Literature DB >> 18157828

Recommendations for locus-specific databases and their curation.

R G H Cotton1, 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.   

Abstract

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome. (c) 2007 Wiley-Liss, Inc.

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Year:  2008        PMID: 18157828      PMCID: PMC2752432          DOI: 10.1002/humu.20650

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


  19 in total

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Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  MUTbase: maintenance and analysis of distributed mutation databases.

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3.  Progress of the HUGO mutation database initiative: a brief introduction to the human mutation MDI special issue.

Authors:  R G Cotton
Journal:  Hum Mutat       Date:  2000       Impact factor: 4.878

4.  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

5.  Genetics. Working the (gene count) numbers: finally, a firm answer?

Authors:  Elizabeth Pennisi
Journal:  Science       Date:  2007-05-25       Impact factor: 47.728

6.  A database of locus-specific databases.

Authors:  Ourania Horaitis; C Conover Talbot; Manyphong Phommarinh; Kate M Phillips; Richard G H Cotton
Journal:  Nat Genet       Date:  2007-04       Impact factor: 38.330

Review 7.  Analysis of published PKD1 gene sequence variants.

Authors:  Alexander M Gout; David Ravine; Peter C Harris; Sandro Rossetti; Dorien Peters; Martijn Breuning; Elizabeth Petri Henske; Akio Koizumi; Sumiko Inoue; Yoshiko Shimizu; Wanna Thongnoppakhun; Pa-thai Yenchitsomanus; Constantinos Deltas; Richard Sandford; Roser Torra; Alberto E Turco; Steve Jeffery; Michel Fontes; Stefan Somlo; Laszlo M Furu; Yvo M Smulders; Bernard Mercier; Claude Ferec; Stéphane Burtey; York Pei; Luba Kalaydjieva; Nadja Bogdanova; Marie McCluskey; Lee Jung Geon; C H Wouters; Jana Reiterova; Jitka Stekrová; Jose L San Millan; Gianluca Aguiari; Laura Del Senno
Journal:  Nat Genet       Date:  2007-04       Impact factor: 38.330

8.  UMD (Universal mutation database): a generic software to build and analyze locus-specific databases.

Authors:  C Béroud; G Collod-Béroud; C Boileau; T Soussi; C Junien
Journal:  Hum Mutat       Date:  2000       Impact factor: 4.878

9.  Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases.

Authors:  Mireille Claustres; Ourania Horaitis; Marijana Vanevski; Richard G H Cotton
Journal:  Genome Res       Date:  2002-05       Impact factor: 9.043

Review 10.  PAHdb 2003: what a locus-specific knowledgebase can do.

Authors:  Charles R Scriver; Mélanie Hurtubise; David Konecki; Manyphong Phommarinh; Lynne Prevost; Heidi Erlandsen; Ray Stevens; Paula J Waters; Shannon Ryan; David McDonald; Christineh Sarkissian
Journal:  Hum Mutat       Date:  2003-04       Impact factor: 4.878

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  23 in total

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Authors:  John-Paul Plazzer; Johan T den Dunnen; Timothy Smith; Finlay Macrae; Richard G Cotton
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2.  Integration of molecular and clinical data of 40 unrelated von Willebrand Disease families in a Spanish locus-specific mutation database: first release including 58 mutations.

Authors:  Irene Corrales; Lorena Ramírez; Júlia Ayats; Carme Altisent; Rafael Parra; Francisco Vidal
Journal:  Haematologica       Date:  2010-08-26       Impact factor: 9.941

Review 3.  Computational approaches to study the effects of small genomic variations.

Authors:  Kamil Khafizov; Maxim V Ivanov; Olga V Glazova; Sergei P Kovalenko
Journal:  J Mol Model       Date:  2015-09-08       Impact factor: 1.810

4.  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

5.  Clinical Variant Classification: A Comparison of Public Databases and a Commercial Testing Laboratory.

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Journal:  Oncologist       Date:  2017-04-13

6.  Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from Qatar.

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Journal:  Mol Genet Genomics       Date:  2018-03-20       Impact factor: 3.291

7.  VIPdb, a genetic Variant Impact Predictor Database.

Authors:  Zhiqiang Hu; Changhua Yu; Mabel Furutsuki; Gaia Andreoletti; Melissa Ly; Roger Hoskins; Aashish N Adhikari; Steven E Brenner
Journal:  Hum Mutat       Date:  2019-08-17       Impact factor: 4.878

8.  Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes.

Authors:  Jennifer J Johnston; Wendy S Rubinstein; Flavia M Facio; David Ng; Larry N Singh; Jamie K Teer; James C Mullikin; Leslie G Biesecker
Journal:  Am J Hum Genet       Date:  2012-06-14       Impact factor: 11.025

Review 9.  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

10.  Locus-specific databases and recommendations to strengthen their contribution to the classification of variants in cancer susceptibility genes.

Authors:  Marc S Greenblatt; Lawrence C Brody; William D Foulkes; Maurizio Genuardi; Robert M W Hofstra; Magali Olivier; Sharon E Plon; Rolf H Sijmons; Olga Sinilnikova; Amanda B Spurdle
Journal:  Hum Mutat       Date:  2008-11       Impact factor: 4.878

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