CNRS, CHU Lille, Institut Pasteur de Lille, UMR 8199 - European Genomic Institute for Diabetes (EGID), University Lille, F-59000, Lille, France
- Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, UK
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Abstract
Obesity and excess weight are a pandemic phenomenon in the modern world. Childhood and adolescent obesity often ends up in obesity in adults. The costs of obesity and its consequences are staggering for any society, crippling for countries in development. Childhood obesity is also widespread in Macedonia. Metabolic syndrome, dyslipidemia and carbohydrate intolerance are found in significant numbers. Parents and grandparents are often obese. Some of the children are either dysmorphic, or slightly retarded. We have already described patients with Prader-Willi syndrome, Bardet-Biedl syndrome or WAGR syndrome. A genetic screening for mutations in monogenic obesity in children with early, rapid-onset or severe obesity, severe hyperphagia, hypogonadism, intestinal dysfunction, hypopigmentation of hair and skin, postprandial hypoglycaemia, diabetes insipidus, abnormal leptin level and coexistence of lean and obese siblings in the family discovers many genetic forms of obesity. There are about 30 monogenic forms of obesity. In addition, obesity is different in ethnic groups, and the types of monogenic obesity differ. In brief, an increasing number of genes and genetic mechanisms in children continue to be discovered. This sheds new light on the molecular mechanisms of obesity and potentially gives a target for new forms of treatment.
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First Report of Diabetes Phenotype due to a Loss-of-Function ABCC8 Mutation Previously Known to Cause Congenital Hyperinsulinism. Case Rep Genet 2019; 2019:3654618. [PMID: 31110826 PMCID: PMC6487141 DOI: 10.1155/2019/3654618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 12/19/2022] Open
Abstract
Monogenic Diabetes is relatively rare, representing only 1-2% of total diabetes cases; nevertheless, it is often misdiagnosed primarily as type 1 diabetes, leading to unnecessary insulin therapy and delayed recognition of affected family members. In the present article, we describe a case of a young, male patient who presented with hyperglycemia in the absence of ketosis and following genetic testing; he proved to harbor the loss-of-function p.Arg1353His (c.4058G>A) mutation in the ABCC8 gene, inherited from his mother. This mutation has been previously described in patients with Congenital Hyperinsulinism. Furthermore, different mutations in the ABCC8 gene have been linked with MODY 12, type 2, and gestational diabetes; however, to the best of our knowledge, this is the first report that associates this specific mutation with diabetes phenotype. ABCC8-related diabetes is characterized by remarkable heterogeneity in terms of clinical presentation and therapeutic approach. Early diagnosis and individualized treatment are essential to achieving metabolic targets and avoiding long-term diabetes complications.
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Abstract
PURPOSE OF REVIEW Monogenic forms of diabetes have received increased attention and genetic testing is more widely available; however, many patients are still misdiagnosed as having type 1 (T1D) or type 2 diabetes. This review will address updates to monogenic diabetes prevalence, identification, treatment, and genetic testing. RECENT FINDINGS The creation of a T1D genetic risk score and the use of noninvasive urinary C-peptide creatinine ratios have provided new tools to aid in the discrimination of possible monogenic diabetes from likely T1D. Early, high-dose sulfonylurea treatment in infants with a KCNJ11 or ABCC8 mutation continues to be well tolerated and effective. As the field moves towards more comprehensive genetic testing methods, there is an increased opportunity to identify novel genetic causes. Genetic testing results continue to allow for personalized treatment but should provide patient information at an appropriate health literacy level. SUMMARY Although there have been clinical and genetic advances in monogenic diabetes, patients are still misdiagnosed. Improved insurance coverage of genetic testing is needed. The majority of data on monogenic diabetes has been collected from Caucasian populations, therefore, research studies should endeavor to include broader ethnic and racial diversity to provide comprehensive information for all populations.
