Werner's Syndrome Data: OLD GENEHUNTER VERSION: 2005

A little background about Werner's Syndrome as well as some references can be found here.

For a full list of data files available, click here.

ApoB on Chromosome 2

ApoB is on chromosome 2 and is unlinked to the Werner's syndrome locus which is known to be on chromosome 8p. Some alleles for ApoB are quite different in frequency in the Japanese compared to frequencies in caucasians. What is interesting is that if caucasian frequencies are used, spurious evidence about linkage can result from the analysis (although a lod score of 3 is not achieved, an "interesting" lod score of over 2 is obtained, while if Japanese frequencies are used, the maximum lod score is under 1).

Homozygosity mapping

In this exercise, we took all inbred affected individuals with ApoB genotype from 19 Japanese families. There are 3 sib pairs (641 and 642, 1741 and 1742, 1541 and 1542) but they are otherwise unrelated. The marker data together with ApoB allele frequencies from different control populations are given in homoApob.dat.

Linkage analysis with Genehunter

We can use Genehunter to calculate lod score based on the pedigree data with the single marker Apob and see what's the influence of using different allele frequency estimates.

1. Data with 19 Japanese families: apob3gh.dat.

   The fields are:

   1. Family Id
   2. Personal ID
   3. Father ID
   4. Mother ID
   5. Sex: 1 = Male, 2 = Female
   6. Disease Status: 1 = Normal, 2 = Diseased, 0 = Unknown
   7. Next two fields are Apob genotypes, 0 = Unknown, 1-9 allele codes


2. Genehunter parameter files, using different sets of allele frequencies. Genehunter output files are also given. Relevant lines in the parameter files are annotated.
   • Standard Caucasian: GH parameter file (output file).
   • UW Caucasian controls: GH parameter file (output file).
   • UW Japanese controls: GH parameter file (output file).

Chromosome 8 Markers

Linkage analysis with Genehunter

Some of the affected individuals in those Japanese families had data on 35 markers close to WRN on Chromosome 35. Some of the markers are very close together and not informative for linkage analysis, so we are only going to use a subset (13) of the markers. Again we have allele frequencies from both Japanese and Caucasian controls.

• Pedigree data for linkage analysis with Genehunter: ws8ped.dat.



• GH Parameter files with two sets of allele frequencies: Japanese: wschr8_Jap.par. Caucasians: wschr8_Cau.par.



• GH output files: Japanese: ghchr8jp.out, Caucasians: ghchr8ca.out.