51
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ePGA: A Web-Based Information System for Translational Pharmacogenomics. PLoS One 2016; 11:e0162801. [PMID: 27631363 PMCID: PMC5025168 DOI: 10.1371/journal.pone.0162801] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022] Open
Abstract
One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a web-based electronic Pharmacogenomics Assistant (ePGA; http://www.epga.gr/) that provides personalized genotype-to-phenotype translation, linked to state of the art clinical guidelines. ePGA's translation service matches individual genotype-profiles with PGx gene haplotypes and infers the corresponding diplotype and phenotype profiles, accompanied with summary statistics. Additional features include i) the ability to customize translation based on subsets of variants of clinical interest, and ii) to update the knowledge base with novel PGx findings. We demonstrate ePGA's functionality on genetic variation data from the 1000 Genomes Project.
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52
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Winkler EC, Wiemann S. Findings made in gene panel to whole genome sequencing: data, knowledge, ethics – and consequences? Expert Rev Mol Diagn 2016; 16:1259-1270. [DOI: 10.1080/14737159.2016.1212662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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53
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Breton A, Theodorou A, Aktuna S, Sonzogni L, Darling D, Chan L, Menzel S, van der Spek PJ, Swagemakers SMA, Grosveld F, Philipsen S, Thein SL. ASH1L (a histone methyltransferase protein) is a novel candidate globin gene regulator revealed by genetic study of an English family with beta-thalassaemia unlinked to the beta-globin locus. Br J Haematol 2016; 175:525-530. [PMID: 27434206 DOI: 10.1111/bjh.14256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/06/2016] [Indexed: 01/14/2023]
Abstract
In 1993, we described an English family with beta-thalassaemia that was not linked to the beta-globin locus. Whole genome sequence analyses revealed potential causative mutations in 15 different genes, of which 4 were consistently and uniquely associated with the phenotype in all 7 affected family members, also confirmed by genetic linkage analysis. Of the 4 genes, which are present in a centromeric region of chromosome 1, ASH1L was proposed as causative through functional mRNA knock-down and chromatin-immunoprecipitation studies in human erythroid progenitor cells. Our data suggest a putative role for ASH1L (Trithorax protein) in the regulation of globin genes.
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Affiliation(s)
- Amandine Breton
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Andria Theodorou
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Suleyman Aktuna
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - Laura Sonzogni
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | - David Darling
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Lucas Chan
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Stephan Menzel
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK
| | | | | | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Consortium for Systems Biology, Erasmus MC, Rotterdam, The Netherlands.,Centre for Biomedical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.,Netherlands Consortium for Systems Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Swee Lay Thein
- Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences and Medicine, London, SE5 9NU, UK. .,Department of Haematological Medicine, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK.
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54
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Krüppeling erythropoiesis: an unexpected broad spectrum of human red blood cell disorders due to KLF1 variants. Blood 2016; 127:1856-62. [PMID: 26903544 DOI: 10.1182/blood-2016-01-694331] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 02/06/2023] Open
Abstract
Until recently our approach to analyzing human genetic diseases has been to accurately phenotype patients and sequence the genes known to be associated with those phenotypes; for example, in thalassemia, the globin loci are analyzed. Sequencing has become increasingly accessible, and thus a larger panel of genes can be analyzed and whole exome and/or whole genome sequencing can be used when no variants are found in the candidate genes. By using such approaches in patients with unexplained anemias, we have discovered that a broad range of hitherto unrelated human red cell disorders are caused by variants in KLF1, a master regulator of erythropoiesis, which were previously considered to be extremely rare causes of human genetic disease.
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Henderson SJ, Timbs AT, McCarthy J, Gallienne AE, Proven M, Rugless MJ, Lopez H, Eglinton J, Dziedzic D, Beardsall M, Khalil MSM, Old JM. Ten Years of Routine α- and β-Globin Gene Sequencing in UK Hemoglobinopathy Referrals Reveals 60 Novel Mutations. Hemoglobin 2015; 40:75-84. [PMID: 26635043 DOI: 10.3109/03630269.2015.1113990] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We review and report here the genotypes and phenotypes of 60 novel thalassemia and abnormal hemoglobin (Hb) mutations discovered following the adoption of routine DNA sequencing of both α- and β-globin genes for all UK hemoglobinopathy samples referred for molecular investigation. This screening strategy over the last 10 years has revealed a total of 11 new β chain variants, 15 α chain variants, 19 β-thalassemia (β-thal) mutations and 15 α(+)-thalassemia (α(+)-thal) mutations. The large number of new thalassemia alleles confirms the wide racial heterogeneity of mutations in the UK immigrant population. Eleven of the new variants ran with Hb A on high performance liquid chromatography (HPLC), demonstrating the value of routine sequencing of both α- and β-globin genes for all hemoglobinopathy investigations. The new β chain variants are: Hb Bury [β22(B4)Glu → Asp (HBB: c.69A > T)], Hb Fulwood [β35(C1)Tyr → His (HBB: c.106T > C)], Hb Little Venice [β42(CD1)Phe → Cys (HBB: c.128T > G)], Hb Cork [β57(E1)Asn → Ser (HBB: c.173A > G), Hb Basingstoke [β118(GH1)Phe → Ser (HBB: c.356T > C)], Hb Howden [β20(B2)Val → Ala (HBB: c.62T > C)], Hb Wilton [β41(C7)Phe → Leu (HBB: c.126C > A)], Hb Belsize Park [β120(GH3)Lys → Asn (HBB: c.363A > T)], Hb Hampstead Heath [β2(NA2)His → Gln;β26(B8)Glu → Lys (HBB: c.[6C > G;79G > A])], Hb Grantham [β85(F1)Phe → Cys (HBB: c.257T > G)] and Hb Calgary [β64(E8)Gly → Val (HBB: c.194G > T). The new α chain variants are: Hb Edinburgh [α70(E19)Val → Gly (HBA2: c.212T > G)], Hb Walsgrave [α116(GH4)Glu → Val (HBA2: c.350A > T)], Hb Wexham [α117(GH5) and 118(H1) insertion Ser (HBA1: c.354-355insTCA)], Hb Coombe Park [α127(H10)Lys → Glu (HBA2: c.382A > G)], Hb Oxford [α17(A15)Val → Asp (HBA2: c.53T > A)], Hb Bridlington [α32(B13)Met → Thr (HBA1: c.98T > C), Hb Wolverhampton [α81(F2)Ser → Tyr (HBA2: c.9245C > A)], Hb Little Waltham [α13(A11)Ala → Asp (HBA2: c.41C > A)], Hb Derby [α61(E10)Lys → Arg (HBA1: c.185A > G)], Hb Uttoxter [α74(EF3)Tyr → Asp (HBA2: c.223G > T)], Hb Harehills [α124(H7)Ser → Cys (HBA1: c.374C > G)], Hb Hekinan II [α27(B8)Glu → Asp (HBA1: c.84G > T)], Hb Manitoba IV [α102(G9)Ser → Arg (HBA1: c.307A > C), Hb Witham [α139(HC1)Lys → Arg (HBA2: c.419A > G) and Hb Farnborough [α9(A7)Asn → Asp (HBA1: c.28A > G). In addition, 10 more paralogous α-globin chain variants have been discovered. The novel β-thal alleles are: HBB: c.-138C > G, HBB: c.-121C > T, HBB: c.-80T > G, HBB: c.18_19delTG, HBB: c.219_220insT, HBB: c.315 + 2_315 + 13delTGAGTCTATGGG, HBB: c.316-70C > G, HBB: c.345_346insTGTGCTG, HBB: c.354delC, HBB: c.376-381delCCAGTG, HBB: c.393T > A, HBB: c.394_395insA, HBB: c.375_376insA, HBB: c.*+95_*+107delTGGATTCTinsC, HBB: c.* + 111_*+112delAA, HBB: c.*+112A > T, HBB: c.394C > T, HBB: c.271delG and HBB: c.316-3C > T. The novel α (+ )-thal alleles are: HBA1: c.95+1G > C, HBA1: c.315C > G [Hb Donnington, α104(G11)Cys → Trp], HBA1: c.327delC, HBA1: c.333_345del, HBA1: c.*+96G > A, HBA2: c.2T > G, HBA2: c.112delC, HBA2: c.143delA, HBA2: c.143_146delACCT, HBA2: c.156_157insG, HBA2: c.220_223delGTGG, HBA2: c.305T > C [Hb Bishopstown, α101(G8)Leu → His], HBA2: c.169_170delAA, HBA2: c.1A > T and HBA2: c.-3delA.
