Literature DB >> 19306393

Sharing data between LSDBs and central repositories.

Johan T den Dunnen1, Rolf H Sijmons, Paal S Andersen, Mauno Vihinen, Jacques S Beckmann, Sandro Rossetti, C Conover Talbot, Ross C Hardison, Sue Povey, Richard G H Cotton.   

Abstract

Several Locus-Specific DataBases (LSDBs) have recently been approached by larger, more general data repositories (including NCBI and UCSC) with the request to share the DNA variant data they have collected. Within the Human Genome Variation Society (HGVS) a document was generated summarizing the issues related to these requests. The document has been circulated in the HGVS/LSDB community and was discussed extensively. Here we summarize these discussions and present the concluded recommendations for LSDB data sharing with central repositories. (c) 2009 Wiley-Liss, Inc.

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Year:  2009        PMID： 19306393      PMCID： PMC4409810          DOI： 10.1002/humu.20977

Source DB:  PubMed          Journal:  Hum Mutat        ISSN： 1059-7794            Impact factor:   4.878


  9 in total

1.  A survey of locus-specific database curation. Human Genome Variation Society.

Authors:  Richard G H Cotton; Kate Phillips; Ourania Horaitis
Journal:  J Med Genet       Date:  2007-04       Impact factor: 6.318

Review 2.  Perspective on genes and mutations causing retinitis pigmentosa.

Authors:  Stephen P Daiger; Sara J Bowne; Lori S Sullivan
Journal:  Arch Ophthalmol       Date:  2007-02

3.  Recommendations for locus-specific databases and their curation.

Authors:  R G H Cotton; A D Auerbach; J S Beckmann; O O Blumenfeld; A J Brookes; A F Brown; P Carrera; D W Cox; B Gottlieb; M S Greenblatt; P Hilbert; H Lehvaslaiho; P Liang; S Marsh; D W Nebert; S Povey; S Rossetti; C R Scriver; M Summar; D R Tolan; I C Verma; M Vihinen; J T den Dunnen
Journal:  Hum Mutat       Date:  2008-01       Impact factor: 4.878

4.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

5.  Genetic interaction between Bardet-Biedl syndrome genes and implications for limb patterning.

Authors:  Marwan K Tayeh; Hsan-Jan Yen; John S Beck; Charles C Searby; Trudi A Westfall; Hilary Griesbach; Val C Sheffield; Diane C Slusarski
Journal:  Hum Mol Genet       Date:  2008-04-01       Impact factor: 6.150

6.  A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes.

Authors:  Douglas F Easton; Amie M Deffenbaugh; Dmitry Pruss; Cynthia Frye; Richard J Wenstrup; Kristina Allen-Brady; Sean V Tavtigian; Alvaro N A Monteiro; Edwin S Iversen; Fergus J Couch; David E Goldgar
Journal:  Am J Hum Genet       Date:  2007-09-06       Impact factor: 11.025

7.  Recommendations of the 2006 Human Variome Project meeting.

Authors:  Richard G H Cotton; William Appelbe; Arleen D Auerbach; Kevin Becker; Walter Bodmer; D Joe Boone; Victor Boulyjenkov; Samir Brahmachari; Lawrence Brody; Anthony Brookes; Alastair F Brown; Peter Byers; Jose Maria Cantu; Jean-Jacques Cassiman; Mireille Claustres; Patrick Concannon; Richard G H Cotton; Johan T den Dunnen; Paul Flicek; Richard Gibbs; Judith Hall; Julia Hasler; Michael Katz; Pui-Yan Kwok; Sandrine Laradi; Annika Lindblom; Donna Maglott; Steven Marsh; Collen Muto Masimirembwa; Shinsei Minoshima; Ana Maria Oller de Ramirez; Roberta Pagon; Raj Ramesar; David Ravine; Sue Richards; David Rimoin; Huijun Z Ring; Charles R Scriver; Stephen Sherry; Nobuyoshi Shimizu; Lincoln Stein; Ghazi Omar Tadmouri; Graham Taylor; Michael Watson
Journal:  Nat Genet       Date:  2007-04       Impact factor: 38.330

8.  PhenCode: connecting ENCODE data with mutations and phenotype.

Authors:  Belinda Giardine; Cathy Riemer; Tim Hefferon; Daryl Thomas; Fan Hsu; Julian Zielenski; Yunhua Sang; Laura Elnitski; Garry Cutting; Heather Trumbower; Andrew Kern; Robert Kuhn; George P Patrinos; Jim Hughes; Doug Higgs; David Chui; Charles Scriver; Manyphong Phommarinh; Santosh K Patnaik; Olga Blumenfeld; Bruce Gottlieb; Mauno Vihinen; Jouni Väliaho; Jim Kent; Webb Miller; Ross C Hardison
Journal:  Hum Mutat       Date:  2007-06       Impact factor: 4.878

9.  Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results.

