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- 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.

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- MIQAS - Minimal Information for QTLs and Association Studies

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  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

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