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Affiliation(s)
- Shirley J Henderson
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Adele T Timbs
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Janice McCarthy
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Alice E Gallienne
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Melanie Proven
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Michelle J Rugless
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Herminio Lopez
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Jennifer Eglinton
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Dariusz Dziedzic
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Matthew Beardsall
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - Mohamed S M Khalil
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
| | - John M Old
- a National Haemoglobinopathy Reference Laboratory, Biomedical Research Centre Molecular Diagnostic Laboratory, Haematology Department, John Radcliffe Hospital , Oxford , Oxfordshire , UK
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56
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Savige J, Dalgleish R, Cotton RG, den Dunnen JT, Macrae F, Povey S. The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease. Pediatr Nephrol 2015; 30:1893-901. [PMID: 25384529 DOI: 10.1007/s00467-014-2994-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/09/2014] [Accepted: 10/15/2014] [Indexed: 02/02/2023]
Abstract
A recent review identified 60 common inherited renal diseases caused by DNA variants in 132 different genes. These diseases can be diagnosed with DNA sequencing, but each gene probably also has a thousand normal variants. Many more normal variants have been characterised by individual laboratories than are reported in the literature or found in publicly accessible collections. At present, testing laboratories must assess each novel change they identify for pathogenicity, even when this has been done elsewhere previously, and the distinction between normal and disease-associated variants is particularly an issue with the recent surge in exomic sequencing and gene discovery projects. The Human Variome Project recommends the establishment of gene-specific DNA variant databases to facilitate the sharing of DNA variants and decisions about likely disease causation. Databases improve diagnostic accuracy and testing efficiency, and reduce costs. They also help with genotype-phenotype correlations and predictive algorithms. The Human Variome Project advocates databases that use standardised descriptions, are up-to-date, include clinical information and are freely available. Currently, the genes affected in the most common inherited renal diseases correspond to 350 different variant databases, many of which are incomplete or have insufficient clinical details for genotype-phenotype correlations. Assistance is needed from nephrologists to maximise the usefulness of these databases for the diagnosis and management of inherited renal disease.
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Affiliation(s)
- Judy Savige
- The University of Melbourne, Melbourne Health, Melbourne, Australia. .,Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia.
| | | | - Richard Gh Cotton
- Human Variome Project, The University of Melbourne, Melbourne, Australia
| | - Johan T den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Finlay Macrae
- The University of Melbourne, Melbourne Health, Melbourne, Australia.,Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Australia
| | - Sue Povey
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
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57
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Douzgou S, Pollalis YA, Vozikis A, Patrinos GP, Clayton-Smith J. Collaborative Crowdsourcing for the Diagnosis of Rare Genetic Syndromes: The DYSCERNE Experience. Public Health Genomics 2015; 19:19-24. [PMID: 26447648 DOI: 10.1159/000440710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
The big-data revolution is creating a challenge for the provision of services in the health sector to keep pace with the expectations of the general population. Utilization of crowdsourcing can impact positively on the quality, cost and speed of healthcare by involving large sections of professionals and the public and creating novel science within an ethical framework. In 2007, the DYSCERNE project was funded by the European Commission Public Health Executive Agency (EU DG Sanco) aimed at setting up a network of expertise for rare dysmorphic disorders. As part of DYSCERNE, a Dysmorphology Diagnostic System was set up to enable clinicians throughout the EU to submit cases electronically for diagnosis using a secure, web-based interface, hosted at specified access points (submitting nodes), in 26 different European countries. DYSCERNE utilized the process of crowdsourcing international expertise for the clinical diagnosis of very rare genetic syndromes of multiple congenital anomalies. This is the first reported account of collaborative crowd sourcing in dysmorphology, as part of a clinical genetics service.
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Affiliation(s)
- Sofia Douzgou
- Department of Economics, University of Piraeus, Piraeus, Greece
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58
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Shooter C, Rooks H, Thein SL, Clark B. Next generation sequencing identifies a novel rearrangement in the HBB cluster permitting to-the-base characterization. Hum Mutat 2015; 36:142-50. [PMID: 25331561 DOI: 10.1002/humu.22707] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/16/2014] [Indexed: 12/29/2022]
Abstract
Genetic testing for hemoglobinopathies is required for prenatal diagnosis, understanding complex cases where multiple pathogenic variants may be present or investigating cases of unexplained anemia. Characterization of disease causing variants that range from single base changes to large rearrangements may require several different labor-intensive methodologies. Multiplex ligation probe amplification analysis is the current method used to detect indels, but the technique does not characterize the breakpoints or detect balanced translocations. Here, we describe a next-generation sequencing (NGS) method that is able to identify and characterize a novel rearrangement of the HBB cluster responsible for εγδβ thalassemia in an English family. The structural variant involved a 59.0 kb inversion encompassing HBG2 exon 3, HBG1, HBD, HBB, and OR51V1, juxtaposed by a deletion of 122.6 kb including 82 bp of the inverted sequence, HBG2 exon 1 and 2, HBE, and the β-locus control region. Identification of reads spanning the breakpoints provided to-the-base resolution of the rearrangement, subsequently confirmed by gap-PCR and Sanger sequence analysis. The same rearrangement, termed Inv-Del English V εγδβ thalassemia (HbVar 2935), was identified in two other unrelated English individuals with a similar hematological phenotype. Our NGS approach should be applicable as a diagnostic tool for other disorders.
