Tuesday, January 27, 2015
YOLO COUNTY NEWS
99 CENTS

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

cat1W

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

Comments

comments

San Francisco Chronicle

.

News

 
Interfaith event focuses on justice

By Fred Gladdis | From Page: A1 | Gallery

In vino veritas: A criminal case and intrigue in Napa Valley

By New York Times News Service | From Page: A1 | Gallery

 
Parking lawsuit may be more than meets the eye

By Dave Ryan | From Page: A1

 
Crash leads to DUI, hit-run arrest

By Lauren Keene | From Page: A2

Senate Dems block GOP effort to wind down pipeline debate

By The Associated Press | From Page: A2

 
New-home sales jump 11.6% in December

By The Associated Press | From Page: A2

Blizzard howls its way into Boston

By The Associated Press | From Page: A2 | Gallery

 
Apply now for Soroptimist service grants

By Enterprise staff | From Page: A3

Share your love (story) with us

By Enterprise staff | From Page: A3

 
Pets of the week

By Enterprise staff | From Page: A3 | Gallery

Workshop offers tips on GoPro cameras

By Enterprise staff | From Page: A3

 
Sutter Davis Hospital seeks volunteer doulas

By Special to The Enterprise | From Page: A3

Winter produce, treats available at Wednesday market

By Enterprise staff | From Page: A3

 
Have a ‘Heart to Heart’ with Dr. G

By Enterprise staff | From Page: A3

Apply now to be on Davis’ coop crawl

By Enterprise staff | From Page: A4

 
Seed swap set Friday at Davis Cemetery

By Enterprise staff | From Page: A4

VFW post plans Valentine’s Day Heroes Breakfast

By Enterprise staff | From Page: A4 | Gallery

 
Storyteller relies on nature as his subject on Saturday

By Enterprise staff | From Page: A4

Vote for your favorites in Readers’ Choice poll

By Enterprise staff | From Page: A4

 
Learn nature photography from an expert

By Enterprise staff | From Page: A4 | Gallery

Thorp receives UCD’s Distinguished Emeritus Award

By Kathy Keatley Garvey | From Page: A4 | Gallery

 
Innovation opportunities on the agenda

By Enterprise staff | From Page: A4

Sutter auxiliary seeks volunteers

By Enterprise staff | From Page: A5

 
A winemaker’s downfall

By New York Times News Service | From Page: A7

Gerber nominations open now

By Enterprise staff | From Page: A10

 
.

Forum

Wife’s attitude costs her friends

By Creators Syndicate | From Page: B5

 
Taking turns as the halfway house

By Creators Syndicate | From Page: B5

Locals will join march for climate change

By Michelle Millet | From Page: A6

 
It’s foggy? Turn on your headlights

By Letters to the Editor | From Page: A6

Damage done to democracy

By Letters to the Editor | From Page: A6

 
A family was torn apart, but we survived

By Special to The Enterprise | From Page: A6 | Gallery

.

Sports

Aggie women almost get a sweep of Portland tennis teams

By Enterprise staff | From Page: B1 | Gallery

 
UCD women need to get in gear for a basketball road trip

By Bruce Gallaudet | From Page: B1 | Gallery

Anatomy of a hoops collapse: Can Aggie men handle the pressure?

By Bruce Gallaudet | From Page: B1 | Gallery

 
Four DHS wrestlers soar at McClellan Air Force Base

By Enterprise staff | From Page: B1

UCD swims past Santa Barbara

By Enterprise staff | From Page: B2 | Gallery

 
Sports briefs: Eat ribs for the Davis Aquadarts

By Enterprise staff | From Page: B8

.

Features

Name Droppers: Lea Rosenberg leads Odd Fellows

By Enterprise staff | From Page: A5

 
.

Arts

‘Ideation’ a funny, dark, thrilling farce — and more

By Bev Sykes | From Page: A9 | Gallery

 
DHS Idol finals will be a tough competition

By Krystal Lau | From Page: A9

Wynonna Judd will perform Feb. 13 in Vacaville

By Enterprise staff | From Page: A9

 
.

Business

.

Obituaries

Death notice: Lorraine Bernice DeGraff

By Special to The Enterprise | From Page: A2

 
.

Comics

Comics: Tuesday, January 27, 2015 (set 1)

By Creator | From Page: B5

 
Comics: Tuesday, January 27, 2015 (set 2)

By Creator | From Page: B7