Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Human Variome Project quality
assessment criteria for variation
databases
Mauno Vihinen on behalf of the Working Group
Pro...
Numerous variation databases are available
Widely used for various purposes (research, diagnosis..)
Their contents, update...
Variation database quality, working group
HVP Working Group for Variant Database Quality Assessment, 2014
Produced a guide...
Components of quality
Two case studies
- BTKbase
- ClinVar
What next?
1) A working group is currently translating the criteria to items that can be
evaluated in practice
Some qualit...
Thanks!
John Hancock
Donna Maglott
Melissa Landrum
Gerard Schaafsma
Peter Taschner
http://www.humanvariomeproject.org/fini...
Upcoming SlideShare
Loading in …5
×

Human variome project quality assessment criteria for variation databases - Mauno Vihinen

154 views

Published on

Numerous databases containing information about DNA, RNA and protein variations are available. Gene-specific variant databases (locus specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database [1]. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. Instructions are available for the developed quality criteria and how implementation of the quality scheme can be achieved ([1], http://www.humanvariomeproject.org/finish/19/255.html). Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance.

Reference: [1] Vihinen, M., Hancock, J. M., Maglott, D. R., Landrum, M. J., Schaafsma, C. P., Taschner, P. Human Variome Project quality assessment scheme for variation databases. Hum. Mutat. (in press).

Published in: Science
  • Be the first to comment

  • Be the first to like this

Human variome project quality assessment criteria for variation databases - Mauno Vihinen

  1. 1. Human Variome Project quality assessment criteria for variation databases Mauno Vihinen on behalf of the Working Group Protein Structure and Bioinformatics Group Department of Experimental Medical Science Lund University, Sweden
  2. 2. Numerous variation databases are available Widely used for various purposes (research, diagnosis..) Their contents, update frequency etc vary So does the quality How to define variation database quality? Quality of databases
  3. 3. Variation database quality, working group HVP Working Group for Variant Database Quality Assessment, 2014 Produced a guideline, accepted by HVP Publication in the Human Mutation 25th anniversary issue
  4. 4. Components of quality Two case studies - BTKbase - ClinVar
  5. 5. What next? 1) A working group is currently translating the criteria to items that can be evaluated in practice Some quality items have simple yes/no evaluation For many others more detailed grading need to be established Design a scheme to measure overall database quality 2) Beta testing with some real databases Refining the quality calculation scheme 3) Database quality evaluation Requires independent group without any conflict of interest Feeback for curators and information for users (electronic seal) 4) Refinement of quality criteria 5) Evaluation of databases every few years Voluntary participation
  6. 6. Thanks! John Hancock Donna Maglott Melissa Landrum Gerard Schaafsma Peter Taschner http://www.humanvariomeproject.org/finish/19/255.html Vihinen et al. Hum Mutat (2016) http://structure.bmc.lu.se mauno.vihinen@med.lu.se

×