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DominantMapper

Requirements

This program is designed to run on Windows XP SP3 or Vista SP1 systems that have the .NET 2.0 framework installed, which is freely available from Microsoft .

Genotyping should be performed using very high density SNP microarrays such as Affymetrix SNP5 or SNP6 chips. SNP6 data files must be annotated with chromosome and positional data, which can conveniently be done using SNPAnnotator.

Assumptions

The basic algorithm used by DominantMapper works on four assumptions:

  1. The disease is a dominant condition.
  2. All the affected individuals have the same mutation.
  3. All the carriers are affected and are not mosaic for a new germline mutation.
  4. If unaffected sib data is included in the analysis the mutation must demonstrate complete penetrance.

Data entry

The data shown in this user guide relates to the pedigree shown in Figure 1, where SNP data is available for the individuals marked with an asterisk. The family has been shown to contain a dominant mutation in the TSPAN12 gene at 120 Mb on Chromosome 7. While the pedigree contains a number of nuclear families, SNP data is only available for both parents in two families (parents 3 - 4, and 11 - 12). The affected children of the other families are not analysed separately as part of a distinct family, but rather as affected relatives of one of the other families.

Figure 1

Figure 1

Adding parents

Figure 2

Figure 2

Each family to be analysed is added sequentially and must include both parents, one of whom is affected, and have at least one affected child. To add the parents, press the appropriate Select button (Figure 2, underlined in blue for an affected parent and red for the unaffected parent) and select the correct SNP data file. The name of the file is then displayed by the program (underlined in Figure 2).

Adding children from affected families

Figure 3

Figure 3

Affected and unaffected children are added using the buttons on the Affected children and Unaffected children panels (highlighted by green and orange rectangles respectively in Figure 2). Data for an affected child is added using the Affected button (underlined in red, Figure 3) and the name of the SNP data file is added to the drop-down list below the button. To remove a genotype file select its name in the drop-down list and press the Delete button (underlined in blue in Figure 3). Similarly, the data for unaffected children is added and removed using the appropriate buttons in the Unaffected children panel.


Adding affected relatives

Figure 4

Figure 4

It is possible to include affected individuals who belong to the same pedigree, but whose parent data is incomplete or absent (e.g. individuals 5, 15 and 17 in Figure 1). These affected relatives are included by pressing the Relative button on the Affected relatives panel (highlighted by the red line, Figure 4) and the file name appears in the drop-down list. Selecting a file name in the drop-down list and pressing the Delete button removes the file.


Adding a family

Figure 5

Figure 5

Once the parents, children and affected relatives have been added, the family can be stored by the program by pressing the Add button (underlined in red, Figure 5) on the Add family panel. The family name is created by combining the affected and unaffected parents’ file names, and is added to the drop-down list in the Add family panel. Families can be removed by selecting their family name and pressing the Delete button (underlined in blue, Figure 5). Pressing the Edit button (underlined in green, Figure 5) removes the selected family from the drop-down list and re-populates the family data into the Parents, Affected children, Unaffected children and Affected relatives panels, from where the family data can be edited and then re-added to the family drop-down list by pressing the Add button again. Once a family has been added the process can be repeated for other nuclear families in the pedigree.


Viewing the analysis results

Analysing and viewing the data

Figure 6

Figure 6

To analyse the SNP genotype data, press the Analyse button (underlined by the red line, Figure 6) and choose which distance units you wish to use on the File details form. Only those distance units present in the affected parent’s SNP data file of the first family are available to be selected. In Figure 6 only the Physical (Mb) option is available, as the file contains no genetic map positions.

Once the mapping units have been selected, the program will load the SNP data and then test each SNP for missing genotypes (nocalls) and non-Mendelian inheritance. SNPs that fail these tests will be excluded from further analysis. The remaining SNPs are then tested against a set of rules to identify SNPs that can be excluded from linkage to the disease loci. Once this analysis is complete the View button (above the blue line in Figure 6) will become active; pressing it will open a new window displaying the results of the analysis (Figure 7).

