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Next-generation sequencing of hereditary hemochromatosis-related genes: Novel likely pathogenic variants found in the Portuguese population. Blood Cells Mol Dis 2016; 61:10-5. [PMID: 27667161 DOI: 10.1016/j.bcmd.2016.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 02/07/2023]
Abstract
Hereditary hemochromatosis (HH) is an autosomal recessive disorder characterized by excessive iron absorption resulting in pathologically increased body iron stores. It is typically associated with common HFE gene mutation (p.Cys282Tyr and p.His63Asp). However, in Southern European populations up to one third of HH patients do not carry the risk genotypes. This study aimed to explore the use of next-generation sequencing (NGS) technology to analyse a panel of iron metabolism-related genes (HFE, TFR2, HJV, HAMP, SLC40A1, and FTL) in 87 non-classic HH Portuguese patients. A total of 1241 genetic alterations were detected corresponding to 53 different variants, 13 of which were not described in the available public databases. Among them, five were predicted to be potentially pathogenic: three novel mutations in TFR2 [two missense (p.Leu750Pro and p.Ala777Val) and one intronic splicing mutation (c.967-1G>C)], one missense mutation in HFE (p.Tyr230Cys), and one mutation in the 5'-UTR of HAMP gene (c.-25G>A). The results reported here illustrate the usefulness of NGS for targeted iron metabolism-related gene panels, as a likely cost-effective approach for molecular genetics diagnosis of non-classic HH patients. Simultaneously, it has contributed to the knowledge of the pathophysiology of those rare iron metabolism-related disorders.
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Porto G, Brissot P, Swinkels DW, Zoller H, Kamarainen O, Patton S, Alonso I, Morris M, Keeney S. EMQN best practice guidelines for the molecular genetic diagnosis of hereditary hemochromatosis (HH). Eur J Hum Genet 2016; 24:479-95. [PMID: 26153218 PMCID: PMC4929861 DOI: 10.1038/ejhg.2015.128] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 12/14/2022] Open
Abstract
Molecular genetic testing for hereditary hemochromatosis (HH) is recognized as a reference test to confirm the diagnosis of suspected HH or to predict its risk. The vast majority (typically >90%) of patients with clinically characterized HH are homozygous for the p.C282Y variant in the HFE gene, referred to as HFE-related HH. Since 1996, HFE genotyping was implemented in diagnostic algorithms for suspected HH, allowing its early diagnosis and prevention. However, the penetrance of disease in p.C282Y homozygotes is incomplete. Hence, homozygosity for p.C282Y is not sufficient to diagnose HH. Neither is p.C282Y homozygosity required for diagnosis as other rare forms of HH exist, generally referred to as non-HFE-related HH. These pose significant challenges when defining criteria for referral, testing protocols, interpretation of test results and reporting practices. We present best practice guidelines for the molecular genetic diagnosis of HH where recommendations are classified, as far as possible, according to the level and strength of evidence. For clarification, the guidelines' recommendations are preceded by a detailed description of the methodology and results obtained with a series of actions taken in order to achieve a wide expert consensus, namely: (i) a survey on the current practices followed by laboratories offering molecular diagnosis of HH; (ii) a systematic literature search focused on some identified controversial topics; (iii) an expert Best Practice Workshop convened to achieve consensus on the practical recommendations included in the guidelines.
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Affiliation(s)
- Graça Porto
- Center for Predictive and Preventive Genetics (CGPP), Institute of Molecular and Cellular Biology (IBMC), Porto, Portugal
- Clinical Haematology, Hospital Santo António (CHP-HAS) and Department of Molecular Pathology and Immunology, Abel Salazar Institute for Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Pierre Brissot
- Liver Disease Unit, Pontchaillou University Hospital, University of Rennes, and National Reference Centre for Rare Iron Overload Diseases of Genetic Origin, Rennes, France
| | - Dorine W Swinkels
- Department of Laboratory Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Heinz Zoller
- Department of Medicine II, Gastroenterology and Hepatology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Simon Patton
- European Molecular Quality Network (EMQN), Manchester, UK
| | - Isabel Alonso
- Center for Predictive and Preventive Genetics (CGPP), Institute of Molecular and Cellular Biology (IBMC), Porto, Portugal
| | - Michael Morris
- European Molecular Quality Network (EMQN), Manchester, UK
- Synlab, Lausanne, Switzerland
| | - Steve Keeney
- European Molecular Quality Network (EMQN), Manchester, UK
- Molecular Diagnostics Centre (Haematology), Manchester Royal Infirmary, Manchester, UK
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Barton JC, Edwards CQ, Acton RT. HFE gene: Structure, function, mutations, and associated iron abnormalities. Gene 2015; 574:179-92. [PMID: 26456104 PMCID: PMC6660136 DOI: 10.1016/j.gene.2015.10.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 10/04/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023]
Abstract
The hemochromatosis gene HFE was discovered in 1996, more than a century after clinical and pathologic manifestations of hemochromatosis were reported. Linked to the major histocompatibility complex (MHC) on chromosome 6p, HFE encodes the MHC class I-like protein HFE that binds beta-2 microglobulin. HFE influences iron absorption by modulating the expression of hepcidin, the main controller of iron metabolism. Common HFE mutations account for ~90% of hemochromatosis phenotypes in whites of western European descent. We review HFE mapping and cloning, structure, promoters and controllers, and coding region mutations, HFE protein structure, cell and tissue expression and function, mouse Hfe knockouts and knockins, and HFE mutations in other mammals with iron overload. We describe the pertinence of HFE and HFE to mechanisms of iron homeostasis, the origin and fixation of HFE polymorphisms in European and other populations, and the genetic and biochemical basis of HFE hemochromatosis and iron overload.
