Human Mutation

Cover image for Vol. 38 Issue 6

Edited By: Garry R. Cutting

Impact Factor: 5.089

ISI Journal Citation Reports © Ranking: 2015: 23/166 (Genetics & Heredity)

Online ISSN: 1098-1004

Virtual Issue: Recommendations and Standards for the Reporting and Databasing of Genetic Variations

Guest Editors: Johan den Dunnen and Mauno Vihinen

Human Mutation actively collaborates with the Human Genome Variation Society (HGVS) and the Human Variome Project (HVP). As part of this activity, the journal promotes publications that suggest recommendations and ultimately standards on all fields covered by the journal. Over the years, Human Mutation has published a range of papers on recommendations and standards for reporting genetic variations and developing variation databases. In this virtual issue we have, for your convenience, collected these papers. Articles related to the functional consequences ("pathogenicity") of variants have been described in another Virtual Issue, Evaluating Mutation Pathogenicity.

Gene variant collection - the issues involved

Best Practice Guidelines for the Use of Next-Generation Sequencing Applications in Genome Diagnostics: A National Collaborative Study of Dutch Genome Diagnostic Laboratories
Marjan M. Weiss, Bert Van der Zwaag, Jan D. H. Jongbloed, Maartje J. Vogel, Hennie T. Brüggenwirth, Ronald H. Lekanne Deprez, Olaf Mook, Claudia A. L. Ruivenkamp, Marjon A. van Slegtenhorst, Arthur van den Wijngaard, Quinten Waisfisz, Marcel R. Nelen and Nienke van der Stoep

Free the Data: One Laboratory's Approach to Knowledge-based Genomic Variant Classification and Preparation for EMR Integration of Genomic Data
Lora J. H. Bean, Stuart W. Tinker, Cristina da Silva and Madhuri R. Hegde

How to catch all those mutations – The report of the third Human Variome Project Meeting, UNESCO Paris, May 2010
Kohonen-Corish, M., Al-Aama, J., Auerbach, A., Axton, M., Barach, C. I., Bernstein, I., Béroud, C., Burn, J., Cunningham, F., Cutting, G., den Dunnen, J., Greenblatt, M., Kaput, J., Katz, M., Lindblom, A., Macrae, F., Maglott, D., Möslein, G., Povey, S., Ramesar, R., Richards, S., Seminara, D., Sobrido, M.-J., Tavtigian, S., Taylor, G., Vihinen, M., Winship, I., and Cotton, R. G. H.

Describing sequence variants

Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion
den Dunnen JT & Antonarakis SE

Describing structural changes by extending HGVS sequence variation nomenclature
Taschner PEM, den Dunnen JT

Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker
Wildeman M, van Ophuizen E, den Dunnen JT, Taschner PEM

General database issues


Practical guidelines addressing ethical issues pertaining to the curation of human locus specific variation databases (LSDBs)
Povey S, Al Aqueel AI, Cambon-Thomsen A, Dalgleish R, Den Dunnen JT, Firth HV, Greenblatt M, Isaacson Barash C, Parker M, Patrinos GP, Savige J, Sobrido MJ, Winship I, Cotton RGH


Curating gene variant databases (LSDBs): Toward a universal standard
Celli, J., Dalgleish, R., Vihinen, M., Taschner, P. E. M. and den Dunnen, J. T.

Sharing LSDB data

Sharing data between LSDBs and central repositories
den Dunnen, J. T., Sijmons, R. H., Andersen, P. S., Vihinen, M., Beckmann, J. S., Rossetti, S., Talbot Jr., C. C., Hardison, R. C., Cotton, R. G. H. and the Human Genome Variation Society (HGVS)

Gene variant databases (LSDBs)

Starting a database

Guidelines for establishing locus specific databases
Vihinen M, den Dunnen JT, Dalgleish R, Cotton RGH

LOVD v.2.0: the next generation in gene variant databases
Fokkema IFAC, Taschner PEM, Schaafsma Gerard CP, Celli J, Laros JFJ, den Dunnen JT

Data models

The Phenotype and Genotype Experiment Object Model (PaGE-OM): A robust data structure for information related to DNA variation
Brookes AJ, Lehvaslaiho H, Muilu J, Shigemoto Y, Oroguchi T, Tomiki T, Mukaiyama A, Konagaya A, Kojima T, Inoue I, Kuroda M, Mizushima H, Thorisson GA, D.Dash, Rajeevan H, Darlison MW, M.Woon, Fredman D, Smith AV, Senger M, Naito K and Sugawara H

Standardised submission forms

A Structured Simple Form for Ordering Genetic Tests Is Needed to Ensure Coupling of Clinical Detail (Phenotype) with DNA Variants (Genotype) to Ensure Utility in Publication and Databases
R.G.H. Cotton, A.D. Auerbach, A.F. Brown, P. Carrera, J. Christodoulou, M. Claustres, J. Compton, D.W. Cox, E. De Baere, J.T. den Dunnen, M. Greenblatt, M. Fujiwara, P. Hilbert, A. Jani, H. Lehvaslaiho, D.W. Nebert, I. Verma, and M. Vihinen, Members of the Human Genome Variation Society and the Human Variome Project Diagnostic Laboratory Working Group

Somatic mutations

Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: practical guidelines for improving data collection, distribution and integration
Olivier, M., Petitjean, A., Teague, J., Forbes, S., Dunnick, J., den Dunnen, J., Langerod, A., Wilkinson, M., Vihinen, M., Cotton, R. G. H., Hainaut, P.

Country specific databases

Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection
Patrinos GP, Al Aama J, Al Aqeel A, Al-Mulla F, Borg J, Devereux A, Felice AE, Macrae F, Marafie MJ, Petersen MB, Qi M, Ramesar RS, Zlotogora J, Cotton RG

Further reading

Guidelines for Reporting and Using Prediction Tools for Genetic Variation Analysis
Mauno Vihinen

Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain
George P. Patrinos, David N. Cooper, Erik van Mulligen, Vassiliki Gkantouna, Giannis Tzimas, Zuotian Tatum, Erik Schultes, Marco Roos and Barend Mons

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical use
Mitropoulou C, Webb AJ, Mitropoulos K, Brookes AJ, Patrinos GP

Recommendations for Locus-Specific Databases and their Curation
Cotton RGH, Auerbach AD, Beckmann JS, Blumenfeld OO, Brookes AJ, Brown AF, Carrera P, Cox DW, Gottlieb B, Greenblatt MS, Hilbert P, Lehvaslaiho H, Liang P, Marsh S, Nebert DW, Povey S, Rossetti S, Scriver CR, Summar M, Tolan DR, Verma IC, Vihinen M, and den Dunnen JT