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Johnson SR, Leo PJ, McInerney-Leo AM, Anderson LK, Marshall M, McGown I, Newell F, Brown MA, Conwell LS, Harris M, Duncan EL. Whole-exome sequencing for mutation detection in pediatric disorders of insulin secretion: Maturity onset diabetes of the young and congenital hyperinsulinism. Pediatr Diabetes 2018; 19:656-662. [PMID: 29417725 DOI: 10.1111/pedi.12638] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 11/18/2017] [Accepted: 12/17/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND To assess the utility of whole-exome sequencing (WES) for mutation detection in maturity-onset diabetes of the young (MODY) and congenital hyperinsulinism (CHI). MODY and CHI are the two commonest monogenic disorders of glucose-regulated insulin secretion in childhood, with 13 causative genes known for MODY and 10 causative genes identified for CHI. The large number of potential genes makes comprehensive screening using traditional methods expensive and time-consuming. METHODS Ten subjects with MODY and five with CHI with known mutations underwent WES using two different exome capture kits (Nimblegen SeqCap EZ Human v3.0 Exome Enrichment Kit, Nextera Rapid Capture Exome Kit). Analysis was blinded to previously identified mutations, and included assessment for large deletions. The target capture of five exome capture technologies was also analyzed using sequencing data from >2800 unrelated samples. RESULTS Four of five MODY mutations were identified using Nimblegen (including a large deletion in HNF1B). Although targeted, one mutation (in INS) had insufficient coverage for detection. Eleven of eleven mutations (six MODY, five CHI) were identified using Nextera Rapid (including the previously missed mutation). On reconciliation, all mutations concorded with previous data and no additional variants in MODY genes were detected. There were marked differences in the performance of the capture technologies. CONCLUSIONS WES can be useful for screening for MODY/CHI mutations, detecting both point mutations and large deletions. However, capture technologies require careful selection.
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Affiliation(s)
- S R Johnson
- Department of Endocrinology, Lady Cilento Children's Hospital, South Brisbane, Australia.,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia.,Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - P J Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - A M McInerney-Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - L K Anderson
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - M Marshall
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - I McGown
- Department of Pathology, Mater Health Services, South Brisbane, Australia
| | - F Newell
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - M A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia
| | - L S Conwell
- Department of Endocrinology, Lady Cilento Children's Hospital, South Brisbane, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - M Harris
- Department of Endocrinology, Lady Cilento Children's Hospital, South Brisbane, Australia.,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Woolloongabba, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - E L Duncan
- Faculty of Medicine, University of Queensland, Brisbane, Australia.,Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia.,Department of Endocrinology, Royal Brisbane and Women's Hospital, Brisbane, Australia
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da Fonseca ACP, Mastronardi C, Johar A, Arcos-Burgos M, Paz-Filho G. Genetics of non-syndromic childhood obesity and the use of high-throughput DNA sequencing technologies. J Diabetes Complications 2017; 31:1549-1561. [PMID: 28735903 DOI: 10.1016/j.jdiacomp.2017.04.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Childhood obesity is a serious public health problem associated with the development of several chronic diseases, such as type 2 diabetes mellitus, dyslipidemia, and hypertension. The elevated prevalence of obesity is mostly due to inadequate diet and lifestyle, but it is also influenced by genetic factors. OBJECTIVES To review recent advances in the field of the genetics of obesity. We summarize the list of genes associated with the rare non-syndromic forms of obesity, and explain their function. Furthermore, we discuss the technologies that are available for the genetic diagnosis of obesity. RESULTS Several studies reported that single gene variants cause Mendelian forms of obesity, determined by mutations of major effect in single genes. Rare, non-syndromic forms of obesity are a result of loss-of-function mutations in genes that act on the development and function of the hypothalamus or the leptin-melanocortin pathway. These variants disrupt enzymes and receptors that play a role in energy homeostasis, resulting in severe early-onset obesity and endocrine dysfunctions. Different approaches and technologies have been used to understand the genetic background of obesity. Currently, whole genome and whole exome sequencing are important diagnostic tools to identify new genes and variants associated with severe obesity, but other approaches are also useful at individual or population levels, such as linkage analysis, candidate gene sequencing, chromosomal microarray analysis, and genome-wide association studies. CONCLUSIONS The understanding of the genetic causes of obesity and the usefulness and limitations of the genetic diagnostic approaches can contribute to the development of new personalized therapeutic targets against obesity.
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Affiliation(s)
| | - Claudio Mastronardi
- Institute of Translational Medicine, Universidad del Rosario, Bogota, Colombia
| | - Angad Johar
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Australia.
| | | | - Gilberto Paz-Filho
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Australia.
