01547-A: Genetic Analysis of Alopecia X in Pomeranians

Grant Amount: $12,960

Tosso Leeb, PhD; University of Bern

May 1, 2011 - April 30, 2012

Sponsor(s): National Beagle Club

Breed(s): Pomeranian

Research Program Area: Dermatology and Allergic Disease

Project Summary

During the project period we collected more than 100 samples from Pomeranians and Keeshonden. Many of these dogs were seen by expert dermatologists, so that their phenotype information should be highly accurate. These samples will facilitate our further research. The main experiment of this application was the targeted re-sequencing of a 1.6 million base pair segment of chromosome 15 in two affected and two non-affected Pomeranians. We performed this sophisticated experiment exactly as planned and identified ~4,320 sequence variants in the investigated part of the genome. Very surprisingly, none of these sequence variants was predicted to affect any of the protein sequences encoded by the genes in the targeted region. This was quite unexpected and disappointing to us as we had hypothesized that the alopecia X mutation most likely causes the complete or partial loss of function of one of these genes. We therefore went back to our original mapping experiment that formed the basis of this research project. In 2008 we had performed a genome-wide association study (GWAS) using the at that time state-of-the art Affymetrix v2 SNP chips with ~50,000 markers. We now repeated this experiment with the same dogs, but using the newer illumina canine_HD SNP chips with ~177,000 markers. The repeated GWAS confirmed the association to alopecia X on chromosome 15. The signal got even stronger with the newer illumina SNP chips. However, the signal also moved 4 million base pairs on chromosome 15 to a new and presumably correct position. We had not been able to pick up the correct position in the original mapping experiment with the Affymetrix chips as they have a rather uneven marker spacing with a lack of markers in the critical region on chromosome 15. We will use the newly gained mapping information in our further search for the causative mutation. We are currently re-sequencing the entire genome of an affected Pomeranian. We hope that we will be able to identify the causative mutation in the newly defined interval, after we get the sequencing data. We would like to thank all people who donated blood samples and money for this research project. We still ask for the submission of blood samples from alopecia X affected dogs as well as from older dogs (>5 years) with good hair quality. Information on sample submission can be found at: http://www.vetsuisse.unibe.ch/genetic/content/e2353/e2479/indexeng.html

Publication(s)

None at this time.