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Affiliation(s)
- Claire Shooter
- King's College London, Faculty of Life Sciences and Medicine, Molecular Haematology, London, UK
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59
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Mitropoulos K, Al Jaibeji H, Forero DA, Laissue P, Wonkam A, Lopez-Correa C, Mohamed Z, Chantratita W, Lee MTM, Llerena A, Brand A, Ali BR, Patrinos GP. Success stories in genomic medicine from resource-limited countries. Hum Genomics 2015; 9:11. [PMID: 26081768 PMCID: PMC4485996 DOI: 10.1186/s40246-015-0033-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/09/2015] [Indexed: 02/08/2023] Open
Abstract
In recent years, the translation of genomic discoveries into mainstream medical practice and public health has gained momentum, facilitated by the advent of new technologies. However, there are often major discrepancies in the pace of implementation of genomic medicine between developed and developing/resource-limited countries. The main reason does not only lie in the limitation of resources but also in the slow pace of adoption of the new findings and the poor understanding of the potential that this new discipline offers to rationalize medical diagnosis and treatment. Here, we present and critically discuss examples from the successful implementation of genomic medicine in resource-limited countries, focusing on pharmacogenomics, genome informatics, and public health genomics, emphasizing in the latter case genomic education, stakeholder analysis, and economics in pharmacogenomics. These examples can be considered as model cases and be readily replicated for the wide implementation of pharmacogenomics and genomic medicine in other resource-limited environments.
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Affiliation(s)
| | - Hayat Al Jaibeji
- University of Maastricht, Maastricht, The Netherlands. .,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.
| | - Paul Laissue
- Unidad de Genética, Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia.
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | | | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Wasun Chantratita
- Department of Pathology, Medical Genomic Center, Ramathibodi Hospital, Faculty of Medicine, Mahidol University, Bangkok, Thailand.
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Adrian Llerena
- CICAB Clinical Research Center, Extremadura University Hospital and Medical School, Badajoz, Spain.
| | - Angela Brand
- University of Maastricht, Maastricht, The Netherlands.
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece.
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60
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A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Sci Rep 2015; 5:10576. [PMID: 26015273 PMCID: PMC4444969 DOI: 10.1038/srep10576] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/20/2015] [Indexed: 12/16/2022] Open
Abstract
Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu
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61
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Sankaran VG, Weiss MJ. Anemia: progress in molecular mechanisms and therapies. Nat Med 2015; 21:221-30. [PMID: 25742458 DOI: 10.1038/nm.3814] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/04/2015] [Indexed: 12/12/2022]
Abstract
Anemia is a major source of morbidity and mortality worldwide. Here we review recent insights into how red blood cells (RBCs) are produced, the pathogenic mechanisms underlying various forms of anemia, and novel therapies derived from these findings. It is likely that these new insights, mainly arising from basic scientific studies, will contribute immensely to both the understanding of frequently debilitating forms of anemia and the ability to treat affected patients. Major worldwide diseases that are likely to benefit from new advances include the hemoglobinopathies (β-thalassemia and sickle cell disease); rare genetic disorders of RBC production; and anemias associated with chronic kidney disease, inflammation, and cancer. Promising new approaches to treatment include drugs that target recently defined pathways in RBC production, iron metabolism, and fetal globin-family gene expression, as well as gene therapies that use improved viral vectors and newly developed genome editing technologies.
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Affiliation(s)
- Vijay G Sankaran
- 1] Division of Hematology and Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [3] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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62
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Nitta T, Kawano F, Yamashiro Y, Takagi F, Murata T, Tanaka T, Ferania M, Adhiyanto C, Hattori Y. A new Krüppel-like factor 1 mutation (c.947G > A or p.C316Y) in humans causes β-thalassemia minor. Hemoglobin 2015; 39:121-6. [PMID: 25690802 DOI: 10.3109/03630269.2015.1008702] [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] [Indexed: 01/12/2023]
Abstract
Here we describe a Japanese patient with mild β-thalassemia (β-thal) with an intact β-globin gene but a new missense mutation of c.947G > A or p.C316Y in the erythroid Krüppel-Like Factor (KLF1) gene which is strongly associated with the expression of the β-globin gene. The association of the KLF1 mutation with β-thal, is here described. The p.C316Y mutation occurred at one of the cysteines that constitute the second zinc finger motif of KLF1, and would have changed the zinc finger conformation to impair the DNA binding properties or the promoter function of the β-globin gene. Our expression study found that the mutant KLF1 gene had a markedly negative effect on the β-globin gene expression, or 7.0% of that of its normal counterpart. A presumed heterozygous state, or equimolar presence of the mutant and normal KLF1s reduced the expression rate to 70.0% of the normal alone. This degree of the decrease may explain the very mild phenotype of the patient's β-thal. Furthermore, the patient's whole-exome analysis using next-generation sequencing revealed that the β-thal defect is caused by only this KLF1 gene mutation. The Hb A2 and Hb F levels that are frequently elevated in KLF1 mutations were elevated by 4.1 and 1.3%, respectively, in this case. The contribution to their elevation by KLF1: p.C316Y is uncertain.
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Affiliation(s)
- Takenori Nitta
- Department of Health Science, Yamaguchi University Graduate School of Medicine , Ube , Japan
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63
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Zaker-Kandjani B, Namdar-Aligoodarzi P, Azarkeivan A, Najmabadi H, Banan M. Mutation Screening of theKrüppel-Like Factor 1Gene Using Single-Strand Conformational Polymorphism in a Cohort of Iranianβ-Thalassemia Patients. Hemoglobin 2015; 39:24-9. [DOI: 10.3109/03630269.2014.991023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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64
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Chao E, Dolinsky J, Pal T. Response to Cragun et al. Clin Genet 2014; 88:201. [PMID: 25381838 DOI: 10.1111/cge.12512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 11/28/2022]
Affiliation(s)
- E Chao
- Department of Pediatrics, University of California, Irvine, CA, USA.,Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - J Dolinsky
- Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - T Pal
- Department of Interdisciplinary Oncology, University of South Florida, Tampa, FL, USA
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65
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Abstract
In this issue of Blood, Liu et al gain an understanding of phenotypic variability in hemoglobinopathies. They find that mutations in Krüppel-like factor-1 (KLF1) are significantly more prevalent in patients with β-thalassemia than previously recognized and correlate with a milder phenotype. This supports the emerging concept that monoallelic KLF1 mutations can play a modulatory role in hemoglobinopathies.
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67
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Thompson R, Johnston L, Taruscio D, Monaco L, Béroud C, Gut IG, Hansson MG, ’t Hoen PBA, Patrinos GP, Dawkins H, Ensini M, Zatloukal K, Koubi D, Heslop E, Paschall JE, Posada M, Robinson PN, Bushby K, Lochmüller H. RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research. J Gen Intern Med 2014; 29 Suppl 3:S780-7. [PMID: 25029978 PMCID: PMC4124112 DOI: 10.1007/s11606-014-2908-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases.
