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Lagoumintzis G, Poulas K, Patrinos GP. Genetic databases and their potential in pharmacogenomics. Curr Pharm Des 2010; 16:2224-31. [PMID: 20459387 DOI: 10.2174/138161210791792804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 05/10/2010] [Indexed: 11/22/2022]
Abstract
The completion of the human genome sequencing project and the establishment of new methods for the detection of point mutations have lead to a remarkable increase of sequence variants identification in a growing number of genes. As a result of this, a new field of research has emerged, pharmacogenomics, which deals with the influence of genetic variation on drug response by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity. Genetic databases are continuously updated online repositories of mutation data, described for a single or more genes or specifically for a population or ethnic group. Genetic databases can also fulfil the mission of pharmacogenomics by helping elucidate gene function, estimate the prevalence of genes in populations, differentiate among subtypes of diseases, trace how genes may predispose to or protect against illnesses, and improve medical intervention. Therefore, it is expected that genetic databases will gradually assume an increasing importance in all aspects of genome medicine. This article aims to provide an update of the current and emerging types of genetic databases relevant to the field of pharmacogenomics. Moreover, the key elements that are holding back the field as well as the challenges that should be addressed in the near future are also commented.
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Squassina A, Manchia M, Manolopoulos VG, Artac M, Lappa-Manakou C, Karkabouna S, Mitropoulos K, Zompo MD, Patrinos GP. Realities and expectations of pharmacogenomics and personalized medicine: impact of translating genetic knowledge into clinical practice. Pharmacogenomics 2010; 11:1149-67. [DOI: 10.2217/pgs.10.97] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The implementation of genetic data for a better prediction of response to medications and adverse drug reactions is becoming a reality in some clinical fields. However, to be successful, personalized medicine should take advantage of an informational structured framework of genetic, phenotypic and environmental factors in order to provide the healthcare system with useful tools that can optimize the effectiveness of specific treatment. The impact of personalized medicine is potentially enormous, but the results that have so far been gathered are often difficult to translate into clinical practice. In this article we have summarized the most relevant applications of pharmacogenomics on diseases to which they have already been applied and fields in which they are currently emerging. The article provides an overview of the opportunities and shortcomings of the implementation of genetic information into personalized medicine and its full adoption in the clinic. In the second instance, it provides readers from different fields of expertise with an accessible interpretation to the barriers and opportunities in the use/adoption of pharmacogenomic testing between the different clinical areas.
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Papachatzopoulou A, Kourakli A, Stavrou EF, Fragou E, Vantarakis A, Patrinos GP, Athanassiadou A. Region-Specific Genetic Heterogeneity ofHBBMutation Distribution in South-Western Greece. Hemoglobin 2010; 34:333-42. [DOI: 10.3109/03630269.2010.486354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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255
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Zukic B, Radmilovic M, Stojiljkovic M, Tosic N, Pourfarzad F, Dokmanovic L, Janic D, Colovic N, Philipsen S, Patrinos GP, Pavlovic S. Functional analysis of the role of the TPMT gene promoter VNTR polymorphism in TPMT gene transcription. Pharmacogenomics 2010; 11:547-57. [PMID: 20350137 DOI: 10.2217/pgs.10.7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIMS Thiopurine S-methyltransferase (TPMT) activity is polymorphic, and a trimodal distribution has been demonstrated in Caucasians (low, intermediate and high methylator groups). The TPMT gene promoter contains a variable number of three GC-rich tandem repeats, namely A, B and C, ranging from three to nine in length in a A(n)B(m)C architecture. MATERIALS & METHODS Here, we investigated the influence of number and type of TPMT gene promoter tandem repeats on human TPMT gene transcription in K562 cells transiently transfected with reporter constructs bearing various variable number of tandem repeats (VNTR) and addressed the interaction of transcription factor binding to the VNTRs by electrophoretic mobility shift assays. RESULTS We found that the distribution patterns of VNTR alleles do not significantly differ among acute lymphoblastic leukemia patients, acute myeloid leukemia patients and normal individuals. We also demonstrated that the A repeat has a negative effect in TPMT gene transcription and that a positive regulatory element, identified immediately upstream to the VNTR region of the TPMT gene promoter, is indispensable for TPMT gene transcription. Our electrophoretic mobility shift assay analysis indicated that the Sp1 and Sp3 transcription factors bind to the VNTR repeats. CONCLUSION Overall, our data underline that both the number and type of VNTRs, as well as the upstream regulatory region of the TPMT gene promoter, determine the overall level of TPMT gene transcription. It remains to be seen whether these VNTRs can be employed as pharmacogenetic markers to individualize thiopurine therapy.
