Canine Genome decoded

BOSTON — The genetic makeup of cancer is the next target for researchers at the Broad Institute after the successful mapping of the canine genome.

Over time blocks of chromosomes travelling together have been broken down into short blocks with different flavors in the whole dog population (top panel). As dog breeds were created, a few chromosomes were selected for each breed. The blocks have not had a chance to break apart and are still long within breeds. This means that it is 50-times easier to find disease genes in dog breeds than in humans.

Scientists at The Broad Institute at MIT and Harvard decoded 99 percent of the canine genome by mapping a purebred female Boxer and sampling the genomes of 10 other dog breeds, coyotes and wolves to unveil 2.5 million individual genetic differences.

The finding is expected to help pinpoint diseased genes in dogs, taking veterinary medicine to another level, says Eric Lander, senior author of the paper, director of the Broad Institute, professor of biology at MIT and systems biology at Harvard Medical School.

"A natural progression of finding diseased genes is the development of a genetic test, furthering veterinarians' ability to predict a defect in a bloodline or caution owners a specific disease might be present in their pet," says Dr. Kerstin Lindblad-Toh, first author of the paper and co-director of the genome sequencing and analysis program at Broad. "I think this discovery will affect veterinarians a lot, especially in the next couple of years as diseased genes are found and genetic tests become available. Veterinarians will be able to give owners advice on what to feed and care for specific pets in effort to deter disease development or progression."

By comparing single nucleotide polymorphisms (SNP's), which serve as markers to locate genetic factors to physical, behavioral and medical traits, scientists can pinpoint the genes responsible for certain diseases.

"Our biggest breakthrough was discovering that very large chunks of genes travel together in dogs," Lindblad-Toh says. "This means it should be relatively easy to find the diseased genes in dogs. Also, the clustering of regulatory sequences is interesting because it means a subset of crucial human genes are under more elaborate control than what was previously thought."

Sequence method

The Whole Genome Shotgun (WGS) method was used to sequence the canine genome. With a total of 31.5 million sequence reads, about 7.5-fold sequence redundancies were assembled using the ARACHNE program with an initial assembly on the structure.

"Hardly any of the functional elements conserved between human and dog have been deleted in the mouse lineage, suggesting there is a common set of functional elements across all three mammalian species, corresponding to 5 percent of the human genome," Lindblad-Toh says.

Breeds

Selective breeding, carrying large genomic regions of several million bases of DNA into breeds, creating haplotype blocks, has reshaped the dog genome. The genomic regions are predicted to find genes responsible for disease, body size and behavior, Lander says.

"Since breeding tends to predispose many dog breeds to genetic diseases, the dog genome and SNP map, veterinarians will have the tools to identify the diseased genes," Lander adds.

Another finding with the research is that the dog, human and mouse share 5 percent of the same genome.

"Some pieces of the genome must stay the same throughout evolution to maintain functions and keep humans-human and dogs-dogs, instead of turning into a completely different animal," Lindblad-Toh says.

Before breeds were created, large variance in chromosomes were noted, says Elinor Karlsson, a graduate student in the bioinformatics program at Boston University, and one of the leading computational scientists on the dog genome analysis and disease-mapping project at the Broad Institute.

"To create a breed, a few chromosomes are selected to alter the initial breed," Karlsson says. "Coat color along with disease mutations can be tracked to specific chromosomes. New methods for identifying disease mutations will be developed using the dog genome and diversity of dog breeds."

In the works

A list of prioritized genetic dog diseases are being researched at laboratories across the nation, Lindblad-Toh says.

"Our lab's priority is cancer. Companies are already interested in the rights for designing genetic tests to market."

Sixteen other mammals are slated for genetic mapping; the feline genome is the closest to being complete, making it the eighth mammalian genome to be decoded.

"I suspect within the next year, we will have completed the feline genome, then we will need time to interpret it," Lindblad-Toh says.

The dog genome was researched in great depth, taking two years from start to finish, the other animals being mapped will likely be at the 80-percent mark, she adds.

Veterinary help

Scientists are asking veterinarians and clients to participate in research by sending blood samples from their purebred dogs — healthy and diseased.

Cancer will be the first genetic disease scientists are working on decoding.

Since humans share eight of the 10 top diseases in dogs, the genetic mapping will help make correlations between dog and human diseases, ultimately helping both species, Lander says.

Dr. Francis Collins, director of the National Human Genome Research Institute (NHGRI), a major financial provider of the project, calls the genomic accomplishment "an instruction book for dog biology," and says the analysis will benefit animal and human medicine through billions of encrypted base pairs making sense of genetic diseases.

"This sequencing of the dog genome is 1,000 times more connected than the last sequencing effort," Lindblad-Toh says. "Humans and dogs have the same gene repertoire and a comparative mutation can be seen in both species genes. This knowledge will help in veterinary and human medicine."

"With sequencing, the number of genetic differences it takes to evolve humans from the last common ancestor can be determined," says Tarjei Mikkelesen, a graduate student in comparative genomics at the Broad Institute and the Harvard MIT Division of Health Sciences and Technology. "Now that we know where to find these genes, we can dissect and know how a single cell uses a blueprint to develop into a dog and what makes the cells grow out of control and become a tumor or some other disease."

Clair Wade, a senior research scientist in the Center for Genetic Research at Massachusetts General Hospital, adds that breeding dogs for specific traits, brought diseases along to that particular breed.

"Out of 10 top dog diseases, humans share eight," Wade says. "Dogs share our lives, environment and food, and this is yet another link in the species' bond."

Dr. Elaine Ostrander has understood the importance of the dog genome sequence since 1990, Collins says.

"It is only now that we will begin to fully understand what the knowledge of the dog genome can do for medicine."

Since Ostrander focuses on the construction of canine linkage and radiation hybrid maps and mapping of loci for several human and canine diseases, her work will be crucial in propelling research using the dog genome in benefiting canine and human patients.

"Two genetic systems deeply intertwined," says Elaine Ostrander, chief of Cancer Genetics Branch of NHGRI. "The dog has now taken its rightful place in the pack of model organisms that are advancing human health and biology. Over the next three years, I advise you to sit back and watch us lead the pack."

Veterinarians interested in submitting canine blood samples to the Canine Health Foundation, visit www.dogdna.org.