AKCCHF grant #01670-A: Pinpointing the causal mutation(s)
underlying a genome-wide association signal for hereditary cataract in
Northern breeds
Grant Status: Closed
Grant Amount: $12,960. SCARF contributed $2000.
Dr. Sally L Ricketts, PhD, Animal Health Trust
Sponsor(s): Alaskan Malamute Club of America, Inc.
Breed(s): Alaskan Malamute, Samoyed, Siberian Husky
Disease(s): Cataracts
Abstract:
This study aims to pinpoint precisely causal mutations for hereditary cataract (HC) in Northern, or Arctic, breeds. It follows on from our recent investigations in which we have found a region of the genome on canine chromosome 18 that shows genome-wide statistical association with HC in the Siberian Husky, and we also have evidence that the same associated region is relevant in the Alaskan Malamute and Samoyed. As the region spans approximately 6.5 million letters of the DNA code and encompasses over 100 genes, we will use new molecular sequencing technologies to search this sequence for mutations in 10 Siberian Huskies (five HC-affected dogs and five clear dogs). We will assess any novel mutations that we identify in a set of over 200 Siberian Huskies to determine the frequency of the mutations and to assess their specific effect on risk of HC. We will then assess whether the Siberian Husky HC causal mutations are also present in the Alaskan Malamute and Samoyed. We expect to find at least one causal mutation for HC that will be relevant in at least these three breeds, but due to the close ancestral relationship among Northern breeds it is likely that mutations will also be shared with additional breeds. Our results will be used to develop a predictive and diagnostic tool for owners, breeders and veterinarians that will identify dogs at increased risk of developing HC, thus enabling better informed breeding decisions to be made to avoid producing clinically affected dogs.
Project Summary from AKCCHF.org website:
“We have conducted a study to resequence a region of the genome on canine chromosome 18 that we previously found to be statistically associated with hereditary cataract (HC) in Northern, or Arctic, breeds in a genome-wide association study, in order to identify causative mutation(s) for HC in these breeds. We defined HC in these breeds as dogs with cataracts in both eyes located within the posterior polar subcapsular region of the lens. We have used molecular targeted sequencing technology to obtain data for approximately 3.8 million letters of DNA spanning the HC-associated region of the genome in ten Siberian Huskies (five HC cases and five control dogs with clear eyes over the age of 6 years). In this dataset we found over 35,000 variants among the ten dogs and the Boxer reference genome sequence. We devised a computer program to examine the segregation of each variant with HC using both a dominant and recessive genetic model and we found 200 variants that showed perfect segregation with HC in our ten dogs. We excluded variants where the potential ‘risk’ allele was the same as the Boxer reference genome sequence, as it is unlikely that these would represent causal mutations. This left us with 78 variants that we checked manually against online databases to assess which were within, or very close to, gene coding regions. This confirmed that ten variants were located in gene coding regions. Two of these coding variants were predicted to cause a change in the protein sequence of the gene and were found to be potentially damaging to protein function by analysis of online databases. Futhermore, the non-risk allele was highly conserved among many different animal species, which is additional evidence to suggest that it is important for normal function of the protein. We assessed these two variants in 200 Siberian Huskies, 200 Alaskan Malamutes and 130 Samoyeds and found that one of the variants showed strong statistical association with HC in two of the breeds. However, this variant is very common in both dogs with HC and in older dogs with clear eyes, and doesn’t completely account for HC in our samples. It may be that this is a susceptibility variant and there is an environmental component to HC that affects how the genetic susceptibility is expressed, however, before we explore this possibility we are continuing with our analysis of the resequencing data to ensure we have completed a fully comprehensive investigation of the region.”