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Mutational Profiles of F8 and F9 in a Cohort of Haemophilia A and Haemophilia B Patients in the Multi-ethnic Malaysian Population. Mediterr J Hematol Infect Dis 2018; 10:e2018056. [PMID: 30210749 PMCID: PMC6131101 DOI: 10.4084/mjhid.2018.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
Background Haemophilia A (HA) and Haemophilia B (HB) are X-linked blood disorders that are caused by various mutations in the factor VIII (F8) and factor IX (F9) genes respectively. Identification of mutations is essential as some of the mutations are associated with the development of inhibitors. This study is the first comprehensive study of the F8 mutational profile in Malaysia. Materials and methods We analysed 100 unrelated HA and 15 unrelated HB patients for genetic alterations in the F8 and F9 genes by using the long-range PCR, DNA sequencing, and the multiplex-ligation-dependent probe amplification assays. The prediction software was used to confirm the effects of these mutations on factor VIII and IX proteins. Results 44 (53%) of the severe HA patients were positive for F8 intron 22 inversion, and three (3.6%) were positive for intron one inversion. There were 22 novel mutations in F8, including missense (8), frameshift (9), splice site (3), large deletion (1) and nonsense (1) mutations. In HB patients, four novel mutations were identified including the splice site (1), small deletion (1), large deletion (1) and missense (1) mutation. Discussion The mutational spectrum of F8 in Malaysian patients is heterogeneous, with a slightly higher frequency of intron 22 inversion in these severe HA patients when compared to other Asian populations. Identification of these mutational profiles in F8 and F9 genes among Malaysian patients will provide a useful reference for the early detection and diagnosis of HA and HB in the Malaysian population.
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González-Porras J, Jiménez C, Benito R, Ordoñez GR, Álvarez-Román M, Fontecha ME, Janusz K, Castillo D, Fisac R, García-Frade L, Aguilar C, Martínez P, Bermejo N, Herrero S, Balanzategui A, Martin-Antorán J, Ramos R, Cebeiro M, Pardal E, Aguilera C, Pérez-Gutierrez B, Prieto M, Riesco S, Mendoza M, Benito A, Benito-Sendin A, Jimenez-Yuste V, Hernández-Rivas J, García-Sanz R, González-Díaz M, Sarasquete M, Bastida J. Application of a molecular diagnostic algorithm for haemophilia A and B using next-generation sequencing of entire F8, F9 and VWF genes. Thromb Haemost 2017; 117:66-74. [DOI: 10.1160/th16-05-0375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/17/2016] [Indexed: 12/30/2022]
Abstract
SummaryCurrently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes. The proposed algorithm includes the detection of inversions of introns 1 and 22, an NGS custom panel (the entire F8, F9 and VWF genes), and multiplex ligation-dependent probe amplification (MLPA) analysis. A total of 102 samples (97 FVIII- and FIX-deficient patients, and five female carriers) were studied. IVS-22 screening identified 11 out of 20 severe HA patients and one female carrier. IVS-1 analysis did not reveal any alterations. The NGS approach gave positive results in 88 cases, allowing the differential diagnosis of mild/moderate HA and VWD in eight cases. MLPA confirmed one large exon deletion. Only one case did have no pathogenic variants. The proposed algorithm had an overall success rate of 99 %. In conclusion, our evaluation demonstrates that this algorithm can reliably identify pathogenic variants and diagnose patients with HA, HB or VWD.Supplementary Material to this article is available online at www.thrombosis-online.com.