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Chen JM, Cooper DN, Férec C, Kehrer-Sawatzki H, Patrinos GP. Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 2010; 20:222-33. [PMID: 20541013 DOI: 10.1016/j.semcancer.2010.05.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/22/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Genomic rearrangements in inherited disease and cancer involve gross alterations of chromosomes or large chromosomal regions and can take the form of deletions, duplications, insertions, inversions or translocations. The characterization of a considerable number of rearrangement breakpoints has now been accomplished at the nucleotide sequence level, thereby providing an invaluable resource for the detailed study of the mutational mechanisms which underlie genomic recombination events. A better understanding of these mutational mechanisms is vital for improving the design of mutation detection strategies. At least five categories of mutational mechanism are known to give rise to genomic rearrangements: (i) homologous recombination including non-allelic homologous recombination (NAHR), gene conversion, single strand annealing (SSA) and break-induced replication (BIR), (ii) non-homologous end joining (NHEJ), (iii) microhomology-mediated replication-dependent recombination (MMRDR), (iv) long interspersed element-1 (LINE-1 or L1)-mediated retrotransposition and (v) telomere healing. Focussing on the first three of these general mechanisms, we compare and contrast their hallmark characteristics, and discuss the role of various local DNA sequence features (e.g. recombination-promoting motifs, repetitive sequences and sequences capable of non-B DNA formation) in mediating the recombination events that underlie gross genomic rearrangements. Finally, we explore how studies both at the level of the gene (using the neurofibromatosis type-1 gene as an example) and the whole genome (using data derived from cancer genome sequencing studies) are shaping our understanding of the impact of genomic rearrangements as a cause of human genetic disease.
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Voutsinas GE, Stavrou EF, Karousos G, Dasoula A, Papachatzopoulou A, Syrrou M, Verkerk AJ, van der Spek P, Patrinos GP, Stöger R, Athanassiadou A. Allelic imbalance of expression and epigenetic regulation within the alpha-synuclein wild-type and p.Ala53Thr alleles in Parkinson disease. Hum Mutat 2010; 31:685-91. [DOI: 10.1002/humu.21248] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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258
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Lederer CW, Basak AN, Aydinok Y, Christou S, El-Beshlawy A, Eleftheriou A, Fattoum S, Felice AE, Fibach E, Galanello R, Gambari R, Gavrila L, Giordano PC, Grosveld F, Hassapopoulou H, Hladka E, Kanavakis E, Locatelli F, Old J, Patrinos GP, Romeo G, Taher A, Traeger-Synodinos J, Vassiliou P, Villegas A, Voskaridou E, Wajcman H, Zafeiropoulos A, Kleanthous M. An electronic infrastructure for research and treatment of the thalassemias and other hemoglobinopathies: the Euro-mediterranean ITHANET project. Hemoglobin 2010; 33:163-76. [PMID: 19657830 DOI: 10.1080/03630260903089177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Hemoglobin (Hb) disorders are common, potentially lethal monogenic diseases, posing a global health challenge. With worldwide migration and intermixing of carriers, demanding flexible health planning and patient care, hemoglobinopathies may serve as a paradigm for the use of electronic infrastructure tools in the collection of data, the dissemination of knowledge, the harmonization of treatment, and the coordination of research and preventive programs. ITHANET, a network covering thalassemias and other hemoglobinopathies, comprises 26 organizations from 16 countries, including non-European countries of origin for these diseases (Egypt, Israel, Lebanon, Tunisia and Turkey). Using electronic infrastructure tools, ITHANET aims to strengthen cross-border communication and data transfer, cooperative research and treatment of thalassemia, and to improve support and information of those affected by hemoglobinopathies. Moreover, the consortium has established the ITHANET Portal, a novel web-based instrument for the dissemination of information on hemoglobinopathies to researchers, clinicians and patients. The ITHANET Portal is a growing public resource, providing forums for discussion and research coordination, and giving access to courses and databases organized by ITHANET partners. Already a popular repository for diagnostic protocols and news related to hemoglobinopathies, the ITHANET Portal also provides a searchable, extendable database of thalassemia mutations and associated background information. The experience of ITHANET is exemplary for a consortium bringing together disparate organizations from heterogeneous partner countries to face a common health challenge. The ITHANET Portal as a web-based tool born out of this experience amends some of the problems encountered and facilitates education and international exchange of data and expertise for hemoglobinopathies.