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Affiliation(s)
- Rachel Thompson
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Louise Johnston
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | | | | | - Christophe Béroud
- />Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France
| | - Ivo G. Gut
- />Centre Nacional d’Anàlisi Genòmica, Barcelona, Spain
| | | | | | | | - Hugh Dawkins
- />Office of Population Health Genomics, Department of Health Western Australia, Perth, Australia
| | - Monica Ensini
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | | | | | - Emma Heslop
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Justin E. Paschall
- />European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Manuel Posada
- />Instituto de Salud Carlos III, Instituto de Investigación de Enfermedades Raras, CIBERER, Madrid, Spain
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin, Berlin, Germany
| | - Kate Bushby
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
| | - Hanns Lochmüller
- />Institute of Genetic Medicine, MRC Centre for Neuromuscular Diseases, Newcastle University, London, UK
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68
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Kountouris P, Lederer CW, Fanis P, Feleki X, Old J, Kleanthous M. IthaGenes: an interactive database for haemoglobin variations and epidemiology. PLoS One 2014; 9:e103020. [PMID: 25058394 PMCID: PMC4109966 DOI: 10.1371/journal.pone.0103020] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 06/27/2014] [Indexed: 02/07/2023] Open
Abstract
Inherited haemoglobinopathies are the most common monogenic diseases, with millions of carriers and patients worldwide. At present, we know several hundred disease-causing mutations on the globin gene clusters, in addition to numerous clinically important trans-acting disease modifiers encoded elsewhere and a multitude of polymorphisms with relevance for advanced diagnostic approaches. Moreover, new disease-linked variations are discovered every year that are not included in traditional and often functionally limited locus-specific databases. This paper presents IthaGenes, a new interactive database of haemoglobin variations, which stores information about genes and variations affecting haemoglobin disorders. In addition, IthaGenes organises phenotype, relevant publications and external links, while embedding the NCBI Sequence Viewer for graphical representation of each variation. Finally, IthaGenes is integrated with the companion tool IthaMaps for the display of corresponding epidemiological data on distribution maps. IthaGenes is incorporated in the ITHANET community portal and is free and publicly available at http://www.ithanet.eu/db/ithagenes.
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Affiliation(s)
- Petros Kountouris
- Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Xenia Feleki
- Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - John Old
- Oxford Radcliffe Hospitals NHS Trust, Oxford, United Kingdom
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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69
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Potamias G, Lakiotaki K, Katsila T, Lee MTM, Topouzis S, Cooper DN, Patrinos GP. Deciphering next-generation pharmacogenomics: an information technology perspective. Open Biol 2014; 4:140071. [PMID: 25030607 PMCID: PMC4118603 DOI: 10.1098/rsob.140071] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/19/2014] [Indexed: 01/12/2023] Open
Abstract
In the post-genomic era, the rapid evolution of high-throughput genotyping technologies and the increased pace of production of genetic research data are continually prompting the development of appropriate informatics tools, systems and databases as we attempt to cope with the flood of incoming genetic information. Alongside new technologies that serve to enhance data connectivity, emerging information systems should contribute to the creation of a powerful knowledge environment for genotype-to-phenotype information in the context of translational medicine. In the area of pharmacogenomics and personalized medicine, it has become evident that database applications providing important information on the occurrence and consequences of gene variants involved in pharmacokinetics, pharmacodynamics, drug efficacy and drug toxicity will become an integral tool for researchers and medical practitioners alike. At the same time, two fundamental issues are inextricably linked to current developments, namely data sharing and data protection. Here, we discuss high-throughput and next-generation sequencing technology and its impact on pharmacogenomics research. In addition, we present advances and challenges in the field of pharmacogenomics information systems which have in turn triggered the development of an integrated electronic 'pharmacogenomics assistant'. The system is designed to provide personalized drug recommendations based on linked genotype-to-phenotype pharmacogenomics data, as well as to support biomedical researchers in the identification of pharmacogenomics-related gene variants. The provisioned services are tuned in the framework of a single-access pharmacogenomics portal.
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Affiliation(s)
- George Potamias
- Institute of Computer Science, Foundation for Research and Technology Hellas, Crete, Greece
| | - Kleanthi Lakiotaki
- Institute of Computer Science, Foundation for Research and Technology Hellas, Crete, Greece
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Stavros Topouzis
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece
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70
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Plazzer JP, Sijmons RH, Woods MO, Peltomäki P, Thompson B, Den Dunnen JT, Macrae F. The InSiGHT database: utilizing 100 years of insights into Lynch syndrome. Fam Cancer 2014; 12:175-80. [PMID: 23443670 DOI: 10.1007/s10689-013-9616-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This article provides a historical overview of the online database ( www.insight-group.org/mutations ) maintained by the International Society for Gastrointestinal Hereditary Tumours. The focus is on the mismatch repair genes which are mutated in Lynch Syndrome. APC, MUTYH and other genes are also an important part of the database, but are not covered here. Over time, as the understanding of the genetics of Lynch Syndrome increased, databases were created to centralise and share the variants which were being detected in ever greater numbers. These databases were eventually merged into the InSiGHT database, a comprehensive repository of gene variant and disease phenotype information, serving as a starting point for important endeavours including variant interpretation, research, diagnostics and enhanced global collection. Pivotal to its success has been the collaborative spirit in which it has been developed, its association with the Human Variome Project, the appointment of a full time curator and its governance stemming from the well established organizational structure of InSiGHT.
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Affiliation(s)
- J P Plazzer
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Australia.
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71
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Staikou C, Stavroulakis E, Karmaniolou I. A narrative review of peri-operative management of patients with thalassaemia. Anaesthesia 2014; 69:494-510. [DOI: 10.1111/anae.12591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2013] [Indexed: 01/19/2023]
Affiliation(s)
- C. Staikou
- Department of Anaesthesia; Aretaieio University Hospital; Athens Greece
| | - E. Stavroulakis
- Department of Anaesthesia; Aretaieio University Hospital; Athens Greece
| | - I. Karmaniolou
- Department of Anaesthesia; Royal National Orthopaedic Hospital; Stanmore UK
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72
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Elliott JH, Turner T, Clavisi O, Thomas J, Higgins JPT, Mavergames C, Gruen RL. Living systematic reviews: an emerging opportunity to narrow the evidence-practice gap. PLoS Med 2014; 11:e1001603. [PMID: 24558353 PMCID: PMC3928029 DOI: 10.1371/journal.pmed.1001603] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The current difficulties in keeping systematic reviews up to date leads to considerable inaccuracy, hampering the translation of knowledge into action. Incremental advances in conventional review updating are unlikely to lead to substantial improvements in review currency. A new approach is needed. We propose living systematic review as a contribution to evidence synthesis that combines currency with rigour to enhance the accuracy and utility of health evidence. Living systematic reviews are high quality, up-to-date online summaries of health research, updated as new research becomes available, and enabled by improved production efficiency and adherence to the norms of scholarly communication. Together with innovations in primary research reporting and the creation and use of evidence in health systems, living systematic review contributes to an emerging evidence ecosystem.
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Affiliation(s)
- Julian H. Elliott
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- * E-mail:
| | - Tari Turner
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- World Vision Australia, Melbourne, Australia
| | - Ornella Clavisi
- National Trauma Research Institute, Alfred Hospital, Melbourne, Australia
| | - James Thomas
- EPPI-Centre, Institute of Education, University of London, London, England
| | - Julian P. T. Higgins
- School of Social and Community Medicine, University of Bristol, Bristol, England
- Centre for Reviews and Dissemination, University of York, York, England
| | - Chris Mavergames
- Informatics and Knowledge Management Department, The Cochrane Collaboration, Freiburg, Germany
| | - Russell L. Gruen
- National Trauma Research Institute, Alfred Hospital, Melbourne, Australia
- Department of Surgery, Monash University, Melbourne, Australia
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73
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Moumni I, Zorai A, Mahjoub S, Mosbahi I, Chaouechi D, Benromdhane N, Abbes S. A New δ Chain Variant, Hb A2-Tunis [δ46(CD5)Gly → Glu;HBD: c.140G>A], Observed in a Tunisian Family in Association with a Compound Heterozygosity for Hb C [β6(A3)Glu → Lys;HBB: c.19G>A] β0-Thalassemia [IVS-I-1 (β143, G>A);HBB: c.92+1G>A]. Hemoglobin 2014; 38:88-90. [DOI: 10.3109/03630269.2013.872123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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74
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Cutting GR. Annotating DNA variants is the next major goal for human genetics. Am J Hum Genet 2014; 94:5-10. [PMID: 24387988 PMCID: PMC3882730 DOI: 10.1016/j.ajhg.2013.12.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Indexed: 12/29/2022] Open
Abstract
Clinical genetic testing has undergone a dramatic transformation in the past two decades. Diagnostic laboratories that previously tested for well-established disease-causing DNA variants in a handful of genes have evolved into sequencing factories identifying thousands of variants of known and unknown medical consequence. Sorting out what does and does not cause disease in our genomes is the next great challenge in making genetics a central feature of healthcare. I propose that closing the gap in our ability to interpret variation responsible for Mendelian disorders provides a grand and unprecedented opportunity for geneticists. Human geneticists are well placed to coordinate a systematic evaluation of variants in collaboration with basic scientists and clinicians. Sharing of knowledge, data, methods, and tools will aid both researchers and healthcare workers in achieving their common goal of defining the pathogenic potential of variants. Generation of variant annotations will inform genetic testing and will deepen our understanding of gene and protein function, thereby aiding the search for molecular targeted therapies.
