estimation of linkage disequilibrium using ggt2 software

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Post on 14-Dec-2014

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A tutorial showing estimation of Linkage Disequilibrium using GGT2 Software.

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  • 1. Awais Khan, University of Illinois, Urbana-Champaign Estimation of LD decay using Graphical GenoTypes (GGT) 2.0 software (van Berloo 2008) By Dr. M. Awais Khan University of Illinois, Urbana-Champaign
  • 2. Awais Khan, University of Illinois, Urbana-Champaign Click on GGT2 to start the software
  • 3. Awais Khan, University of Illinois, Urbana-Champaign Click on excel icon, it will open excel data exchange window to enter data
  • 4. Awais Khan, University of Illinois, Urbana-Champaign Copy data from tabsheet Demonstration data GAS of excel file Demonstration data-LD-GGT Click import into GGT to import data pasted into GGT Click on Yes for Show Headers and then Click on Past Excel data to paste data into Excel data exchange window
  • 5. Awais Khan, University of Illinois, Urbana-Champaign Each bar represents the genome of a single individual. Right Click individual bar or Click as shown above to see the detailed view of the genome of each individual
  • 6. Awais Khan, University of Illinois, Urbana-Champaign View of one individual
  • 7. Awais Khan, University of Illinois, Urbana-Champaign Click LD Calculation of LD Select LD Measurement as Lewontin D` and Click on Calc LD for all loci
  • 8. Awais Khan, University of Illinois, Urbana-Champaign Click on LD diallel to view LD values in diallel format
  • 9. Awais Khan, University of Illinois, Urbana-Champaign Click on LD pairwise data to view pairwise distance between markers and pairwise LD values for different LD measurements
  • 10. Awais Khan, University of Illinois, Urbana-Champaign Look at Dist column and D` column and observe the LD trend and distance between markers
  • 11. Awais Khan, University of Illinois, Urbana-Champaign To look at heat plot view of LD pattern Click on HeatPlot
  • 12. LD between the 5 SNPs in 1.64 kb region of a gene . The values in colored squares represent D between SNP pairs. Summary of the results Awais Khan, University of Illinois, Urbana-Champaign Marker_1-Marker_2 Dist R D` M1-M2 0.42 0.4 0.76 M1-M3 1.21 0.17 0.41 M1-M4 1.3 0.17 0.41 M1-M5 1.64 0.1 0.32 M2-M3 0.78 0.45 0.58 M2-M4 0.88 0.46 0.58 M2-M5 1.21 0.29 0.42 M3-M4 0.1 1 1 M3-M5 0.43 0.6 0.73 M4-M5 0.33 0.59 0.73
  • 13. Awais Khan, University of Illinois, Urbana-Champaign Reference: van Berloo R. 2008. GGT 2.0: versatile software for visualization and analysis of genetic data. J. Hered. 99:232236

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