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Sheu C, Paramithiotis E. Towards a personalized assessment of pancreatic function in diabetes. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2017.1385391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Carey Sheu
- Caprion Biosciences Inc - Translational Research, Montreal, Canada
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12
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Astuti D, Sabir A, Fulton P, Zatyka M, Williams D, Hardy C, Milan G, Favaretto F, Yu-Wai-Man P, Rohayem J, López de Heredia M, Hershey T, Tranebjaerg L, Chen JH, Chaussenot A, Nunes V, Marshall B, McAfferty S, Tillmann V, Maffei P, Paquis-Flucklinger V, Geberhiwot T, Mlynarski W, Parkinson K, Picard V, Bueno GE, Dias R, Arnold A, Richens C, Paisey R, Urano F, Semple R, Sinnott R, Barrett TG. Monogenic diabetes syndromes: Locus-specific databases for Alström, Wolfram, and Thiamine-responsive megaloblastic anemia. Hum Mutat 2017; 38:764-777. [PMID: 28432734 PMCID: PMC5535005 DOI: 10.1002/humu.23233] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 12/24/2022]
Abstract
We developed a variant database for diabetes syndrome genes, using the Leiden Open Variation Database platform, containing observed phenotypes matched to the genetic variations. We populated it with 628 published disease-associated variants (December 2016) for: WFS1 (n = 309), CISD2 (n = 3), ALMS1 (n = 268), and SLC19A2 (n = 48) for Wolfram type 1, Wolfram type 2, Alström, and Thiamine-responsive megaloblastic anemia syndromes, respectively; and included 23 previously unpublished novel germline variants in WFS1 and 17 variants in ALMS1. We then investigated genotype-phenotype relations for the WFS1 gene. The presence of biallelic loss-of-function variants predicted Wolfram syndrome defined by insulin-dependent diabetes and optic atrophy, with a sensitivity of 79% (95% CI 75%-83%) and specificity of 92% (83%-97%). The presence of minor loss-of-function variants in WFS1 predicted isolated diabetes, isolated deafness, or isolated congenital cataracts without development of the full syndrome (sensitivity 100% [93%-100%]; specificity 78% [73%-82%]). The ability to provide a prognostic prediction based on genotype will lead to improvements in patient care and counseling. The development of the database as a repository for monogenic diabetes gene variants will allow prognostic predictions for other diabetes syndromes as next-generation sequencing expands the repertoire of genotypes and phenotypes. The database is publicly available online at https://lovd.euro-wabb.org.
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Affiliation(s)
- Dewi Astuti
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ataf Sabir
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Edgbaston, Birmingham, UK
| | - Piers Fulton
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Edgbaston, Birmingham, UK
| | - Malgorzata Zatyka
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Edgbaston, Birmingham, UK
| | - Carol Hardy
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Edgbaston, Birmingham, UK
| | - Gabriella Milan
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | | | - Patrick Yu-Wai-Man
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Newcastle Eye Centre, Royal Victoria Infirmary, Newcastle upon Tyne, UK.,NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London, UK.,Cambridge Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Julia Rohayem
- Centrum für Reproduktionsmedizin und Andrologie, WHO Kollaborationszentrum, EAA, Ausbildungszentrum, Universitätsklinikum Münster, Münster, Germany
| | - Miguel López de Heredia
- IDIBELL, Hospital Duran i Reynals, 3ª Planta, Gran Via de L'Hospitalet, 199, E-08908- L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Raras (CIBERER), U-730, Hospital Duran i Reynals, 3ª Planta, Gran Via de L'Hospitalet, 199, E-08908-L'Hospitalet de Llobregat, Barcelona, Spain
| | - Tamara Hershey
- Departments of Psychiatry, Neurology and Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Lisbeth Tranebjaerg
- Department of Clinical Genetics, University Hospital/The Kennedy Centre, Glostrup, Denmark.,Institute of Clinical Medicine, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jian-Hua Chen
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge, UK
| | - Annabel Chaussenot
- School of Medicine, IRCAN, UMR CNRS 7284/INSERM U1081/UNS, Nice Sophia-Antipolis University, Nice, France
| | - Virginia Nunes
- IDIBELL, Hospital Duran i Reynals, 3ª Planta, Gran Via de L'Hospitalet, 199, E-08908- L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Raras (CIBERER), U-730, Hospital Duran i Reynals, 3ª Planta, Gran Via de L'Hospitalet, 199, E-08908-L'Hospitalet de Llobregat, Barcelona, Spain.,Genetics Section, Physiological Sciences Department, Health Sciences and Medicine Faculty, University of Barcelona
| | - Bess Marshall
- Department of Pediatrics, Washington University School of Medicine, One Children's Place, St. Louis, Missouri
| | | | | | - Pietro Maffei
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | | | - Tarekign Geberhiwot
- Department of Metabolism, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical Centre, Birmingham, UK
| | | | - Kay Parkinson
- Alström Syndrome Europe, Woodpecker Cottage, Paignton, S. Devon, UK
| | - Virginie Picard
- Association syndrome de Wolfram, Residence Gauguin, Grand-Champ, France
| | - Gema Esteban Bueno
- Unidad de Géstion Clínica de Garrucha, Área de Gestión Sanitaria Norte de Almería, Avd. Dra. Parra, Almería, Spain
| | - Renuka Dias
- Birmingham Women's and Children's Hospital, Birmingham, UK
| | - Amy Arnold