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Affiliation(s)
- Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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75
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 363] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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76
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Papadopoulos P, Viennas E, Gkantouna V, Pavlidis C, Bartsakoulia M, Ioannou ZM, Ratbi I, Sefiani A, Tsaknakis J, Poulas K, Tzimas G, Patrinos GP. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2013; 42:D1020-6. [PMID: 24234438 PMCID: PMC3964978 DOI: 10.1093/nar/gkt1125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft’s PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.
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Affiliation(s)
- Petros Papadopoulos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece, Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, GR-26504, Patras, Greece, Faculty of Medicine and Pharmacy, Human Genomic Center, University Mohammed V Souissi, 11400, Rabat, Morocco and Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-26334, Patras, Greece
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77
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Makrythanasis P, Antonarakis SE. Pathogenic variants in non-protein-coding sequences. Clin Genet 2013; 84:422-428. [DOI: 10.1111/cge.12272] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- P Makrythanasis
- Department of Genetic Medicine and Development; University of Geneva Medical School; Geneva Switzerland
| | - SE Antonarakis
- Department of Genetic Medicine and Development; University of Geneva Medical School; Geneva Switzerland
- Service of Genetic Medicine; University Hospitals of Geneva; Geneva Switzerland
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78
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Toma S, Tenorio M, Oakley M, Thein SL, Clark BE. Two Novel Mutations (HBG1: c.-250C>T andHBG2: c.-250C>T) Associated With Hereditary Persistence of Fetal Hemoglobin. Hemoglobin 2013; 38:67-9. [DOI: 10.3109/03630269.2013.848365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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79
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Giardine B, Borg J, Viennas E, Pavlidis C, Moradkhani K, Joly P, Bartsakoulia M, Riemer C, Miller W, Tzimas G, Wajcman H, Hardison RC, Patrinos GP. Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res 2013; 42:D1063-9. [PMID: 24137000 PMCID: PMC3964999 DOI: 10.1093/nar/gkt911] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for α-, and β-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.
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Affiliation(s)
- Belinda Giardine
- The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, PA, USA, Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta, MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, Rotterdam, The Netherlands, Department of Computer Engineering and Informatics, University of Patras, Faculty of Engineering, Patras, Greece, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece, Department of Medical Genetics, Laboratory of Cytogenetics, Institute of Biology, Nantes, France, Hôpital Edouard Herriot, Unité de Pathologie Moléculaire du Globule Rouge, Lyon, France, Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, Patras, Greece, INSERM U955, CHU Henri Mondor, Creteil, France and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
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80
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Weinkam P, Sali A. Mapping polymerization and allostery of hemoglobin S using point mutations. J Phys Chem B 2013; 117:13058-68. [PMID: 23957820 DOI: 10.1021/jp4025156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hemoglobin is a complex system that undergoes conformational changes in response to oxygen, allosteric effectors, mutations, and environmental changes. Here, we study allostery and polymerization of hemoglobin and its variants by application of two previously described methods: (i) AllosMod for simulating allostery dynamics given two allosterically related input structures and (ii) a machine-learning method for dynamics- and structure-based prediction of the mutation impact on allostery (Weinkam et al. J. Mol. Biol. 2013, 425, 647-661), now applicable to systems with multiple coupled binding sites, such as hemoglobin. First, we predict the relative stabilities of substates and microstates of hemoglobin, which are determined primarily by entropy within our model. Next, we predict the impact of 866 annotated mutations on hemoglobin's oxygen binding equilibrium. We then discuss a subset of 30 mutations that occur in the presence of the sickle cell mutation and whose effects on polymerization have been measured. Seven of these HbS mutations occur in three predicted druggable binding pockets that might be exploited to directly inhibit polymerization; one of these binding pockets is not apparent in the crystal structure, but only in structures generated by AllosMod. For the 30 mutations, we predict that mutation-induced conformational changes within a single tetramer tend not to significantly impact polymerization; instead, these mutations more likely impact polymerization by directly perturbing a polymerization interface. Finally, our analysis of allostery allows us to hypothesize why hemoglobin evolved to have multiple subunits and a persistent low frequency sickle cell mutation.
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Affiliation(s)
- Patrick Weinkam
- Department of Bioengineering and Therapeutic Sciences, ‡Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco , San Francisco, California 94158, United States
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81
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Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 2013; 45:1160-7. [PMID: 23974870 PMCID: PMC3874936 DOI: 10.1038/ng.2745] [Citation(s) in RCA: 432] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 07/30/2013] [Indexed: 12/16/2022]
Abstract
Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation to clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 cystic fibrosis patients in registries and clinics in North America and Europe. Among these patients, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of cystic fibrosis patients enabled assignment of 12 of the remaining 32 variants as neutral while the other 20 variants remained indeterminate. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically-relevant genomic variation.
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82
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Wang T, He Y, Zhou JY, Xie XM, Li J, Li R, Liao C, Li DZ. KLF1 gene mutations in Chinese adults with increased fetal hemoglobin. Hemoglobin 2013; 37:501-6. [PMID: 23806141 DOI: 10.3109/03630269.2013.805304] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We investigated the Krüppel-like factor 1 (KLF1) gene mutations in Chinese adults with increased Hb F levels (>1.5%) referred to our laboratory for thalassemia screening. Functionally effective KLF1 mutations were identified in five out of 140 samples with an elevated Hb F (1.9-11.4%). Only two different KLF1 mutations were detected. Functional KLF1 mutations were not identified in the matched cohort of 110 samples with normal Hb F values (<1.0%). The KLF1 mutations could be one of the causes of hereditary persistence of fetal hemoglobin (HPFH) in regions where thalassemias are common.
