IBDelphi Duo
IBDelphi Duo was developed to more accurately calculate the chance that both members of a consanguineous couple are carriers for an unknown recessive autosomal disease. While it is possible to determine this probability based on the pedigree structure, due to the manner in which chromosomes are inherited this figure could significantly over or under estimate its real value. IBDelphi Duo works by analysing the genotype data for the consanguineous couple to find regions that may be IBD by identifying regions that lack SNPs that exclude its possibility.
Data analysis
Analysing the couples data files
Figure 1
A genotype data file for each member of the couple is added by pressing the appropriate button in the upper panel of the main form. When two files have been selected, the button becomes active. To analyse the SNP genotype data, click the in the middle panel of the main form and choose the unit of distance you wish to use. Only distance units present in the males data file can be selected. IBDelphi Duo then creates the SNP database, loads the couples genotype data and then analyses the data. When complete the three buttons in the lower panel become active.
Figure 2
Viewing the analysis results
Viewing a summary of the analysis
To view a visual summary of the couples IBD regions, click the button in the lower panel. This opens a new window which displays the results for all the chromosomes (Figure 3). The black lines represent SNPs that exclude the flanking sequences from having IBD in the couple, while the yellow lines highlight SNPs that do not exclude IBD. Consequently, regions of possible IBD appear as blocks of yellow with the occasional black line which suggests a misscalled SNP genotype. Non-IBD regions appear as a combination of yellow and black lines, while white areas show regions with no SNP coverage. Each chromosome may be flanked by blue and red lines, these represents autozygous regions in the male (blue lines) and female (red lines) genomes. This image can be saved by pressing the in the lower left corner of the window.
Figure 3
Viewing a detailed display of IBD regions on each chromosome
The IBD regions on each chromosome can be viewed by pressing the button; this opens a new window that displays the results for a single chromosome (Figure 4). The current chromosome is identified in the windows title bar and is selected using the drop down list in the lower left hand corner of the window. As in the previous window possible IBD regions are identified by an extended region of yellow lines with few if any black vertical lines. Each vertical yellow line shows the position 'of non-excluding SNP, where as vertical black lines identify SNPs that exclude possible IBD between the couple's genomes. If either the male or female contain extended regions of homozygosity they are shown as blue (male genome) or red (female genome) rectangles flanking the chromosome (figure 5). In consanguineous couples from outbreed populations it is unlikely IBD regions will occur on both copies of a chromosome pair. However in couples from an inbreed population it is possible for a region to have IBD from two distinct common ancestors. Ticking the check box displays a second chromosome in which extended regions of yellow suggest both chromosome copies show IBD (Figure 6).
Figure 4
Figure 5
Figure 6
Due to the limited screen resolution, compared to the large number of SNPs per chromosome, multiple SNPs are likely to occupy the same pixel on the screen. It is consequently difficult to discern whether a region has been excluded by just a few or by many SNPs. To give an indication of the number of SNPs that exclude a region, the window also shows a graph of the number of non-excluding SNPs in a sliding SNP window of 900 SNPs. Since most SNPs are uninformative, the graph only shows regions that have 25 or fewer excluding SNPs. If the check box is ticked the graph also shows a red curve which indicates the number of SNPs that exclude a regions from been a region of dual IBD (Figure 6). Since the graph shows the score across the sliding window of 900 SNP, the IBD region may project either side of the region indicated by the graph. Ticking the check box highlights the true extent of the predicted IBD and predicted dual IBD regions as a thick black and red line.
It is possible to save this window as an image file by pressing the button. Clicking the button creates a web page that contains images of possible IBD regions on all the autosomal chromosomes, an example web page can be seen here.
Viewing a text summary of the possible IBD regions in a couple
Figure 7
Pressing the on the main window opens a new form which summarizes the analysis (Figure 7). The summary includes the name of the SNP genotype data files used and the size of the autosomal genome covered by the SNP data. This values does not include the sex chromosomes or the regions with no SNP coverage in the data file such as the P arm of chromosomes 13, 14, 15, 21 and 22. The total length of IBD regions found in the couple is stated as both a physical size and as a proportion of the autosomal genome. Finally each region found is annotated with the chromosome it's on, it's size, start and end points and the total size of any gaps found in the region. The gap size is important in IBD fragments that span regions of very low SNP coverage, such as the regions flanking the centromere on chromosomes 1 and 9. These gaps are automatically removed from the total size of IBD regions found. This text can be either copied and pasted to a new document or saved as a text file by clicking the in the lower left corner of the form.