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Patrinos GP, Innocenti F. Conference Scene: Pharmacogenomics: paving the path to personalized medicine. Pharmacogenomics 2010; 11:141-6. [DOI: 10.2217/pgs.09.174] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 2009 Golden Helix® Symposium on Pharmacogenomics and Personalized medicine was held in Athens, Greece, where approximately 150 participants from 21 countries were updated on recent developments in the fields of pharmacogenetics and pharmacogenomics. The meeting was supported by ten corporate entities, of which three were major pharmaceutical and two were technology companies. It was endorsed by the University of Chicago and partly funded by the University of Patras. Here, we report some highlights of this meeting.
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Chuzhanova N, Chen JM, Bacolla A, Patrinos GP, Férec C, Wells RD, Cooper DN. Gene conversion causing human inherited disease: evidence for involvement of non-B-DNA-forming sequences and recombination-promoting motifs in DNA breakage and repair. Hum Mutat 2009; 30:1189-98. [PMID: 19431182 DOI: 10.1002/humu.21020] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A variety of DNA sequence motifs including inverted repeats, minisatellites, and the chi recombination hotspot, have been reported in association with gene conversion in human genes causing inherited disease. However, no methodical statistically based analysis has been performed to formalize these observations. We have performed an in silico analysis of the DNA sequence tracts involved in 27 nonoverlapping gene conversion events in 19 different genes reported in the context of inherited disease. We found that gene conversion events tend to occur within (C+G)- and CpG-rich regions and that sequences with the potential to form non-B-DNA structures, and which may be involved in the generation of double-strand breaks that could, in turn, serve to promote gene conversion, occur disproportionately within maximal converted tracts and/or short flanking regions. Maximal converted tracts were also found to be enriched (P<0.01) in a truncated version of the chi-element (a TGGTGG motif), immunoglobulin heavy chain class switch repeats, translin target sites and several novel motifs including (or overlapping) the classical meiotic recombination hotspot, CCTCCCCT. Finally, gene conversions tend to occur in genomic regions that have the potential to fold into stable hairpin conformations. These findings support the concept that recombination-inducing motifs, in association with alternative DNA conformations, can promote recombination in the human genome.
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Georgoulias P, Wozniak G, Samara M, Chiotoglou I, Kontos A, Tzavara C, Valotassiou V, Georgitsi M, Aleporou-Marinou V, Patrinos GP, Kollia P. Impact of ACE and ApoE polymorphisms on myocardial perfusion: correlation with myocardial single photon emission computed tomographic imaging. J Hum Genet 2009; 54:595-602. [PMID: 19713976 DOI: 10.1038/jhg.2009.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Coronary artery disease is associated with multiple genetic and environmental risk factors. In this study, we evaluated the correlation of angiotensin l-converting enzyme (ACE) (I/D) and ApoE gene polymorphisms (E2, E3, E4 and g.-219G/T) with myocardial perfusion. We examined 410 patients using exercise-rest myocardial perfusion single photon emission computed tomography (SPECT), in which the summed stress score (SSS), summed rest score (SRS) and summed difference score (SDS) indexes were calculated. Homozygotes for the ACE D allele had greater mean values of SSS (P<0.001) and SDS (P<0.001). In addition, E3 homozygotes, E4 heterozygotes and E4 homozygotes had significantly higher values of SSS and SDS compared with E3 heterozygotes (P<0.001); E4 homozygotes had significantly higher values of SSS and SDS compared with E3 homozygotes. Furthermore, for the g.-219G>T polymorphic site at the promoter region of ApoE gene, the mean values of SSS and SDS were significantly higher for T heterozygotes/homozygotes than for GG homozygotes. Adjusting for all demographic and clinical data using multiple linear regression analysis it was found that ACE D and both ApoE genotypes were independent predictors with a cumulative contribution for the prediction of SSS and SDS. Furthermore, logistic regression analysis revealed that all three genotypes had an independent predictive ability for abnormal SSS (SSS>2). These data provide the first evidence of an association and significant cumulative contribution of the aforementioned genotypes in myocardial perfusion with E4 allele having the strongest association followed by ACE D and ApoE g.-219T alleles.