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Affiliation(s)
- Ting Wang
- Prenatal Diagnostic Center, Guangzhou Women & Children Medical Center affiliated to Guangzhou Medical College , Guangzhou, Guangdong, People's Republic of China
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83
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Harteveld CL. State of the art and new developments in molecular diagnostics for hemoglobinopathies in multiethnic societies. Int J Lab Hematol 2013; 36:1-12. [PMID: 23721114 DOI: 10.1111/ijlh.12108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/17/2013] [Indexed: 12/01/2022]
Abstract
For detecting carriers of thalassemia traits, the basic part of diagnostics consists of measurement of the hematological indices followed by mostly automatic separation and measurement of the Hb fractions, while direct Hb separation either on high pressure liquid chromatography or capillary electrophoresis is sufficient to putatively identify carriers of the common Hb variants like HbS, C, E, D, and O-Arab. A putative positive result is reported together with an advice for parents, partner, or family analysis. For couples, presumed at-risk confirmation at the DNA level is essential. In general, this part of diagnostics is done in specialized centers provided with sufficient experience and the technical tools needed to combine hematological and biochemical interpretation with identification of the mutations at the molecular level. State-of-the-art tools are usually available in centers that also provide prenatal diagnosis and should consist of gap-PCR for the common deletions, direct DNA sequencing for all kind of point-mutations and the capacity to uncover novel or rare mutations or disease mechanisms. New developments are MLPA for large and eventually unknown deletion defects and microarray technology for fine mapping and primer design for breakpoint analysis. Gap-PCR primers designed in the region flanking the deletion breakpoints can subsequently be used to facilitate carrier detection of uncommon deletions in family members or isolated populations in laboratories where no microarray technology or MLPA is available.
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Affiliation(s)
- C L Harteveld
- Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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84
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Abstract
PURPOSE OF REVIEW This review describes the genetics of unusual blood group phenotypes, particularly those with altered expression of Lutheran antigens, and how this area of study has informed our understanding of erythropoiesis in general and haemoglobin switching in particular. RECENT FINDINGS Mutations in erythroid transcription factors GATA1 (GATA1 binding protein 1) and KLF1 (Kruppel-like factor 1) cause benign and disease phenotypes in humans [X-linked Lu(a-b-) phenotype, In(Lu) blood group phenotype, hereditary persistence of foetal haemoglobin, borderline HbA(2), and congenital dyserythropoietic anaemia (CDA)]. These studies explain the occurrence of rare blood group phenotypes with simultaneous altered expression of antigens from several blood group systems and illuminate the role of KLF1 in gamma and delta globin gene regulation. SUMMARY The study of rare blood group phenotypes is a potent tool for discovery of mutations in human genes. Elucidation of the molecular basis of the rare In(Lu) phenotype revealed the first mutations in human KLF1. Subsequently, numerous additional mutations have been described, one of which causes a rare form of CDA. Analysis of the X-linked Lu(a-b-) phenotype revealed a mutation in the C-terminal domain of human GATA1. The apparent sensitivity of the Lutheran glycoprotein to alterations in GATA1 and KLF1 activity suggest that it could be a useful biomarker of erythroid transcription factor mutation.
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85
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Piel FB, Howes RE, Nyangiri OA, Moyes CL, Williams TN, Weatherall DJ, Hay SI. Online biomedical resources for malaria-related red cell disorders. Hum Mutat 2013; 34:937-44. [PMID: 23568771 PMCID: PMC3738938 DOI: 10.1002/humu.22330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/01/2013] [Indexed: 01/01/2023]
Abstract
Warnings about the expected increase of the global public health burden of malaria-related red cell disorders are accruing. Past and present epidemiological data are necessary to track spatial and temporal changes in the frequencies of these genetic disorders. A number of open access biomedical databases including data on malaria-related red cell disorders have been launched over the last two decades. Here, we review the content of these databases, most of which focus on genetic diversity, and we describe a new epidemiological resource developed by the Malaria Atlas Project. To tackle upcoming public health challenges, the integration of epidemiological and genetic data is important. As many countries are considering implementing national screening programs, strategies to make such data more accessible are also needed.
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Affiliation(s)
- Frédéric B Piel
- Spatial Ecology and Epidemiology Group, Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom.
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86
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Abstract
The β-thalassemias are characterized by a quantitative deficiency of β-globin chains underlaid by a striking heterogeneity of molecular defects. Although most of the molecular lesions involve the structural β gene directly, some down-regulate the gene through distal cis effects, and rare trans-acting mutations have also been identified. Most β-thalassemias are inherited in a Mendelian recessive fashion but there is a subgroup of β-thalassemia alleles that behave as dominant negatives. Unraveling the molecular basis of β-thalassemia has provided a paradigm for understanding of much of human genetics.
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Affiliation(s)
- Swee Lay Thein
- Department of Haematological Medicine, King's College London School of Medicine/King's College Hospital NHS Foundation Trust, London SE5 9NU, United Kingdom.
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87
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Thom CS, Dickson CF, Gell DA, Weiss MJ. Hemoglobin variants: biochemical properties and clinical correlates. Cold Spring Harb Perspect Med 2013; 3:a011858. [PMID: 23388674 DOI: 10.1101/cshperspect.a011858] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Diseases affecting hemoglobin synthesis and function are extremely common worldwide. More than 1000 naturally occurring human hemoglobin variants with single amino acid substitutions throughout the molecule have been discovered, mainly through their clinical and/or laboratory manifestations. These variants alter hemoglobin structure and biochemical properties with physiological effects ranging from insignificant to severe. Studies of these mutations in patients and in the laboratory have produced a wealth of information on hemoglobin biochemistry and biology with significant implications for hematology practice. More generally, landmark studies of hemoglobin performed over the past 60 years have established important paradigms for the disciplines of structural biology, genetics, biochemistry, and medicine. Here we review the major classes of hemoglobin variants, emphasizing general concepts and illustrative examples.
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Affiliation(s)
- Christopher S Thom
- Cell and Molecular Biology Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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88
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Yien YY, Bieker JJ. EKLF/KLF1, a tissue-restricted integrator of transcriptional control, chromatin remodeling, and lineage determination. Mol Cell Biol 2013; 33:4-13. [PMID: 23090966 PMCID: PMC3536305 DOI: 10.1128/mcb.01058-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Erythroid Krüppel-like factor (EKLF or KLF1) is a transcriptional regulator that plays a critical role in lineage-restricted control of gene expression. KLF1 expression and activity are tightly controlled in a temporal and differentiation stage-specific manner. The mechanisms by which KLF1 is regulated encompass a range of biological processes, including control of KLF1 RNA transcription, protein stability, localization, and posttranslational modifications. Intact KLF1 regulation is essential to correctly regulate erythroid function by gene transcription and to maintain hematopoietic lineage homeostasis by ensuring a proper balance of erythroid/megakaryocytic differentiation. In turn, KLF1 regulates erythroid biology by a wide variety of mechanisms, including gene activation and repression by regulation of chromatin configuration, transcriptional initiation and elongation, and localization of gene loci to transcription factories in the nucleus. An extensive series of biochemical, molecular, and genetic analyses has uncovered some of the secrets of its success, and recent studies are highlighted here. These reveal a multilayered set of control mechanisms that enable efficient and specific integration of transcriptional and epigenetic controls and that pave the way for proper lineage commitment and differentiation.
