Progress Report

September 21, 2001
Patrick J. Venta, Ph.D., Vilma Yuzbasiyan-Gurkan, Ph.D., and William D. Schall, D.V.M.
Michigan State University

We currently have DNA samples from 20 chondrodysplasia-affected dogs and 81 samples from relatives. Most of the samples for the affected dogs are in pedigrees that have reasonable statistical power for linkage analysis. The number of samples we have should be just enough to detect linkage between a nearby genetic marker and the disease gene using a relatively high marker density. However, if pedigrees with additional affected animals are discovered, and DNA samples can be obtained, it will make the search to find the causative gene more efficient.

We have been testing the hypothesis that one promising candidate gene, called the CHH gene, is the culprit. This gene was chosen because it causes dwarfism and a particular type of anemia in humans, features that are also prominent signs of Alaskan Malamute chondrodysplasia. At the time that our examination of this gene was underway, the chromosomal location of the human gene was known, but which gene was causative out of about 100 genes in the region remained a mystery. We searched for variation in five canine genes contained in the chromosomal interval in dogs so that we could determine if the region (and thus the same gene) was causative for canine chondrodysplasia. Although we normally find two to three variations among five genes, we found only one. The lack of variability may be because the region is poor in genetic variation in dogs, or more likely because of chance. The marker found was also not particularly variable in the study population, but gave very weak support to the exclusion of this gene as being causative.

Recently, the human CHH gene was identified in humans. It is a rare type of gene because the final product is an RNA molecule rather than a protein (the usual product of most genes). This makes direct examination of the gene more difficult for technical reasons. However, we are able to search for new genetic markers in genes that are extremely close it, given the availability of the complete human genome sequence and our ability to isolate portions of any protein-coding dog gene. We are now testing five genes in two places per gene to help ensure that we get a more variable marker this time. We anticipate a final verdict on the CHH gene in the near future. We are also testing one other moderately interesting candidate gene called EPB72 and plan to have results on it at about the same time as for the CHH gene.

We are concurrently developing genetic markers in gene-dense regions of the genome, in preparation for a whole genome scan in case the candidate genes are excluded. Targeting gene-dense regions for examination before looking at gene-poor regions increases the probability that we will find a linked marker earlier rather than later. We have been able to identify these markers due to recent scientific publications on the map of the dog genome and because of the availability of the human genome sequence. Although extracting the information from these sources has taken some effort, it may help us to find the chondrodysplasia gene sooner than would a purely a random search. About half of the markers covering the gene-rich regions have been identified and the specific chemicals (small pieces of DNA called primers) needed to test them have been manufactured. We are now in the process of developing the second half of the markers.

We will continue to scan the human medical literature for other potential candidate genes that may lead to an earlier discovery of the chondrodysplasia gene. We are also currently developing a promising new method to do whole genome linkage scans that, if successful, should make scans much more efficient for all disease gene searches. The method takes into account the unique population structures found in most dog breeds. Although refinements of the method may take some time, the usefulness should become apparent during the upcoming year of work and we will immediately apply it to help in the search for the Alaskan malamute chondrodysplasia gene.