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Affiliation(s)
- James C Barton
- Southern Iron Disorders Center, Birmingham, AL, USA and Department of Medicine; University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Corwin Q Edwards
- Department of Medicine, Intermountain Medical Center and University of Utah, Salt Lake City, UT, USA.
| | - Ronald T Acton
- Southern Iron Disorders Center, Birmingham, AL, USA and Department of Medicine; Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
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van Gammeren A, de Baar E, Schrauwen L, van Wijngaarden P. Compound heterozygous C282Y/Q283P and Q283P/H63D mutations in haemochromatosis. Br J Haematol 2015; 171:650-1. [PMID: 25850353 DOI: 10.1111/bjh.13417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ellen de Baar
- Department of Clinical Chemistry and Haematology, Breda, the Netherlands
| | - Lianne Schrauwen
- Department of Clinical Chemistry and Haematology, Breda, the Netherlands
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Silva B, Martins R, Proença D, Fleming R, Faustino P. The functional significance of E277K and V295A HFE mutations. Br J Haematol 2012; 158:399-408. [DOI: 10.1111/j.1365-2141.2012.09164.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/15/2012] [Indexed: 12/12/2022]
Affiliation(s)
- Bruno Silva
- Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa; Portugal
| | - Rute Martins
- Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa; Portugal
| | - Daniela Proença
- Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa; Portugal
| | - Rita Fleming
- Serviço de Imuno-hemoterapia; Hospital de Santa Maria; Lisboa; Portugal
| | - Paula Faustino
- Departamento de Genética; Instituto Nacional de Saúde Dr. Ricardo Jorge; Lisboa; Portugal
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Aguilar-Martinez P, Grandchamp B, Cunat S, Cadet E, Blanc F, Nourrit M, Lassoued K, Schved JF, Rochette J. Iron overload in HFE C282Y heterozygotes at first genetic testing: a strategy for identifying rare HFE variants. Haematologica 2011; 96:507-14. [PMID: 21228038 DOI: 10.3324/haematol.2010.029751] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Heterozygotes for the p.Cys282Tyr (C282Y) mutation of the HFE gene do not usually express a hemochromatosis phenotype. Apart from the compound heterozygous state for C282Y and the widespread p.His63Asp (H63D) variant allele, other rare HFE mutations can be found in trans on chromosome 6. DESIGN AND METHODS We performed molecular investigation of the genes implicated in hereditary hemochromatosis in six patients who presented with iron overload but were simple heterozygotes for the HFE C282Y mutation at first genetic testing. Functional impairment of new variants was deduced from computational methods including molecular modeling studies. RESULTS We identified four rare HFE mutant alleles, three of which have not been previously described. One mutation is a 13-nucleotide deletion in exon 6 (c.1022_1034del13, p.His341_Ala345 > LeufsX119), which is predicted to lead to an elongated and unstable protein. The second one is a substitution of the last nucleotide of exon 2 (c.340G > A, p.Glu114Lys) which modifies the relative solvent accessibility in a loop interface. The third mutation, p.Arg67Cys, also lies in exon 2 and introduces a destabilization of the secondary structure within a loop of the α1 domain. We also found the previously reported c.548T > C (p.Leu183Pro) missense mutation in exon 3. No other known iron genes were mutated. We present an algorithm at the clinical and genetic levels for identifying patients deserving further investigation. Conclusions Our results suggest that additional mutations in HFE may have a clinical impact in C282Y carriers. In conjunction with results from previously described cases we conclude that an elevated transferrin saturation level and elevated hepatic iron index should indicate the utility of searching for further HFE mutations in C282Y heterozygotes prior to other iron gene studies.