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Affiliation(s)
- Yvette Y. Yien
- Department of Developmental and Regenerative Biology
- Graduate School of Biological Sciences
| | - James J. Bieker
- Department of Developmental and Regenerative Biology
- Black Family Stem Cell Institute
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA
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89
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Georgitsi M, Patrinos GP. Genetic databases in pharmacogenomics: the Frequency of Inherited Disorders Database (FINDbase). Methods Mol Biol 2013; 1015:321-336. [PMID: 23824866 DOI: 10.1007/978-1-62703-435-7_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pharmacogenomics studies how the variations of the individuals' genetic makeup are correlated with a person's response to certain drugs in relation to the therapeutic efficiency, clinical outcome, or even survival, and how they affect drug metabolism, transport, or clearance. Yet, since the incidence of these polymorphisms, being either single-point variations or small insertions/deletions, varies among different populations, a systematic collection and documentation of these variations is warranted, in order to facilitate implementation of pharmacogenomics in different populations. Here we review the existing electronic databases related to pharmacogenomics and pay particular attention in the description of the pharmacogenomics module Frequency of Inherited Disorders database (FINDbase), which documents curated allelic frequency data pertaining to 144 pharmacogenomics markers across 14 genes, representing approximately 87,000 individuals from 150 populations and ethnic groups worldwide. Long-term sustainability of these resources aims to contribute to the design, development, and implementation of pharmacogenomics testing towards the application of personalized approaches in medical treatment.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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90
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Abstract
The globin gene disorders including the thalassemias are among the most common human genetic diseases with more than 300,000 severely affected individuals born throughout the world every year. Because of the easy accessibility of purified, highly specialized, mature erythroid cells from peripheral blood, the hemoglobinopathies were among the first tractable human molecular diseases. From the 1970s onward, the analysis of the large repertoire of mutations underlying these conditions has elucidated many of the principles by which mutations occur and cause human genetic diseases. This work will summarize our current knowledge of the α-thalassemias, illustrating how detailed analysis of this group of diseases has contributed to our understanding of the general molecular mechanisms underlying many orphan and common diseases.
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Affiliation(s)
- Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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91
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Costa FC, Fedosyuk H, Chazelle AM, Neades RY, Peterson KR. Mi2β is required for γ-globin gene silencing: temporal assembly of a GATA-1-FOG-1-Mi2 repressor complex in β-YAC transgenic mice. PLoS Genet 2012; 8:e1003155. [PMID: 23284307 PMCID: PMC3527334 DOI: 10.1371/journal.pgen.1003155] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 10/18/2012] [Indexed: 12/12/2022] Open
Abstract
Activation of γ-globin gene expression in adults is known to be therapeutic for sickle cell disease. Thus, it follows that the converse, alleviation of repression, would be equally effective, since the net result would be the same: an increase in fetal hemoglobin. A GATA-1-FOG-1-Mi2 repressor complex was recently demonstrated to be recruited to the −566 GATA motif of the Aγ-globin gene. We show that Mi2β is essential for γ-globin gene silencing using Mi2β conditional knockout β-YAC transgenic mice. In addition, increased expression of Aγ-globin was detected in adult blood from β-YAC transgenic mice containing a T>G HPFH point mutation at the −566 GATA silencer site. ChIP experiments demonstrated that GATA-1 is recruited to this silencer at day E16, followed by recruitment of FOG-1 and Mi2 at day E17 in wild-type β-YAC transgenic mice. Recruitment of the GATA-1–mediated repressor complex was disrupted by the −566 HPFH mutation at developmental stages when it normally binds. Our data suggest that a temporal repression mechanism is operative in the silencing of γ-globin gene expression and that either a trans-acting Mi2β knockout deletion mutation or the cis-acting −566 Aγ-globin HPFH point mutation disrupts establishment of repression, resulting in continued γ-globin gene transcription during adult definitive erythropoiesis. Sickle cell disease (SCD) is one of the most common genetic diseases, affecting millions of people worldwide. SCD affects red blood cells' shape and renders them ineffective, resulting in anemia along with attendant complications. The disease is caused by a single point mutation in the coding sequence of the adult β-globin gene that changes normal adult hemoglobin (HbA) to sickle hemoglobin (HbS). Scientific evidence has demonstrated that continued expression of the fetal γ-globin genes (fetal hemoglobin, HbF), which are normally silenced after birth, is the best treatment for SCD, since the pathophysiology is largely ameliorated. Our therapeutic goal is to reactivate the γ-globin genes to substitute for the defective adult β-globin gene. We identified a novel γ-globin gene silencer sequence and demonstrated that a GATA-1-FOG-1-Mi2 repressor complex binds to this sequence and silences γ-globin synthesis. However, data regarding the requirement of Mi2 for silencing is controversial. We demonstrate that γ-globin synthesis increases as Mi2 expression decreases. We also show that repressor complex components assemble sequentially during development; completion of assembly coincides with γ-globin gene silencing. Disruption of either the repressor complex or mutation of its binding site induces γ-globin. Understanding this mechanism will reveal potential new targets for treating SCD.
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Affiliation(s)
- Flávia C. Costa
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Halyna Fedosyuk
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Allen M. Chazelle
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Renee Y. Neades
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Kenneth R. Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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92
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Beck T, Free RC, Thorisson GA, Brookes AJ. Semantically enabling a genome-wide association study database. J Biomed Semantics 2012; 3:9. [PMID: 23244533 PMCID: PMC3579732 DOI: 10.1186/2041-1480-3-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 08/22/2012] [Indexed: 01/03/2023] Open
Abstract
Background The amount of data generated from genome-wide association studies (GWAS) has grown rapidly, but considerations for GWAS phenotype data reuse and interchange have not kept pace. This impacts on the work of GWAS Central – a free and open access resource for the advanced querying and comparison of summary-level genetic association data. The benefits of employing ontologies for standardising and structuring data are widely accepted. The complex spectrum of observed human phenotypes (and traits), and the requirement for cross-species phenotype comparisons, calls for reflection on the most appropriate solution for the organisation of human phenotype data. The Semantic Web provides standards for the possibility of further integration of GWAS data and the ability to contribute to the web of Linked Data. Results A pragmatic consideration when applying phenotype ontologies to GWAS data is the ability to retrieve all data, at the most granular level possible, from querying a single ontology graph. We found the Medical Subject Headings (MeSH) terminology suitable for describing all traits (diseases and medical signs and symptoms) at various levels of granularity and the Human Phenotype Ontology (HPO) most suitable for describing phenotypic abnormalities (medical signs and symptoms) at the most granular level. Diseases within MeSH are mapped to HPO to infer the phenotypic abnormalities associated with diseases. Building on the rich semantic phenotype annotation layer, we are able to make cross-species phenotype comparisons and publish a core subset of GWAS data as RDF nanopublications. Conclusions We present a methodology for applying phenotype annotations to a comprehensive genome-wide association dataset and for ensuring compatibility with the Semantic Web. The annotations are used to assist with cross-species genotype and phenotype comparisons. However, further processing and deconstructions of terms may be required to facilitate automatic phenotype comparisons. The provision of GWAS nanopublications enables a new dimension for exploring GWAS data, by way of intrinsic links to related data resources within the Linked Data web. The value of such annotation and integration will grow as more biomedical resources adopt the standards of the Semantic Web.
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Affiliation(s)
- Tim Beck
- Department of Genetics, University of Leicester, University Road, Leicester, UK.
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93
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Impact of mutations on the allosteric conformational equilibrium. J Mol Biol 2012; 425:647-61. [PMID: 23228330 DOI: 10.1016/j.jmb.2012.11.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/21/2022]
Abstract
Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and effector-unbound protein structures. These simulations can be performed using our web server (http://salilab.org/allosmod/). We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a data set of 10 proteins and 179 mutations, we predict both the magnitude and the sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1k(B)T. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction.