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Guo ZP, Yang LH, Qin XY, Liu XE, Chen JF, Zhang YF. Comprehensive analysis of phenotypes and genetics in 21 Chinese families with haemophilia B: characterization of five novel mutations. Haemophilia 2014; 20:859-65. [PMID: 25251685 DOI: 10.1111/hae.12534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Abstract
Molecular characterization of haemophilia B (HB) at the factor IX gene (F9) is essential to establish diagnosis, confirm genotype-phenotype correlations and to advise in genetic counselling. This study aimed to identify the causative mutations in 21 Chinese families with HB and to analyse the association of these mutations with clinical phenotype. Phenotypic analyses were performed using one-stage assay for factor IX (FIX) activity (FIX: C) and enzyme-linked immunosorbent assay for FIX antigen (FIX: Ag). Direct sequencing of the F9 gene was carried out. For those suspected to have a large deletion, multiplex ligation-dependent probe amplification (MLPA) was performed. Predicting the causal impact of new changes was studied by bioinformatics approaches. We also assessed the effect of the F9 mutations on the FIX protein structure and function. Causative mutations were detected in all study patients. There were 14 point mutations, three small deletions, one large deletion and one small in-frame duplication that together comprised a total of 19 unique variants, of which five were novel. The structural and functional defects of novel missense and in-frame deletion/duplication mutations were demonstrated by bioinformatics approaches. The 12 missense mutations include five purely quantitative mutations, five predominantly qualitative abnormalities and two combined defects. Our data confirmed the genetic heterogeneity of the F9 mutations. Quantitative missense mutations were found to be in different regions of precursor FIX compared with qualitative and combined ones.
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Affiliation(s)
- Z-P Guo
- Department of Hematology, the Second Hospital of Shanxi Medical University, Taiyuan, China
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Belvini D, Salviato R, Acquila M, Bicocchi MP, Frusconi S, Garagiola I, Sanna V, Santacroce R, Rocino A, Tagariello G. Prenatal diagnosis of haemophilia B: the Italian experience. Haemophilia 2013; 19:898-903. [PMID: 23809776 DOI: 10.1111/hae.12219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2013] [Indexed: 11/29/2022]
Abstract
This article describes prenatal diagnosis (PND) of haemophilia B (HB) within the framework of Italian haemophilia centres and genetics laboratories. The study details the experience from six haemophilia genetic centres (three in the North, one in the Centre and two in the South of Italy) and summarizes the different techniques used to perform PND of HB during the last 15 years. To date, the Italian HB database includes 373 characterized unrelated patients and their genetic information has permitted the identification of 274 carriers of childbearing age. This database represents the main instrument for timely and precise PND. Sixty-six prenatal diagnoses were performed on 52 HB carriers whose average age at the time was 34 (ranging from 24 to 44 years). In 44 cases, genetic counselling for carrier status determination was performed before pregnancy, while eight were not studied prior to pregnancy. Foetal samples were obtained by chorionic villus sampling in 52 cases, by amniocentesis in 12 while two were diagnosed by analysis of free foetal DNA obtained from maternal peripheral blood. In 35 (53%) pregnancies the foetus was female. For 31 men (47%), haemophilia status was determined by analysis of previously determined informative markers or familial mutations (12 affected and 19 unaffected). There may be more than one laboratory involved in the PND diagnostic pathway (providing DNA extraction, karyotype analysis, gender determination, maternal contamination detection, molecular diagnosis and sequencing). Good communication between all the parties, coordinated by the haemophilia centre, is essential for a successful and rapid process.