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Christopoulou G, Tserga A, Patrinos GP, Papadakis MN. Molecular Characterization and Diagnosis of Hb Crete [β129(H7)Ala→Pro]. Hemoglobin 2009; 28:339-42. [PMID: 15658190 DOI: 10.1081/hem-200037796] [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: 11/03/2022]
Abstract
We report the molecular characterization of Hb Crete [beta129(H7)Ala-->Pro] in a female subject from the Greek island of Crete. DNA sequence analysis revealed a 1368 GCC-->CCC base substitution in exon 3 of the beta-globin gene, leading to the Ala-->Pro amino acid change at codon 129. Both the proband and her mother, who were found to be heterozygotes for Hb Crete, presented with mild microcytic anemia and normal Hb A2 levels and iron metabolism indices. This is the first description of an heterozygous Hb Crete case, and also the first report on the molecular basis of Hb Crete. Moreover, the proposed NlaVI restriction enzyme-based detection of Hb Crete at the DNA level is a fast and accurate approach, useful for molecular diagnostics.
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Kalamaras A, Chassanidis C, Samara M, Chiotoglou I, Vamvakopoulos NK, Papadakis MN, Kollia* P, Patrinos GP. The 5′ Regulatory Region of the Human Fetal Globin Genes is a Gene Conversion Hotspot. Hemoglobin 2009; 32:572-81. [DOI: 10.1080/03630260802507824] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zlotogora J, van Baal S, Patrinos GP. The Israeli National Genetic Database. THE ISRAEL MEDICAL ASSOCIATION JOURNAL : IMAJ 2009; 11:373-375. [PMID: 19697591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The Israeli National Genetic Database http//www.goldenhelix. org/israeli is a continuously updated depository on monogenic genetic disorders that are present in the various Israeli populations. It provides the means of obtaining information for clinical purposes, genetic counseling and research.
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Moradkhani K, Préhu C, Old J, Henderson S, Balamitsa V, Luo HY, Poon MC, Chui DHK, Wajcman H, Patrinos GP. Mutations in the paralogous human alpha-globin genes yielding identical hemoglobin variants. Ann Hematol 2009; 88:535-43. [PMID: 18923834 PMCID: PMC2690850 DOI: 10.1007/s00277-008-0624-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 09/25/2008] [Indexed: 11/25/2022]
Abstract
The human alpha-globin genes are paralogues, sharing a high degree of DNA sequence similarity and producing an identical alpha-globin chain. Over half of the alpha-globin structural variants reported to date are only characterized at the amino acid level. It is likely that a fraction of these variants, with phenotypes differing from one observation to another, may be due to the same mutation but on a different alpha-globin gene. There have been very few previous examples of hemoglobin variants that can be found at both HBA1 and HBA2 genes. Here, we report the results of a systematic multicenter study in a large multiethnic population to identify such variants and to analyze their differences from a functional and evolutionary perspective. We identified 14 different Hb variants resulting from identical mutations on either one of the two human alpha-globin paralogue genes. We also showed that the average percentage of hemoglobin variants due to a HBA2 gene mutation (alpha2) is higher than the percentage of hemoglobin variants due to the same HBA1 gene mutation (alpha1) and that the alpha2/alpha1 ratio varied between variants. These alpha-globin chain variants have most likely occurred via recurrent mutations, gene conversion events, or both. Based on these data, we propose a nomenclature for hemoglobin variants that fall into this category.
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Zaimidou S, van Baal S, Smith TD, Mitropoulos K, Ljujic M, Radojkovic D, Cotton RG, Patrinos GP. A1ATVar: a relational database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency and application of the VariVis software. Hum Mutat 2009; 30:308-13. [PMID: 19021233 DOI: 10.1002/humu.20857] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have developed a relational database of human SERPINA1 gene mutations, leading to alpha(1)-antitrypsin (AAT) deficiency, called A(1)ATVar, which can be accessed over the World Wide Web at www.goldenhelix.org/A1ATVar. Extensive information has been extracted from the literature and converted into a searchable database, including genotype information, clinical phenotype, allelic frequencies for the commonest AAT variant alleles, methods of detection, and references. Mutation summaries are automatically displayed and user-generated queries can be formulated based on fields in the database. A separate module, linked to the FINDbase database for frequencies of inherited disorders allows the user to access allele frequency information for the three most frequent AAT alleles, namely PiM, PiS, and PiZ. The available experimental protocols to detect AAT variant alleles at the protein and DNA levels have been archived in a searchable format. A visualization tool, called VariVis, has been implemented to combine A(1)ATVar variant information with SERPINA1 sequence and annotation data. A direct data submission tool allows registered users to submit data on novel AAT variant alleles as well as experimental protocols to explore SERPINA1 genetic heterogeneity, via a password-protected interface. Database access is free of charge and there are no registration requirements for querying the data. The A(1)ATVar database is the only integrated database on the Internet offering summarized information on AAT allelic variants and could be useful not only for clinical diagnosis and research on AAT deficiency and the SERPINA1 gene, but could also serve as an example for an all-in-one solution for locus-specific database (LSDB) development and curation.
