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Scientists set out to map genome of cats — 99 of them

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From left, UC Davis graduate Jennifer Lyons plays with Simba while holding Milkdud, Dr. Niels Pedersen, and head animal caretaker Monica Durden show cats at Durden's office on the UCD on Friday. Lyons will be joining the doctor heading the 99 Lives Cat Whole Genome Sequencing Initiative. Liz Hafalia/San Francisco Chronicle photo

By
From page A7 | February 05, 2014 |

By Stephanie M. Lee
Cats may not have nine lives, as the myth goes, but they do have 38 chromosomes.

And a team led by a former UC Davis professor is trying to understand those genes by sequencing a lot of cats — 99 cats, to be precise.

Leslie Lyons is fond of cats — she is the proud owner of two — but that’s not why she is pursuing this project. As sequencing technology grows faster, more comprehensive and more precise, scientists in general are mapping the genomes of humans, dogs, cows and other mammals.

But Lyons, who now works at the University of Missouri, says the cat genome remains relatively un-deciphered. A full mapping of those 20,000 genes in various breeds could help pinpoint the genetic cause of distinguishing marks, like fur and eye colors, but also of cat health problems, she says. It could even shed light on diseases that can occur in cats and humans alike.

“When a sick cat comes along, you could genetically sequence it and say, ‘Hey, look, this has a variation we’ve never seen before,’ ” said Lyons, who is collaborating on the project with San Mateo company Maverix Biomics. “It might give us clues very quickly as to what genes to focus on for this cat’s health care.”

Right now, it’s too early to tell whether protective pet owners or veterinarians would be willing to fork over the cash to sequence their cats’ genomes, said David Kirkpatrick, a spokesman for the American Veterinary Medical Association.

But pet owners in the United States do go to great lengths to take care of their animals, spending $26 billion on supplies, over-the-counter medicine and veterinary care in 2012, according to the American Pet Production Association.

In the not-too-distant future, perhaps, a trip to the vet could include a DNA test.

“We want to bring the health care standards of our pets to a comparable standard for humans,” Lyons said.

From 9 cats to 99
The project, called the 99 Lives Cat Whole Genome Sequencing Initiative, grew out of an original plan to sequence just nine cats. But Lyon and her colleagues decided that nine lives were not enough to build a truly complete genetic portrait, so they upped the sample size.

The work requires samples from kitties that are spayed and neutered. The cats’ leftover ovaries, uteruses and testicles contain DNA that can be easily extracted.

So the scientists are seeking cat samples from Greece, India, China, Russia, the Galapagos and Madagascar, to name a few. They want all kinds of breeds: the silky-haired Maine Coon and the American shorthair, the spotted Egyptian Mau and the blue-eyed Siamese. They want both purebreds and housecats that are a little bit of everything.

12 racial groups of cats
Like humans, cats belong to different racial populations, Lyons said. Felines from the United States, Britain and Canada tend to match up genetically with each other — not surprising, because most share a fluffy ancestry that originated in Western Europe.

Their genetic profile differs from that of cats in Egypt, which in turn are distinct from their counterparts in Southeast Asia and the Middle East. All in all, there are about 12 racial groups, Lyons said.

“What (humans) really want to do is figure out all the genetic variations in our genomes,” she said. “It varies with where you live in the world and what ethnic group you are, and that’s true with cats, too.”

Assisting in the sequencing are UC Davis, the University of Missouri, Cornell University and Texas A&M University. Funding also comes from Zoetis, an animal health company; the Winn Feline Foundation, a cat health nonprofit; and Procter and Gamble, which makes cat and dog food.

An Abyssinian named Cinnamon was the first cat to be genetically sequenced in 2007, but the technology then was more primitive and picked up only about 60 percent of her total DNA.

The technology Lyons uses now will pick up virtually all of it, but mapping each genome will take weeks or months and cost about $8,000. Sequencing all 99 whiskered creatures will generate a huge amount of data — 168 terabytes. (A typical desktop computer has 1 terabyte of capacity.)

All that data will be uploaded into a cloud-based website that will allow anyone to view, search and annotate it.

“They can share that information very easily among researchers, rather than having to ship it around to researchers from lab to lab,” said Dave Mandelkern, president and co-founder of Maverix Biomics, which is operating the website.

Implications for humans
The data could have implications for humans who suffer from illnesses such as polycystic kidney disease and spinal muscular atrophy — diseases that also affect cats.

More immediately, the project could help researchers like Niels Pedersen, a UCD professor emeritus who helped with the sequencing. Pedersen, for example, is trying to better understand the genetic causes of feline infectious peritonitis, a fatal illness in cats.

“Using the tools we had at the time, we can see that there are some genetic factors that might be important,” he said. “To really define them … we really need to move to the whole genome sequencing.”

— Reach Stephanie M. Lee iat slee@sfchronicle.com

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