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Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics 2010; 11:548. [PMID: 21059217 PMCID: PMC2992548 DOI: 10.1186/1471-2105-11-548] [Citation(s) in RCA: 690] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/08/2010] [Indexed: 11/24/2022] Open
Abstract
Background Many newly detected point mutations are located in protein-coding regions of the human genome. Knowledge of their effects on the protein's 3D structure provides insight into the protein's mechanism, can aid the design of further experiments, and eventually can lead to the development of new medicines and diagnostic tools. Results In this article we describe HOPE, a fully automatic program that analyzes the structural and functional effects of point mutations. HOPE collects information from a wide range of information sources including calculations on the 3D coordinates of the protein by using WHAT IF Web services, sequence annotations from the UniProt database, and predictions by DAS services. Homology models are built with YASARA. Data is stored in a database and used in a decision scheme to identify the effects of a mutation on the protein's 3D structure and function. HOPE builds a report with text, figures, and animations that is easy to use and understandable for (bio)medical researchers. Conclusions We tested HOPE by comparing its output to the results of manually performed projects. In all straightforward cases HOPE performed similar to a trained bioinformatician. The use of 3D structures helps optimize the results in terms of reliability and details. HOPE's results are easy to understand and are presented in a way that is attractive for researchers without an extensive bioinformatics background.
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Genetic and metabolic factors are associated with increased hepatic iron stores in a selected population of p.Cys282Tyr heterozygotes. Blood Cells Mol Dis 2010; 44:159-63. [DOI: 10.1016/j.bcmd.2010.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 11/30/2009] [Accepted: 12/18/2009] [Indexed: 12/31/2022]
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Abstract
Haemochromatosis should currently refer to hereditary iron overload disorders presenting with a definite and common phenotype characterised by normal erythropoiesis, increased transferrin saturation and ferritin and primarily parenchymal iron deposition related to innate low (but normally regulated) production of the hepatic peptide hormone hepcidin. Since the discovery of the haemochromatosis gene (HFE) in 1996, several novel gene defects have been detected, explaining the mechanism and diversity of iron overload diseases. Overall, at least four main types of hereditary haemochromatosis (HH) have been identified. This review describes the systematic diagnostic and therapeutic strategy and pitfalls for patients suspected for HH and their relatives.
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Affiliation(s)
- M C H Janssen
- Radboud University Medical Centre, Department of General Internal Medicine 463, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
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Mendes AI, Ferro A, Martins R, Picanço I, Gomes S, Cerqueira R, Correia M, Nunes AR, Esteves J, Fleming R, Faustino P. Non-classical hereditary hemochromatosis in Portugal: novel mutations identified in iron metabolism-related genes. Ann Hematol 2008; 88:229-34. [PMID: 18762941 DOI: 10.1007/s00277-008-0572-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 07/21/2008] [Indexed: 12/01/2022]
Abstract
The most frequent genotype associated with Hereditary hemochromatosis is the homozygosity for C282Y, a common HFE mutation. However, other mutations in HFE, transferrin receptor 2 (TFR2), hemojuvelin (HJV) and hepcidin (HAMP) genes, have also been reported in association with this pathology. A mutational analysis of these genes was carried out in 215 Portuguese iron-overloaded individuals previously characterized as non-C282Y or non-H63D homozygous and non-compound heterozygous. The aim was to determine the influence of these genes in the development of iron overload phenotypes in our population. Regarding HFE, some known mutations were found, as S65C and E277K. In addition, three novel missense mutations (L46W, D129N and Y230F) and one nonsense mutation (Y138X) were identified. In TFR2, besides the I238M polymorphism and the rare IVS5 -9T-->A mutation, a novel missense mutation was detected (F280L). Concerning HAMP, the deleterious mutation 5'UTR -25G-->A was found once, associated with Juvenile Hemochromatosis. In HJV, the A310G polymorphism, the novel E275E silent alteration and the novel putative splicing mutation (IVS2 +395C-->G) were identified. In conclusion, only a few number of mutations which can be linked to iron overload was found, revealing their modest contribution for the development of this phenotype in our population, and suggesting that their screening in routine diagnosis is not cost-effective.
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Affiliation(s)
- Ana Isabel Mendes
- Human Genetics Centre, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
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