Authors:  Sharon E Plon; Diana M Eccles; Douglas Easton; William D Foulkes; Maurizio Genuardi; Marc S Greenblatt; Frans B L Hogervorst; Nicoline Hoogerbrugge; Amanda B Spurdle; Sean V Tavtigian
Journal:  Hum Mutat       Date:  2008-11       Impact factor: 4.878
  9 in total
  8 in total

1.  Human Variome Project Quality Assessment Criteria for Variation Databases.

Authors:  Mauno Vihinen; John M Hancock; Donna R Maglott; Melissa J Landrum; Gerard C P Schaafsma; Peter Taschner
Journal:  Hum Mutat       Date:  2016-03-21       Impact factor: 4.878

Review 2.  The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease.

Authors:  Judy Savige; Raymond Dalgleish; Richard Gh Cotton; Johan T den Dunnen; Finlay Macrae; Sue Povey
Journal:  Pediatr Nephrol       Date:  2014-11-11       Impact factor: 3.714

3.  ClinGen--the Clinical Genome Resource.

Authors:  Heidi L Rehm; Jonathan S Berg; Lisa D Brooks; Carlos D Bustamante; James P Evans; Melissa J Landrum; David H Ledbetter; Donna R Maglott; Christa Lese Martin; Robert L Nussbaum; Sharon E Plon; Erin M Ramos; Stephen T Sherry; Michael S Watson
Journal:  N Engl J Med       Date:  2015-05-27       Impact factor: 91.245

4.  Practical guidelines addressing ethical issues pertaining to the curation of human locus-specific variation databases (LSDBs).

Authors:  Sue Povey; Aida I Al Aqeel; Anne Cambon-Thomsen; Raymond Dalgleish; Johan T den Dunnen; Helen V Firth; Marc S Greenblatt; Carol Isaacson Barash; Michael Parker; George P Patrinos; Judith Savige; Maria-Jesus Sobrido; Ingrid Winship; Richard G H Cotton
Journal:  Hum Mutat       Date:  2010-11       Impact factor: 4.878

5.  VarioML framework for comprehensive variation data representation and exchange.

Authors:  Myles Byrne; Ivo Fac Fokkema; Owen Lancaster; Tomasz Adamusiak; Anni Ahonen-Bishopp; David Atlan; Christophe Béroud; Michael Cornell; Raymond Dalgleish; Andrew Devereau; George P Patrinos; Morris A Swertz; Peter Em Taschner; Gudmundur A Thorisson; Mauno Vihinen; Anthony J Brookes; Juha Muilu
Journal:  BMC Bioinformatics       Date:  2012-10-03       Impact factor: 3.169

6.  Towards linked open gene mutations data.

Authors:  Achille Zappa; Andrea Splendiani; Paolo Romano
Journal:  BMC Bioinformatics       Date:  2012-03-28       Impact factor: 3.169

7.  Ensembl's 10th year.

Authors:  Paul Flicek; Bronwen L Aken; Benoit Ballester; Kathryn Beal; Eugene Bragin; Simon Brent; Yuan Chen; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Julio Fernandez-Banet; Leo Gordon; Stefan Gräf; Syed Haider; Martin Hammond; Kerstin Howe; Andrew Jenkinson; Nathan Johnson; Andreas Kähäri; Damian Keefe; Stephen Keenan; Rhoda Kinsella; Felix Kokocinski; Gautier Koscielny; Eugene Kulesha; Daniel Lawson; Ian Longden; Tim Massingham; William McLaren; Karine Megy; Bert Overduin; Bethan Pritchard; Daniel Rios; Magali Ruffier; Michael Schuster; Guy Slater; Damian Smedley; Giulietta Spudich; Y Amy Tang; Stephen Trevanion; Albert Vilella; Jan Vogel; Simon White; Steven P Wilder; Amonida Zadissa; Ewan Birney; Fiona Cunningham; Ian Dunham; Richard Durbin; Xosé M Fernández-Suarez; Javier Herrero; Tim J P Hubbard; Anne Parker; Glenn Proctor; James Smith; Stephen M J Searle
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

8.  Collection of variation causing disease--the Human Variome Project.

Authors:  Richard G H Cotton
Journal:  Hum Genomics       Date:  2009-07       Impact factor: 4.639
  8 in total

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