- Birmingham Women's and Children's Hospital, Birmingham, UK
| | | | - Richard Paisey
- Diabetes Research Unit, Horizon Centre, Torbay Hospital NHS Foundation Trust, Devon, UK
| | - Fumihiko Urano
- Department of Medicine, Division of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine, St. Louis, Missouri
| | - Robert Semple
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Box 289, Addenbrooke's Hospital, Cambridge, UK
| | - Richard Sinnott
- Department of information and computing systems, The University of Melbourne, Parkville, Australia
| | - Timothy G Barrett
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.,Birmingham Women's and Children's Hospital, Birmingham, UK
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13
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Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clin Sci (Lond) 2017; 130:943-86. [PMID: 27154742 DOI: 10.1042/cs20160136] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
In high-, middle- and low-income countries, the rising prevalence of obesity is the underlying cause of numerous health complications and increased mortality. Being a complex and heritable disorder, obesity results from the interplay between genetic susceptibility, epigenetics, metagenomics and the environment. Attempts at understanding the genetic basis of obesity have identified numerous genes associated with syndromic monogenic, non-syndromic monogenic, oligogenic and polygenic obesity. The genetics of leanness are also considered relevant as it mirrors some of obesity's aetiologies. In this report, we summarize ten genetically elucidated obesity syndromes, some of which are involved in ciliary functioning. We comprehensively review 11 monogenic obesity genes identified to date and their role in energy maintenance as part of the leptin-melanocortin pathway. With the emergence of genome-wide association studies over the last decade, 227 genetic variants involved in different biological pathways (central nervous system, food sensing and digestion, adipocyte differentiation, insulin signalling, lipid metabolism, muscle and liver biology, gut microbiota) have been associated with polygenic obesity. Advances in obligatory and facilitated epigenetic variation, and gene-environment interaction studies have partly accounted for the missing heritability of obesity and provided additional insight into its aetiology. The role of gut microbiota in obesity pathophysiology, as well as the 12 genes associated with lipodystrophies is discussed. Furthermore, in an attempt to improve future studies and merge the gap between research and clinical practice, we provide suggestions on how high-throughput '-omic' data can be integrated in order to get closer to the new age of personalized medicine.
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14
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Genetic Factors of Diabetes. Arch Immunol Ther Exp (Warsz) 2017; 64:157-160. [DOI: 10.1007/s00005-016-0432-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/24/2016] [Indexed: 12/30/2022]
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15
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Vaxillaire M, Froguel P. Monogenic diabetes: Implementation of translational genomic research towards precision medicine. J Diabetes 2016; 8:782-795. [PMID: 27390143 DOI: 10.1111/1753-0407.12446] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/13/2016] [Accepted: 06/29/2016] [Indexed: 12/18/2022] Open
Abstract
Various forms of early onset non-autoimmune diabetes are recognized as monogenic diseases, each subtype being caused by a single highly penetrant gene defect at the individual level. Monogenic diabetes (MD) is clinically and genetically heterogeneous, including maturity onset diabetes of the young and infancy-onset and neonatal diabetes mellitus, which are characterized by functional defects of insulin-producing pancreatic β-cells and hyperglycemia early in life. Depending on the genetic cause, MD differs in the age at diabetes onset, the severity of hyperglycemia, long-term diabetic complications, and extrapancreatic manifestations. In this review we discuss the many challenges of molecular genetic diagnosis of MD in the face of a substantial genetic heterogeneity, as well as the clinical benefit and cost-effectiveness of an early genetic diagnosis, as demonstrated by simulation models based on lifetime complications and treatment costs. We also discuss striking examples of proof-of-concept of genomic medicine, which have enabled marked improvement in patient care and long-term clinical management. Recent advances in genome editing and pluripotent stem cell reprogramming technologies provide new opportunities for in vitro diabetes modeling and the discovery of novel drug targets and cell-based diabetes therapies. A review of these future directions makes the case for exciting translational research to further our understanding of the pathophysiology of early onset diabetes.
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Affiliation(s)
- Martine Vaxillaire
- CNRS-UMR 8199, Integrative Genomics and Modelling of Metabolic Diseases, Pasteur Institute of Lille, Lille, France.
- Lille University, Lille, France.
- European Genomic Institute for Diabetes (EGID), Lille, France.
| | - Philippe Froguel
- CNRS-UMR 8199, Integrative Genomics and Modelling of Metabolic Diseases, Pasteur Institute of Lille, Lille, France
- Lille University, Lille, France
- European Genomic Institute for Diabetes (EGID), Lille, France
- Department of Genomics of Common Diseases, School of Public Health, Imperial College London, Hammersmith Hospital, London, UK
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