1 / 16

- MIQAS - Minimal Information for QTLs and Association Studies

Rules and file format Jan Aerts jan.aerts@bbsrc.ac.uk. - MIQAS - Minimal Information for QTLs and Association Studies. current practice QTL data handling. what we want to do. get info from QTL: genes, markers, microarray probes, ... find QTN -> narrow down QTL regions in silico.

tmalone
Download Presentation

- MIQAS - Minimal Information for QTLs and Association Studies

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Rules and file format Jan Aerts jan.aerts@bbsrc.ac.uk - MIQAS -Minimal Information for QTLs and Association Studies

  2. current practice QTL data handling

  3. what we want to do • get info from QTL: genes, markers, microarray probes, ... • find QTN -> narrow down QTL regions • in silico within species between species

  4. issues (1) • described in manuscripts as free text... • “From the 17th generation 15 males from the L line and 15 females from the H line were selected to create a reciprocal cross.” • ... or as printed tables (PDF)

  5. issues (2) • existing or custom map • position in cM or by flanking markers • from the beginning of the map or as distance from one of the flanking markers • confidence interval

  6. practice needed

  7. what this means... • need for set of rules that define minimal information for QTLs -> submission • need for file format for easy synchronization between QTL databases -> exchange

  8. A. set of rules • to enable research with QTLs as starting point: • trait investigated • experiment • population • type of analysis • QTL position • map-positions of markers used • way of linking markers between different maps (marker identity!) • position

  9. B. file format - top-level

  10. B. file format - position-level cM

  11. ...in more detail • data submission authors • export function for QTL analysis software • tool (website?) that walks authors through the collection of the relevant data • submit to “MIQAS-compliant” database • data exchange between databases • doesn't matter if it's XML, YAML, Boulder or tab-delimited

  12. keys to success • not • actual nitty gritty of data format • but • support by QTL community • low threshold to use • encouragement by journals

  13. issues/possibilities • legacy data • centrally assigned accession numbers • central repository maps and populations • causative genes within QTL -> maybe in future

  14. status • draft version of rule set and XML format • to do: • discuss rule set with community/set up special interest group • finalize XML format with a limited group of data curators • involve QTL analysis software programmers and journal editors • create wizard and input/output filters for QTL databases

  15. acknowledgements • Roslin Institute • Dave Burt • Wilfrid Carre • DJ DeKoning • Paul Hocking • Ian Dunn • Andy Law • Iowa State University • Zhi-Liang Hu • Jim Reecy

More Related