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Affiliation(s)
- D Belvini
- Dipartimento di Laboratorio, Servizio Trasfusionale, Centro per le Malattie del Sangue e Presidio Regionale Malattie rare per le Coagulopatie Congenite, Castelfranco Veneto Hospital (TV), Castelfranco Veneto, Italy
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Spectrum of F9 mutations in Chinese haemophilia B patients: identification of 20 novel mutations. Pathology 2012; 44:342-347. [DOI: 10.1097/pat.0b013e328353443d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 10/23/2011] [Accepted: 11/06/2011] [Indexed: 12/30/2022]
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Doss C GP. In silico profiling of deleterious amino acid substitutions of potential pathological importance in haemophlia A and haemophlia B. J Biomed Sci 2012; 19:30. [PMID: 22423892 PMCID: PMC3361463 DOI: 10.1186/1423-0127-19-30] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 03/16/2012] [Indexed: 01/08/2023] Open
Abstract
Background In this study, instead of current biochemical methods, the effects of deleterious amino acid substitutions in F8 and F9 gene upon protein structure and function were assayed by means of computational methods and information from the databases. Deleterious substitutions of F8 and F9 are responsible for Haemophilia A and Haemophilia B which is the most common genetic disease of coagulation disorders in blood. Yet, distinguishing deleterious variants of F8 and F9 from the massive amount of nonfunctional variants that occur within a single genome is a significant challenge. Methods We performed an in silico analysis of deleterious mutations and their protein structure changes in order to analyze the correlation between mutation and disease. Deleterious nsSNPs were categorized based on empirical based and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for analysis of protein structure stability. Results Out of 510 nsSNPs in F8, 378 nsSNPs (74%) were predicted to be 'intolerant' by SIFT, 371 nsSNPs (73%) were predicted to be 'damaging' by PolyPhen and 445 nsSNPs (87%) as 'less stable' by I-Mutant2.0. In F9, 129 nsSNPs (78%) were predicted to be intolerant by SIFT, 131 nsSNPs (79%) were predicted to be damaging by PolyPhen and 150 nsSNPs (90%) as less stable by I-Mutant2.0. Overall, we found that I-Mutant which emphasizes support vector machine based method outperformed SIFT and PolyPhen in prediction of deleterious nsSNPs in both F8 and F9. Conclusions The models built in this work would be appropriate for predicting the deleterious amino acid substitutions and their functions in gene regulation which would be useful for further genotype-phenotype researches as well as the pharmacogenetics studies. These in silico tools, despite being helpful in providing information about the nature of mutations, may also function as a first-pass filter to determine the substitutions worth pursuing for further experimental research in other coagulation disorder causing genes.
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Affiliation(s)
- George Priya Doss C
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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Xiao L, Sun W, Zhang J, Zhou Y, Chen L, Gao H, Sirois P, Li K. An excess of G over C nucleotides in mutagenesis of human genetic diseases. Mol Biotechnol 2011; 48:1-6. [PMID: 20878503 DOI: 10.1007/s12033-010-9341-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Strand asymmetries in DNA evolution, including indel and single nucleotide substitutions, were reported in prokaryotes. Recently, an excess of G>A over C>T substitutions in hemophilia B patients was recognized in our molecular diagnostic practices. Further analysis demonstrated biased point mutations between sense and antisense strands when unique changes in factor IX were counted. Similar mutation spectra of factor IX and the HGMD prompted us to speculate that the excess of G>A over C>T may be present in genes other than factor IX. Data from nine genes (each has ≥ 100 missense mutations) retrieved from HGMD, international factor IX database, and Dr. Sommer's lab database in the City of Hope National Medical Center, Duarte, CA, USA were analyzed for their point mutation spectra. Similar to factor IX, all genes selected in this study have biased G>A over C>T unique mutations when nonsense mutations were excluded. The biased missense point mutations were recently convincingly documented by the statistic data of categorized missense mutation in HGMD. The consistence of the genetic observation and the genomic data from HGMD strongly indicate that biased point mutations, possibly a phenotypic selection, are more widespread than previously thought. The biased mutations have immediate clinical impact in molecular diagnostics.
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Affiliation(s)
- Li Xiao
- Department of Molecular Diagnostics, College of Pharmacy, Soochow University, Suzhou 215004, Jiangsu, China
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Affiliation(s)
- P Green
- Department of Medical & Molecular Genetics, Kings College London, London, UK.
