How to Catch All Those Mutations—The Report of the Third Human Variome Project Meeting, UNESCO Paris, May 2010
Maija R.J. Kohonen-Corish,Jumana Y. Al-Aama,Arleen D. Auerbach,Myles Axton,Carol Isaacson Barash,Inge Bernstein,Christophe Béroud,John Burn,Fiona Cunningham,Garry R. Cutting,Johan T. den Dunnen,Marc S. Greenblatt,Jim Kaput,Michael Katz,Annika Lindblom,Finlay A. Macrae,Donna Maglott,Gabriela Möslein,Sue Povey,Raj Ramesar,Sue Richards,Daniela Seminara,María Jesús Sobrido,Sean V. Tavtigian,Graham R. Taylor,Mauno Vihinen,Ingrid Winship,Richard G.H. Cotton +27 more
TLDR
The third Human Variome Project (HVP) Meeting “Integration and Implementation” was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10–14, 2010, and addressed the 12 key areas that form the current framework of HVP activities.Abstract:
The third Human Variome Project (HVP) Meeting "Integration and Implementation" was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10-14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access-Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access-Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium.read more
Citations
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Exome sequencing as a tool for Mendelian disease gene discovery
Michael J. Bamshad,Sarah B. Ng,Abigail W. Bigham,Abigail W. Bigham,Holly K. Tabor,Holly K. Tabor,Mary J. Emond,Deborah A. Nickerson,Jay Shendure +8 more
TL;DR: Experimental and analytical approaches relating to exome sequencing have established a rich framework for discovering the genes underlying unsolved Mendelian disorders and set the stage for applying exome and whole-genome sequencing to facilitate clinical diagnosis and personalized disease-risk profiling.
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How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis
Mauno Vihinen,Mauno Vihinen +1 more
TL;DR: Six main performance evaluation measures are introduced and together with receiver operating characteristics (ROC) analysis they provide a good picture about the performance of methods and allow their objective and quantitative comparison.
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Variation Interpretation Predictors: Principles, Types, Performance, and Choice.
Abhishek Niroula,Mauno Vihinen +1 more
TL;DR: The different types of predictors and their applications for variation interpretation are discussed, including generic tolerance (pathogenicity) predictors for filtering harmful variants and Gene/protein/disease‐specific tools available for some applications.
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Deep sequencing of patient genomes for disease diagnosis: when will it become routine?
TL;DR: Whether and how genome sequencing might become routine for clinical diagnosis may be discussed, as well as whether and how whole-genome sequencing could be routine for diagnostic purposes.
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Correlating disease related mutations to their effect on protein stability: a large scale analysis of the human proteome
TL;DR: Statistically validated analysis of the different P/Pd correlations indicate that Pd best correlates with Pp, corroborates the assumption that protein stability changes can also be disease associated at the proteome level and rationalizes in a nutshell the complexity of the question.
References
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Recommendations of the 2006 Human Variome Project meeting.
Richard G.H. Cotton,Appelbe W,Arleen D. Auerbach,Kevin G. Becker,Walter F. Bodmer,Boone Dj,Boulyjenkov,Samir K. Brahmachari,Larry Brody,Anthony J. Brookes,AF Brown,Peter H. Byers,José María Cantú,Jean Jacques Cassiman,Mireille Claustres,Patrick Concannon,den Dunnen Jt,Paul Flicek,Richard A. Gibbs,Judith G. Hall,Hasler J,Michael Katz,Pui-Yan Kwok,Sandrine Laradi,Annika Lindblom,Donna Maglott,Sge Marsh,Collen Masimirembwa,Shinsei Minoshima,de Ramirez Am,Roberta A Pagon,Rajkumar Ramesar,David Ravine,Sue Richards,David L. Rimoin,Ring Hz,Scriver Cr,Sherry S,Nobuyoshi Shimizu,Lincoln Stein,Ghazi O. Tadmouri,Graham R. Taylor,Michael S. Watson +42 more
TL;DR: The background of the project, the meeting and its recommendations, which addressed all areas of human genetics relevant to collection of information on variation and its effects, are summarized.
Journal ArticleDOI
Human Variome Project: an international collaboration to catalogue human genetic variation.
TL;DR: This research focuses on the development of a single gene-based treatment for central giant cell granuloma, which is a very simple and straightforward procedure to treat central nervous system disorders.
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Recommendations for locus-specific databases and their curation.
Richard G.H. Cotton,Arleen D. Auerbach,Jacques S. Beckmann,Olga O. Blumenfeld,Anthony J. Brookes,Angus Brown,Paola Carrera,Diane W. Cox,Bruce Gottlieb,Marc S. Greenblatt,Pascale Hilbert,Heikki Lehväslaiho,Ping Liang,Sharon Marsh,Daniel W. Nebert,Sue Povey,Sandro Rossetti,Charles R. Scriver,Marshall L. Summar,Dean R. Tolan,I. Verma,Mauno Vihinen,J.T. den Dunnen +22 more
TL;DR: Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there are no formal recommendations for the ideal form of these entities.