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94
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Radmilovic M, Zukic B, Petrovic MS, Bartsakoulia M, Stankovic B, Kotur N, Dokmanovic L, Georgitsi M, Patrinos GP, Pavlovic S. Functional analysis of a novel KLF1 gene promoter variation associated with hereditary persistence of fetal hemoglobin. Ann Hematol 2012; 92:53-8. [PMID: 23161389 DOI: 10.1007/s00277-012-1625-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/05/2012] [Indexed: 11/30/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) is a rare hereditary condition resulting in elevated levels of fetal hemoglobin (HbF) in adults. Typical HPFH is associated with promoter mutations or large deletions affecting the human fetal globin (HBG1 and HBG2) genes, while genetic defects in other genes involved in human erythropoiesis, e.g. KLF1, also result in atypical HPFH. Here, we report the first KLF1 gene promoter mutation (KLF1:g.-148G > A) that is associated with increased HbF level. This mutation was shown to result in drastically reduced CAT reporter gene expression in K562 cells, compared to the wild-type sequence (p = 0.009) and also in reduced KLF1 gene expression in vivo. Furthermore, consistent with in silico analysis, electrophoretic mobility shift analysis showed that the KLF1:g.-148G > A mutation resides in a Sp1 binding site and further that this mutation leads to the ablation of Sp1 binding in vitro. These data suggest that the KLF1:g-148G > A mutation could play a role in increasing HbF levels in adults and further underlines the role of KLF1 as one of the key transcription factors involved in human fetal globin gene switching.
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Affiliation(s)
- Milena Radmilovic
- Institute of Molecular Genetics and Genetic Engineering, Laboratory for Molecular Hematology, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
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95
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Byrne M, Fokkema IF, Lancaster O, Adamusiak T, Ahonen-Bishopp A, Atlan D, Béroud C, Cornell M, Dalgleish R, Devereau A, Patrinos GP, Swertz MA, Taschner PE, Thorisson GA, Vihinen M, Brookes AJ, Muilu J. VarioML framework for comprehensive variation data representation and exchange. BMC Bioinformatics 2012; 13:254. [PMID: 23031277 PMCID: PMC3507772 DOI: 10.1186/1471-2105-13-254] [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: 05/14/2012] [Accepted: 09/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. RESULTS The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. CONCLUSIONS VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.
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Affiliation(s)
- Myles Byrne
- Institute for Molecular Medicine Finland-FIMM, University of Helsinki, Helsinki, Finland.
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96
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Thein SL. The emerging role of fetal hemoglobin induction in non-transfusion-dependent thalassemia. Blood Rev 2012; 26 Suppl 1:S35-9. [PMID: 22631042 DOI: 10.1016/s0268-960x(12)70011-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Patients with beta (β)-thalassemia who have high levels of fetal hemoglobin (HbF) have less severe anemia and are often transfusion-independent. Therefore, augmentation of HbF production has been a longstanding therapeutic objective. Three classes of HbF-inducing agents have been investigated for the treatment of β-thalassemia including chemotherapeutics, short-chain fatty acid derivatives, and recombinant erythropoietin. These agents have several different mechanisms of action and have been shown to increase total hemoglobin levels by 1-5 g/dL above baseline, but none has been able to sustain the therapeutic levels needed to maintain transfusion independence. Recent findings have provided new insights regarding HbF regulatory pathways, providing new opportunities for derepression of fetal globin gene expression and HbF induction.
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Affiliation(s)
- Swee Lay Thein
- King's College Hospital/King's College London School of Medicine, London, UK.
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97
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Machina HK, Wild DJ. Laboratory informatics tools integration strategies for drug discovery: integration of LIMS, ELN, CDS, and SDMS. JOURNAL OF LABORATORY AUTOMATION 2012; 18:126-36. [PMID: 22895535 DOI: 10.1177/2211068212454852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There are technologies on the horizon that could dramatically change how informatics organizations design, develop, deliver, and support applications and data infrastructures to deliver maximum value to drug discovery organizations. Effective integration of data and laboratory informatics tools promises the ability of organizations to make better informed decisions about resource allocation during the drug discovery and development process and for more informed decisions to be made with respect to the market opportunity for compounds. We propose in this article a new integration model called ELN-centric laboratory informatics tools integration.
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98
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Patrinos GP, Cooper DN, van Mulligen E, Gkantouna V, Tzimas G, Tatum Z, Schultes E, Roos M, Mons B. Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain. Hum Mutat 2012; 33:1503-12. [PMID: 22736453 DOI: 10.1002/humu.22144] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/23/2012] [Indexed: 11/07/2022]
Abstract
The advances in bioinformatics required to annotate human genomic variants and to place them in public data repositories have not kept pace with their discovery. Moreover, a law of diminishing returns has begun to operate both in terms of data publication and submission. Although the continued deposition of such data in the public domain is essential to maximize both their scientific and clinical utility, rewards for data sharing are few, representing a serious practical impediment to data submission. To date, two main strategies have been adopted as a means to encourage the submission of human genomic variant data: (1) database journal linkups involving the affiliation of a scientific journal with a publicly available database and (2) microattribution, involving the unambiguous linkage of data to their contributors via a unique identifier. The latter could in principle lead to the establishment of a microcitation-tracking system that acknowledges individual endeavor and achievement. Both approaches could incentivize potential data contributors, thereby encouraging them to share their data with the scientific community. Here, we summarize and critically evaluate approaches that have been proposed to address current deficiencies in data attribution and discuss ways in which they could become more widely adopted as novel scientific publication modalities.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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99
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Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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100
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Induction of Fetal Hemoglobin In Vivo Mediated by a Synthetic γ-Globin Zinc Finger Activator. Anemia 2012; 2012:507894. [PMID: 22778925 PMCID: PMC3384929 DOI: 10.1155/2012/507894] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/17/2012] [Accepted: 04/24/2012] [Indexed: 12/28/2022] Open
Abstract
Sickle cell disease (SCD) and β-thalassemia patients are phenotypically normal if they carry compensatory hereditary persistence of fetal hemoglobin (HPFH) mutations that result in increased levels of fetal hemoglobin (HbF, γ-globin chains) in adulthood. Thus, research has focused on manipulating the reactivation of γ-globin gene expression during adult definitive erythropoiesis as the most promising therapy to treat these hemoglobinopathies. Artificial transcription factors (ATFs) are synthetic proteins designed to bind at a specific DNA sequence and modulate gene expression. The artificial zinc finger gg1-VP64 was designed to target the −117 region of the Aγ-globin gene proximal promoter and activate expression of this gene. Previous studies demonstrated that HbF levels were increased in murine chemical inducer of dimerization (CID)-dependent bone marrow cells carrying a human β-globin locus yeast artificial chromosome (β-YAC) transgene and in CD34+ erythroid progenitor cells from normal donors and β-thalassemia patients. Herein, we report that gg1-VP64 increased γ-globin gene expression in vivo, in peripheral blood samples from gg1-VP64 β-YAC double-transgenic (bigenic) mice. Our results demonstrate that ATFs function in an animal model to increase gene expression. Thus, this class of reagent may be an effective gene therapy for treatment of some inherited diseases.
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