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JENKINS PV, EGAN H, KEENAN C, OSHEA E, SMITH OP, NOLAN B, WHITE B, ODONNELL J. Mutation analysis of haemophilia B in the Irish population: increased prevalence caused by founder effect. Haemophilia 2008; 14:717-22. [DOI: 10.1111/j.1365-2516.2008.01765.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Karimipoor M, Zeinali S, Nafissi N, Tuddenham EGD, Lak M, Safaee R. Identification of factor IX mutations in Iranian haemophilia B patients by SSCP and sequencing. Thromb Res 2007; 120:135-9. [PMID: 17014892 DOI: 10.1016/j.thromres.2006.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2006] [Revised: 06/10/2006] [Accepted: 07/23/2006] [Indexed: 10/24/2022]
Abstract
Different kinds of mutations, mostly point mutations, in the coagulation factor IX (FIX) gene F9 result in a recessive X-linked bleeding disorder known as haemophilia B. In this study, molecular analysis of 76 unrelated Iranian haemophilia B patients was performed by PCR, single strand conformational polymorphism (SSCP) on important functional regions of the F9 gene followed by sequencing on samples with different migration pattern. Using this approach we found mutation in 52 out of 76 patients. Our data showed that the pathologic mechanisms are heterogeneous as recorded for patients in haemophilia B mutation database and seven of the mutations are previously undescribed.
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Affiliation(s)
- Morteza Karimipoor
- Biotechnology Research Centre, Pasteur Institute of Iran, Tehran 13164, Iran.
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Mitchell M, Keeney S, Goodeve A. The molecular analysis of haemophilia B: a guideline from the UK haemophilia centre doctors' organization haemophilia genetics laboratory network. Haemophilia 2005; 11:398-404. [PMID: 16011594 DOI: 10.1111/j.1365-2516.2005.01112.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Haemophilia B is one of the most common inherited bleeding disorders and has a well understood pathophysiology. Our understanding of the molecular genetics of the disease has allowed the development of comprehensive carrier and prenatal diagnosis for this single gene disorder. Continuing technological developments improve our ability to provide genetic analysis in a rapid and cost-effective manner. This guideline aims to provide advice on current best laboratory practice when approaching genetic diagnosis of haemophilia B.
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Affiliation(s)
- M Mitchell
- Molecular Genetics Unit, Reference Centre for Haemostatic and Thrombotic Disorders, St. Thomas' Hospital, London, UK.
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Castaldo G, Nardiello P, Bellitti F, Rocino A, Coppola A, di Minno G, Salvatore F. Denaturing HPLC procedure for factor IX gene scanning. Clin Chem 2003; 49:815-8. [PMID: 12709378 DOI: 10.1373/49.5.815] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Giuseppe Castaldo
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli "Federico II" and CEINGE-Biotecnologie Avanzate, I-80131 Napoli, Italy
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Castaldo G, Nardiello P, Bellitti F, Santamaria R, Rocino A, Coppola A, di Minno G, Salvatore F. Haemophilia B: from molecular diagnosis to gene therapy. Clin Chem Lab Med 2003; 41:445-51. [PMID: 12747585 DOI: 10.1515/cclm.2003.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Thanks to its typical expression, haemophilia can be identified in writings from the second century AD. Haemophilia B, an X-linked recessive bleeding disorder due to factor IX (FIX) deficiency, has an incidence of about 1:30,000 live male births. The factor 9 (F9) gene was mapped in 1984 on Xq27.1. Haemophilia is diagnosed from prothrombin time, activated partial thromboplastin time, and FIX levels. Carrier females are usually asymptomatic and must be identified only with molecular analysis. Linkage analysis of F9 polymorphisms is rapid and inexpensive but limited by non-informative families, recombinant events, and the high incidence of germline mutations; thus, various procedures have been used for the direct scan of F9 mutations. We set up a novel denaturing high performance liquid chromatographic procedure to scan the F9 gene. This rapid, reproducible procedure detected F9 mutations in 100% of a preliminary cohort of 18 haemophilia B patients. Parallel to the development of more efficient diagnostic tools, the life expectancy and reproductive fitness of haemophilic patients have greatly improved and will continue to improve thanks to the use of less immunogenic recombinant FIX. Hopefully, new approaches based on gene therapy now being evaluated in clinical trials will revolutionise haemophilia B treatment.
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Affiliation(s)
- Giuseppe Castaldo
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II and CEINGE-Biotecnologie avanzate, Napoli, Italy.
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