Would you have thought that the beloved tail-wagging pet resting on your couch could serve as a source for human genetic discoveries? Few people know or even come to think that the genome and diseases of dogs are 95% the same as those of humans. The genetic research conducted by Professor Hannes Lohi at the University of Helsinki brings forwards significant information regarding the eye, bone and neurological diseases of both dogs and humans. The field of study represented by Lohi is promoted by a Europe-wide bio and medical research infrastructure (ELIXIR) for which Finland is a co-founder.
The “Eureka!” moment occurred about ten years ago when research fellow Hannes Lohi pinpointed the epilepsy gene of miniature dachshunds with his research group in Toronto. At the same time elsewhere, the gene was also found in humans. This coincidence was the starting point of the cross-disciplinary canine genetic research led by the professor at the Faculty of Veterinary Medicine and Medicine of the University and Helsinki and the Folkhälsan Research Center. Since 2006, DNA samples from almost 50,000 Finnish dogs have been collected in the DNA bank established by Lohi.
“Dog breeds provide a genetically excellent structure especially for behavioural studies and research into canine and human diseases in general. What animal species is socially gifted, shares the same environment and is exposed to the same pathogens other than man’s best friend?”, Lohi realised at the time.
Lohi noted that inbreeding within dog breeds, in particular, facilitates the identification of disease genes.
“It is easier to discover genes from bloodlines using smaller study cohorts. Compared with the mice and rats typically used in studies, dogs are closer to humans also in terms of vital functions due to their size”, Lohi says.
The spectrum of the canine genetic research led by Lohi is extensive. The subjects include eye diseases, autoimmune diseases, neurological diseases as well as skeletal muscle diseases. The group has identified several new disease genes in dogs from factors causing, for example, epilepsy, dwarfism and anxiety disorders. With the genetic areas found, conditions such as anxiety disorders, from which about 5% of the human population will suffer at some point during their life, gain a new research basis for the study of, for example, the genetic background and environmental factors in obsessive-compulsive behaviours.
“We look for the gene causing a disease in a dog breed and, at the same time, the breed provides a canine model for identifying the disease mechanism of human diseases”, Lohi says, describing the benefits of the research.
The group identified the CNGB1 gene that causes retinal degeneration and, at worst, blindness in Papillon dogs. The same gene has been found in human patients. One in ten people over the age of 65 suffers from this disease during retirement. The condition involves blind spots that limit the area of sharp vision, preventing the renewal of a driving licence, for example.
“With the further development of partially developed drugs, the degeneration of the human retina could be treated externally with gene therapy, for example, by applying to the retina a cream containing viruses carrying normal gene copies that would correct the functioning of the cells and may correct vision”, Lohi describes the possibilities.
“After identifying the gene, it becomes possible to study the disease mechanism and make comparisons between humans and dogs. The gene may not always be the same in humans and the mutation can be located elsewhere, in another gene of the cell pathway. Understanding the gene function and disease mechanism are prerequisites for inventing treatments for the disease. On the other hand, when a mutation is found, it is possible to develop a genetic test for dogs and see which dogs are carriers of the disease. This allows dog breeders to quickly benefit from the research”, Lohi says.
He is involved in Genoscoper Laboratories Ltd, a company that, under his leadership, has built a unique and affordable genome-wide genetic test for dogs, MyDogDNA, which tests the dog’s carrier status for over 100 diseases and traits in one go, as well as genomic diversity and structure.
“The genetic diversity of dogs has been weakened by breeding. The number of dogs carrying disease genes has increased, and because many diseases arise in adulthood, sick dogs will have already been used for breeding. To counter the negatives, breeding may lead to the gene causing the disease becoming more common in a particular dog breed. The candidate gene is more easily identified in dogs than in humans and with fewer samples.”
A large number of veterinarians and dog lovers around Finland have not been enthusiastic about participating in a DNA sampling effort for the benefit of a passing project. The aim of the research group is to build a separate, extensive sequence and variant database for Finnish dogs and cats, similar to the one that already exists for humans (1000 Genomes).
“Genetic research has always been the flagship of Finnish science. We have uniquely accurate health information on patients, including family trees. Equivalent pedigree databases and health data are available on dogs, and soon also on cats. Few countries have such a good, centralised system”, Lohi says.
“There are 400 breeds of dogs. At present, a total of 700 diseases have been depicted in dogs and more are found all the time. The aim is to have a database with the entire genome of each breed sequenced. This will speed up genetic discoveries”, Lohi says.
Lohi believes that the benefit of a large sequence database is a kind of consensus. This is achieved once hundreds or thousands of genomes have been sequenced and the large number of variants can be accurately mapped. There may be many diseases in the same breed.
“For example, if the genomes of 1,000 dogs from 50 breeds have been sequenced into the database, it will include an estimated 25 million variants from the different breeds. The database will facilitate future projects in that a small family of dogs or cats can be studied with just a few of the individual animals sequenced to provide a sufficiently reliable result on the correct disease variant. The variants of a dog patient are compared with the variants of the thousand samples in the database and, if a particular variant is found in the patient but not in the reference samples in the database, it can be inferred to be disease-causing. After this, the matter is confirmed using a larger file.”
“An efficient and nationally significant database will help us catch disease genes faster. As things are now, you have to do a lot work in research to obtain a sufficient picture of the location of a variant in the chromosomes. Going forward, a sample will be taken, the entire genome sequenced and compared directly with the variants in the database.”
It is estimated that new biotechnical methods will produce a million times the amount of data produced today by 2020. Lohi states that large amounts of computing resources are needed for both the methods and tools used in research.
“Before, short sections of the genome were sequenced. Now, genome lists are so long that managing them manually is completely impossible. If 200 dogs are studied and the entire genome, i.e. 39 pairs of chromosomes, is sequenced from each dog, the analysis would take several months with the traditional method. A single genome affords hundreds of gigabytes of raw data.”
“As we have shifted from the traditional Sanger method of sequencing to Next-Generation Sequencing (NGS) of the entire genome, huge quantities of data are being analysed using new methods. The genome is first split into sections in the database, sequenced and assembled. The sequencing of a genome involves the processing of three billion pairs of genes for humans and 2.5 billion pairs for dogs as well as different variants and insertions that complicate the interpretation of the sequence”, Lohi says, describing the challenges of the research data.
“After the variants have been identified, it is examined whether the variant is pathogenic. Computing resources are required at this stage, too. Bioinformatics tools can be used to predict which amino acid change the variant causes in the genome. After that, the effects of the amino acid change are studied more closely, switching to use protein-level tools and various algorithms.”
The research group pinpointed the gene causing retinal degeneration in Papillon dogs with six sick and 14 control animals. The genetic defect was identified using exome sequencing technology, analysing all of the protein-coding areas at once. Many disease-causing mutations are located in the exome, even though it only accounts for 1.5% of the genome. This technology, which is used especially to find disease forms present in the database, led to the identification of a mutation carried by almost one in five Papillon dogs in their genome.
Lohi’s research group participated as a pilot organisation in a project of CSC – IT Center for Science exploring what kinds of materials are created for researchers with extensive computing capacity and memory space. The aim of the project was to pilot models and solutions for the kinds of resources needed by researchers in the ELIXIR research infrastructure.
Tiina Autio
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ELIXIR is partly funded by the European Commission