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Kaput J, Cotton RGH, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MRN, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SGE, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AMO, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS. Planning the human variome project: the Spain report. Hum Mutat 2009; 30:496-510. [PMID: 19306394 PMCID: PMC5879779 DOI: 10.1002/humu.20972] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.
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Patrinos GP, Petersen MB. Copy number variation and genomic alterations in health and disease. Genome Med 2009; 1:21. [PMID: 19341492 PMCID: PMC2664954 DOI: 10.1186/gm21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A report of the 1st GOLDEN HELIX Symposium 'Copy number variation and genomic alterations in health and disease', Athens, Greece, 28-29 November 2008.
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Patrinos GP, Petricoin EF. A new scientific journal linked to a genetic database: towards a novel publication modality. HUMAN GENOMICS AND PROTEOMICS : HGP 2008; 2009. [PMID: 20948565 PMCID: PMC2950282 DOI: 10.4061/2009/597478] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Accepted: 06/17/2008] [Indexed: 01/23/2023]
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271
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Polymenidis Z, Patrinos GP. Towards a hybrid model for the cryopreservation of umbilical cord blood stem cells. Nat Rev Cancer 2008; 8:823. [PMID: 18813322 DOI: 10.1038/nrc2418-c4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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272
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Kalamaras A, Chassanidis C, Samara M, Papadakis MN, Vagena A, Aleporou-Marinou V, Patrinos GP, Kollia P. Compound heterozygosity of non-deletional hereditary persistence of fetal hemoglobin and deltabeta-thalassemia. Am J Hematol 2008; 83:760. [PMID: 18615450 DOI: 10.1002/ajh.21243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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273
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Papachatzopoulou A, Kaimakis P, Pourfarzad F, Menounos PG, Evangelakou P, Kollia P, Grosveld FG, Patrinos GP. Increased gamma-globin gene expression in beta-thalassemia intermedia patients correlates with a mutation in 3'HS1. Am J Hematol 2007; 82:1005-9. [PMID: 17654503 DOI: 10.1002/ajh.20979] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report a novel set of genetic markers in the DNaseI hypersensitive sites comprising the human beta-globin locus chromatin hub (CH), namely HS-111 and 3'HS1. The HS-111 (-21 G>A) and 3'HS1 (+179 C>T) transitions form CH haplotypes, which occur at different frequencies in beta-thalassemia intermedia and major patients and normal (nonthalassemic) individuals. We also show that the 3'HS1 (+179 C>T) variation results in a GATA-1 binding site and correlates with increased fetal hemoglobin production in beta-thalassemia intermedia patients. In contrast, the HS-111 (+126 G>A) transition, found in three normal chromosomes, is simply a rare polymorphism. We conclude that the CH haplotypes are useful genetic determinants for beta-thalassemia major and intermedia patients, while the 3'HS1 (+179 C>T) mutation may have functional consequences in gamma-globin genes expression.
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Cremonesi L, Ferrari M, Giordano PC, Harteveld CL, Kleanthous M, Papasavva T, Patrinos GP, Traeger-Synodinos J. An overview of current microarray-based human globin gene mutation detection methods. Hemoglobin 2007; 31:289-311. [PMID: 17654067 DOI: 10.1080/03630260701459366] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The panoply of human globin gene mutation detection methods could become significantly enriched with the advent of microarray-based genotyping platforms. The aim of this article is to provide an overview of the current medium and high-throughput microarray-based globin gene mutation detection platforms, namely the microelectronic array, the "thalassochip" arrayed primer extension (APEX) technology and the single base extension methods. This article also outlines an emerging method based on multiple ligation probe amplification (MLPA) and discusses the implications of customized solutions for resequencing of genomic loci in relation to molecular genetic testing of hemoglobinopathies.
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Chen JM, Cooper DN, Chuzhanova N, Férec C, Patrinos GP. Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet 2007; 8:762-75. [PMID: 17846636 DOI: 10.1038/nrg2193] [Citation(s) in RCA: 449] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gene conversion, one of the two mechanisms of homologous recombination, involves the unidirectional transfer of genetic material from a 'donor' sequence to a highly homologous 'acceptor'. Considerable progress has been made in understanding the molecular mechanisms that underlie gene conversion, its formative role in human genome evolution and its implications for human inherited disease. Here we assess current thinking about how gene conversion occurs, explore the key part it has played in fashioning extant human genes, and carry out a meta-analysis of gene-conversion events that are known to have caused human genetic disease.
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