IBDelphi populations was developed as an extension to IBDelphi Duo, so that it is possible to automatically perform non-redundant pair wise analysis of genotype data from a large number of individuals, from one or two distinct populations.
Genotyping should be performed using very high density SNP microarrays such as Affymetrix SNP5 or SNP6 chips. These data files must be annotated with chromosome and positional data, which can conveniently be done using SNP6Annotator.
Computer requirements
This program is designed to run on Windows XP SP3 ,Vista SP1 and Windows 7 systems that have the .NET 2.0 framework installed, which is freely available from Microsoft .
Data analysis
Inter-population analysis
Figure 1
When analysing data from two populations, place the genotype files in two folders so that each folder contains data for only one population. Next select each folder in turn using the buttons in the and panels (figure 1). After both folders have been selected the button in the panel will be activated. Pressing this button will prompt the user for the name of the results file and start the analysis. IBDeplhi populations will compare each genotype data file in the first folder to each data file in the second folder. Since the analysis may take some time IBDelphi populations automatically minimises to an icon in the taskbar (figure 2a). To restore the IBDelphi populations window right click its icon in the taskbar and select (figure 2b), because IBDelhi populations is analysing the data it may be slow to respond. Selecting the option will save the present analysis results and then close IBDElphi populations.
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Figure 2
Intra-population analysis
Figure 3
To analyse data form a single population select the tab option (figure 3) and enter the folder containing the genotype data. The button in the panel will be activated, pressing it will prompt the user to enter the name of the results file and then start the analysis. IBDelphi population will then compare each pair of data files in the folder to find the total length of IBD between the two individuals and save the result to the results file. Since the analysis may take some time then IBDelphi populations automatically minimises to an icon in the taskbar (figure 2). To restore the IBDelphi populations window right click its icon in the taskbar and select , because IBDelhi populations is analysing the data it may be slow to respond.
Viewing the results of the analysis
Since it is expected that the results from the analysis will be analysed in a number of different ways, the export file structure has been kept simple with both analysis options creating tab delimited text files which can be opened in a spread sheet program such as Excel. In each, the first column lists the total length of IBD (in Mb's) between the two files listed in the second and third columns. IBDelphi population reads the file in column 2 once and then compares it to all the other files listed in column 3, consequently the data is grouped around the file in second column. Tables 1 and 2 show the first six rows of data from a inter-population and intra-population analysis respectively.
| Total length of IBD (Mb) | File from first population | File from second population | ||
|---|---|---|---|---|
| 10,294,540 | NA06984 CEU.birdseed-v2_anot.xls | NA18939 JPT.birdseed-v2_anot.xls | ||
| 5,369,343 | NA06984 CEU.birdseed-v2_anot.xls | NA18946 JPT.birdseed-v2_anot.xls | ||
| 4,299,804 | NA06984 CEU.birdseed-v2_anot.xls | NA18954 JPT.birdseed-v2_anot.xls | ||
| 3,715,222 | NA06984 CEU.birdseed-v2_anot.xls | NA18955 JPT.birdseed-v2_anot.xls | ||
| 4,353,238 | NA06984 CEU.birdseed-v2_anot.xls | NA18957 JPT.birdseed-v2_anot.xls | ||
| 0 | NA06984 CEU.birdseed-v2_anot.xls | NA18962 JPT.birdseed-v2_anot.xls |
Table 1
| Total length of IBD (Mb) | File A | File B | ||
|---|---|---|---|---|
| 3,520,845 | NA19625 ASW.birdseed-v2_anot.xls | NA19700 ASW.birdseed-v2_anot.xls | ||
| 0 | NA19625 ASW.birdseed-v2_anot.xls | NA19701 ASW.birdseed-v2_anot.xls | ||
| 12,600,070 | NA19625 ASW.birdseed-v2_anot.xls | NA19703 ASW.birdseed-v2_anot.xls | ||
| 5,852,790 | NA19625 ASW.birdseed-v2_anot.xls | NA19704 ASW.birdseed-v2_anot.xls | ||
| 0 | NA19625 ASW.birdseed-v2_anot.xls | NA19711 ASW.birdseed-v2_anot.xls |
Table 2