Journal ArticleDOI
Planning the Human Variome Project: The Spain Report
Jim Kaput,Richard G.H. Cotton,Lauren Hardman,Michael S. Watson,Aida I. Al Aqeel,Jumana Y. Al-Aama,Fahd Al-Mulla,Santos Alonso,Stefan Aretz,Arleen D. Auerbach,Bharati Bapat,Inge Bernstein,Jong Bhak,Stacey L. Bleoo,Helmut Blöcer,Steven E. Brenner,John Burn,Mariona Bustamante,Rita Calzone,Anne Cambon-Thomsen,Michele Cargill,Paola Carrera,Lawrence Cavedon,Yoon Shin Cho,Yeun Jun Chung,Mireille Claustres,Garry R. Cutting,Raymond Dalgleish,Johan T. den Dunnen,Carlos Díaz,Steven F. Dobrowolski,M. Rosário N.Dos Santos,Rosemary Ekong,Simon B. Flanagan,Paul Flicek,Yoichi Furukawa,Maurizio Genuardi,Ho Ghang,M. V. Golubenko,Marc S. Greenblatt,Ada Hamosh,John M. Hancock,Ross C. Hardison,Terence M. Harrison,Robert Hoffmann,Rania Horaitis,Heather J. Howard,Carol Isaacson Barash,Neskuts Izagirre,Jongsun Jung,Toshio Kojima,Sandrine Laradi,Yeon Su Lee,Jong-Young Lee,Vera Lúcia Gil-da-Silva-Lopes,Finlay A. Macrae,Donna Maglott,Makia J. Marafie,Steven G.E. Marsh,Yoichi Matsubara,Ludwine Messiaen,Gabriela Möslein,Mihai G. Netea,Melissa L. Norton,Peter J. Oefner,William S. Oetting,James O'Leary,Ana María Oller de Ramirez,Mark H. Paalman,Jillian S. Parboosingh,George P. Patrinos,Giuditta Perozzi,Ian Phillips,Sue Povey,Suyash Prasad,Ming Qi,Ming Qi,David J. Quin,Rajkumar Ramesar,C. Sue Richards,Judith Savige,D. Scheible,Rodney J. Scott,Daniela Seminara,Elizabeth A. Shephard,Rolf H. Sijmons,Timothy D. Smith,María Jesús Sobrido,Toshihiro Tanaka,Sean V. Tavtigian,Graham R. Taylor,Jon W. Teague,Thoralf Töpel,Mollie Ullman-Cullere,Joji Utsunomiya,Henk J van Kranen,Mauno Vihinen,Elizabeth Webb,Thomas K. Weber,Meredith Yeager,Young Ii Yeom,Seon Hee Yim,Hyang Sook Yoo +102 more
TL;DR: 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).
Planning the human variome project: the Spain report
Jim Kaput,Richard G.H. Cotton,Lauren Hardman,Maggie Watson,AI Al Aqeel,Jumana Y. Al-Aama,Fahd Al-Mulla,Santos Alonso,Stefan Aretz,Arleen D. Auerbach,Bharati Bapat,Inge Bernstein,Jong Bhak,Stacey L. Bleoo,H Blocker,Steven E. Brenner,John Burn,Mariona Bustamante,Rita Calzone,Anne Cambon-Thomsen,M Cargill,Paola Carrera,Lawrence Cavedon,Yoon Shin Cho,YJ Chung,Mireille Claustres,Garry R. Cutting,Raymond Dalgleish,J.T. den Dunnen,C Diaz,Steven F. Dobrowolski,dos Santos,Rosemary Ekong,SB Flanagan,Paul Flicek,Yoichi Furukawa,Maurizio Genuardi,Ho Ghang,M. V. Golubenko,Greenblatt,Ada Hamosh,John M. Hancock,Ross C. Hardison,Terence M. Harrison,Robert Hoffmann,R Horaitis,Heather J. Howard,Carol Isaacson Barash,Neskuts Izagirre,Jongsun Jung,T Kojima,Sandrine Laradi,YS Lee,Jy Lee,Vera Lúcia Gil-da-Silva-Lopes,Finlay A. Macrae,Donna Maglott,Makia J. Marafie,Sharon Marsh,Yoichi Matsubara,Ludwine Messiaen,G Moslein,Mihai G. Netea,ML Norton,Peter J. Oefner,William S. Oetting,James O'Leary,AM de Ramirez,Mark H. Paalman,Jillian S. Parboosingh,George P. Patrinos,Giuditta Perozzi,Ian Phillips,Susan Povey,Suyash Prasad,Ming Qi,DJ Quin,Rajkumar Ramesar,Carolyn Sue Richards,Judy Savige,D. Scheible,Rodney J. Scott,Daniela Seminara,Elizabeth A. Shephard,Rolf H. Sijmons,Timothy D. Smith,María-Jesús Sobrido,Toshihiro Tanaka,Sean V. Tavtigian,Graham R. Taylor,Jon W. Teague,Thoralf Töpel,Mollie Ullman-Cullere,Joji Utsunomiya,HJ van Kranen,Mauno Vihinen,Emily L. Webb,Thomas K. Weber,Meredith Yeager,Young Ii Yeom +99 more
TL;DR: The Human Variome Project was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB) and the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008 are reported.