The results window displays data for one chromosome at a time, and is composed of two regions which display the analysis results (Figure 7). The upper region (orange bar to the right of Figure 7) shows the results of the rule-based analysis for each SNP, while the lower region (black bar to the right of Figure 7) shows a graph of an empirically derived score, plotted against chromosome position. The chromosomal map position is shown between the two regions; the units are either Mb or cM, according to the unit selection made at the start of the analysis. The discontinuous thick blue line below the scale represents the positions of the SNPs, with gaps identifying regions with no SNP coverage.


Figure 7

Figure 7


As with SAMPLE, IBDfinder and AutoSNPa, the results are intended to be assessed visually, and have not undergone statistical analysis. Rather, these programs perform comparisons of genotypes across large segments of the genome, in order to make inferences about common ancestry of such regions. Since these chromosomal fragments have undergone relatively few recombinational events, their size is very variable, and not of itself an indicator of the likelihood of harbouring a disease gene.

Results window – upper region

The upper region is composed of 5 horizontal ribbons on which vertical bars representing SNPs are displayed; the colour of the bar represents the linkage status of the SNPs as follows:

Green: Uninformative SNPs.
Orange: SNPs excluded because an affected relative and an affected child are homozygous for different alleles.
Yellow: SNPs excluded because an affected child and unaffected child are homozygous for the same allele, while their affected parent is heterozygous.
Red: SNPs excluded because affected children are homozygous for different alleles.

The lowest strip combines all the information for each exclusion criterion, with regions that show an extended run of green markers being consistent with linkage to the disease gene.

N.B. The data used to create Figure 7 does not contain any unaffected children; consequently there are no yellow markers in this figure.

Results window – lower region

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 visually 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 lower region of the display shows a graph of the number of non-excluding SNPs in a sliding SNP window. The size of this window is set using the Window size drop-down list box (Figure 7, underlined in red). Since most SNPs are uninformative, the graph only shows regions that have 25 or fewer excluding SNPs. The horizontal gridlines indicate the number of excluding SNPs in the window, at intervals of 5 excluding SNPs. Figures 8–10 show the results for Chromosome 7 (which in this family is known to carry a dominant TSPAN12 mutation located at ~120 Mbp.


A

Figure 8a

B

Figure 8b

C

Figure 8b

Figure 8


By default, this graph is plotted as a line graph, with the points positioned at the centre of each SNP window. However, since SNP density is not uniform along the chromosome, it is alternatively possible to view the graph as a series of Tapes or Bars that indicate the extents of the windows (Figures 8B, C). While the Bars view displays the width of a window, it is possible for regions to overlap, making them appear to be one wide region. To overcome this, the Tape plot highlights points where regions overlap. These different plots are selected using the Plot type drop-down menu (underlined in green in Figure 7).

View options

Below the graph is a series of controls for changing the view options of the two display regions, and for saving the underlying data. These include the Window size and Plot type controls described above, while the Chromo listbox (underlined in blue in Figure 7) allows selection of which used to select which chromosome is displayed. (The current chromosome is also indicated at the left-hand side of the title bar.) For example, to view Chr. 7, select 7 from the list (Figure 7, blue underlining).

A

Figure 9a

B

Figure 9b

C

Figure 9d

Figure 9


The Window size list controls the display of the plot of the number of non-excluding SNPs in the lower part of the display. The size of the sliding window can be set to 100, 200, 300 or 400 SNPs; the latter three settings are illustrated in Figure 9A-C respectively).


Export data

Figure 10

Figure 10


The data underlying a region of interest can be exported either to a colour-coded web page or to a tab-delimited text file. To select such a region, place the mouse cursor at the start of the region and while holding down the left mouse button, drag the cursor to the end of the region. The currently selected region will be delimited by two black vertical lines (Figure 10). To save the data, press Save data (underlined in red, Figure 10) and enter the name of the output file and filename extension.


It is also possible to create a web page containing the image of the analysis for each of the chromosomes (Figure 11) by clicking the Images button (underlined in blue in Figure 10).

Figure 11

Figure 11




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