Dataset Information

Planning the human variome project: the Spain report.

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.

SUBMITTER: Kaput J

PROVIDER: S-EPMC5879779 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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Planning the human variome project: the Spain report.

Kaput Jim J Cotton Richard G H RG Hardman Lauren L Watson Michael M Al Aqeel Aida I AI Al-Aama Jumana Y JY Al-Mulla Fahd F Alonso Santos S Aretz Stefan S Auerbach Arleen D AD Bapat Bharati B Bernstein Inge T IT Bhak Jong J Bleoo Stacey L SL Blöcker Helmut H Brenner Steven E SE Burn John J Bustamante Mariona M Calzone Rita R Cambon-Thomsen Anne A Cargill Michele M Carrera Paola P Cavedon Lawrence L Cho Yoon Shin YS Chung Yeun-Jun YJ Claustres Mireille M Cutting Garry G Dalgleish Raymond R den Dunnen Johan T JT Díaz Carlos C Dobrowolski Steven S dos Santos M Rosário N MR Ekong Rosemary R Flanagan Simon B SB Flicek Paul P Furukawa Yoichi Y Genuardi Maurizio M Ghang Ho H Golubenko Maria V MV Greenblatt Marc S MS Hamosh Ada A Hancock John M JM Hardison Ross R Harrison Terence M TM Hoffmann Robert R Horaitis Rania R Howard Heather J HJ Barash Carol Isaacson CI Izagirre Neskuts N Jung Jongsun J Kojima Toshio T Laradi Sandrine S Lee Yeon-Su YS Lee Jong-Young JY Gil-da-Silva-Lopes Vera L VL Macrae Finlay A FA Maglott Donna D Marafie Makia J MJ Marsh Steven G E SG Matsubara Yoichi Y Messiaen Ludwine M LM Möslein Gabriela G Netea Mihai G MG Norton Melissa L ML Oefner Peter J PJ Oetting William S WS O'Leary James C JC de Ramirez Ana Maria Oller AM Paalman Mark H MH Parboosingh Jillian J Patrinos George P GP Perozzi Giuditta G Phillips Ian R IR Povey Sue S Prasad Suyash S Qi Ming M Quin David J DJ Ramesar Rajkumar S RS Richards C Sue CS Savige Judith J Scheible Dagmar G DG Scott Rodney J RJ Seminara Daniela D Shephard Elizabeth A EA Sijmons Rolf H RH Smith Timothy D TD Sobrido María-Jesús MJ Tanaka Toshihiro T Tavtigian Sean V SV Taylor Graham R GR Teague Jon J Töpel Thoralf T Ullman-Cullere Mollie M Utsunomiya Joji J van Kranen Henk J HJ Vihinen Mauno M Webb Elizabeth E Weber Thomas K TK Yeager Meredith M Yeom Young I YI Yim Seon-Hee SH Yoo Hyang-Sook HS

Human mutation 20090401 4

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 envi ...[more]

PMID: 19306394

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Project description:In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target proteins to be included in a vaccine formulation have to accomplish several genetic and immunological characteristics, (such as conservation, distribution, immunogenicity and protective effect), in order to ensure its suitability and effectiveness. This study aimed to get comprehensive insights into the genomic organization, population distribution and genetic conservation of all pneumococcal surface-exposed proteins, genetic regulators and other virulence factors, whose important function and role in pathogenesis has been demonstrated or hypothesized.After retrieving the complete set of DNA and protein sequences reported in the databases GenBank, KEGG, VFDB, P2CS and Uniprot for pneumococcal strains whose genomes have been fully sequenced and annotated, a comprehensive bioinformatic analysis and systematic comparison has been performed for each virulence factor, stand-alone regulator and two-component regulatory system (TCS) encoded in the pan-genome of S. pneumoniae. A total of 25 S. pneumoniae strains, representing different pneumococcal phylogenetic lineages and serotypes, were considered. A set of 92 different genes and proteins were identified, classified and studied to construct a pan-genomic variability map (variome) for S. pneumoniae. Both, pneumococcal virulence factors and regulatory genes, were well-distributed in the pneumococcal genome and exhibited a conserved feature of genome organization, where replication and transcription are co-oriented. The analysis of the population distribution for each gene and protein showed that 49 of them are part of the core genome in pneumococci, while 43 belong to the accessory-genome. Estimating the genetic variability revealed that pneumolysin, enolase and Usp45 (SP_2216 in S. p. TIGR4) are the pneumococcal virulence factors with the highest conservation, while TCS08, TCS05, and TCS02 represent the most conserved pneumococcal genetic regulators.The results identified well-distributed and highly conserved pneumococcal virulence factors as well as regulators, representing promising candidates for a new generation of serotype-independent protein-based vaccine(s) to combat pneumococcal infections.

Dataset Information

Planning the human variome project: the Spain report.

Publications

Planning the human variome project: the Spain report.

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