TDT-data

A TDT-dataset consists of trios where the parents are usually unaffected while the offspring is affected (Spielman et al., 1993). Therefore half of the chromosomes are observed twice in the sample, even though they occur only once independently. To apply TreeLD to TDT-data, those duplicated chromosomes must be removed from the sample. To this end, the user must include only the non-transmitted chromosomes of the parental generation in the input file, while the offspring generation is still presented as diploid individuals. For example the trio depicted in figure 6.1 would be included in an input file as shown in 6.2. It is not possible at present to apply TreeLD to families with more than one offspring.

Figure 6: Example of an input-file generated from a TDT-Trio. NM is the haplotype on the non-transmitted maternal chromosome, NP is the haplotype on the non-transmitted paternal chromosome, while TM and TP are the transmitted paternal and maternal chromosomes.

6.1Trio

6.2 Input file for one trio.