Category Archives: Genome

ScienceDaily (Oct. 7, 2012) Researchers at the RIKEN Center for Genomic Medicine (CGM) and their colleagues have identified 8 new loci associated with susceptibility to atopic dermatitis in the Japanese population. The findings, which appear in the journal Nature Genetics, advance our understanding of the genetic basis of the skin disorder, which affects millions of children and adults around the world.

Atopic dermatitis (often called ecszema) is a chronic, relapsing inflammatory skin condition affecting as much as one-fifth of children and 1-3% of adults in industrialized countries. Those with the condition have skin that reacts easily to the environment and becomes flaky and itchy. While treatment can alleviate some of these symptoms, current techniques remain ineffective in many cases, due in part to a limited scientific understanding of the origins of the condition.

The research group set out to shed light on these origins using a genome-wide association study (GWAS), an approach which identifies gene loci associated with a particular trait. With its strong genetic basis, atopic dermatitis is well suited to the GWAS approach. Three previous GWAS on European and Chinese populations identified 7 loci associated with the condition, but no such studies have been conducted on Japanese people.

To fill this gap, the group conducted a thorough GWAS on 1472 subjects with atopic dermatitis and 7971 controls from among the Japanese population, and then validated their results in a separate study on 1856 subjects with atopic dermatitis and 7021 controls. Analyzing a total of roughly 600,000 genetic variants (called Single Nucleotide Polymorphisms or SNPs), they identified 8 new genetic regions associated with atopic dermatitis and confirmed the 7 loci observed in earlier studies. Among these regions, they identified variants at the IL1RL1/IL18R1/IL18RAP and human leukocyte antigen (HLA) loci, both of which have been associated with bronchial asthma in recent GWAS.

The group's findings thus suggest that atopic dermatitis and asthma have overlapping susceptibility regions, and thus that these regions contain common genetic factors for many allergic diseases. Other loci reveal a wide variety of additional factors possibly involved in the condition, suggesting paths for future research and pointing the way to more effective treatment techniques.

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The above story is reprinted from materials provided by RIKEN, via EurekAlert!, a service of AAAS.

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Genome-wide study identifies eight new susceptibility loci for atopic dermatitis

Public release date: 7-Oct-2012 [ | E-mail | Share ]

Contact: RIKEN Global Relations Office pr@riken.jp RIKEN

Researchers at the RIKEN Center for Genomic Medicine (CGM) and their colleagues have identified 8 new loci associated with susceptibility to atopic dermatitis in the Japanese population. The findings, which appear in the journal Nature Genetics, advance our understanding of the genetic basis of the skin disorder, which affects millions of children and adults around the world.

Atopic dermatitis (often called ecszema) is a chronic, relapsing inflammatory skin condition affecting as much as one-fifth of children and 1-3% of adults in industrialized countries. Those with the condition have skin that reacts easily to the environment and becomes flaky and itchy. While treatment can alleviate some of these symptoms, current techniques remain ineffective in many cases, due in part to a limited scientific understanding of the origins of the condition.

The research group set out to shed light on these origins using a genome-wide association study (GWAS), an approach which identifies gene loci associated with a particular trait. With its strong genetic basis, atopic dermatitis is well suited to the GWAS approach. Three previous GWAS on European and Chinese populations identified 7 loci associated with the condition, but no such studies have been conducted on Japanese people.

To fill this gap, the group conducted a thorough GWAS on 1472 subjects with atopic dermatitis and 7971 controls from among the Japanese population, and then validated their results in a separate study on 1856 subjects with atopic dermatitis and 7021 controls. Analyzing a total of roughly 600,000 genetic variants (called Single Nucleotide Polymorphisms or SNPs), they identified 8 new genetic regions associated with atopic dermatitis and confirmed the 7 loci observed in earlier studies. Among these regions, they identified variants at the IL1RL1/IL18R1/IL18RAP and human leukocyte antigen (HLA) loci, both of which have been associated with bronchial asthma in recent GWAS.

The group's findings thus suggest that atopic dermatitis and asthma have overlapping susceptibility regions, and thus that these regions contain common genetic factors for many allergic diseases. Other loci reveal a wide variety of additional factors possibly involved in the condition, suggesting paths for future research and pointing the way to more effective treatment techniques.

###

Reference

Tomomitsu Hirota, et al. "Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population." Nature Genetics, 2012, DOI: 10.1038/ng.2438

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Genome-wide study identifies 8 new susceptibility loci for atopic dermatitis

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Each strand of DNA is written in a simple language composed of four letters: A, T, C and G.

Each strand of DNA is written in a simple language composed of four letters: A, T, C and G.

The news that the cost of personal genome sequencing will soon drop as low as $1,000 has generated a quite a bit of interest and concern from medical researchers, biotech companies, bioethicists and the average consumer alike.

NPR's Rob Stein explored many of the implications of this technology in his four-part series "The $1,000 Genome." They're complicated, to say the least.

How many people out there would be willing to get their entire genome mapped? And are they prepared for the revelations it could make about their health and risk for disease?

So we decided to ask you, readers of Shots, in an online survey we added to Stein's posts from the series. The survey is certainly not scientific. But given the interest in the series, we thought a few questions would be worth a try. It turns out the respondents leaned strongly in favor of the tests, and the insight they may lend to understanding health.

First, we asked: "Would you have your genome sequenced if you could afford it?"

Of the 6,627 people who participated, 81 percent said yes. About 10 percent were undecided, while 9 percent said no.

Next, we asked, "If you had your genome sequenced, would you want to know everything?" As Stein reported, even James Watson, who shared a Nobel Prize for discovering the structure of DNA, told the researchers who sequenced his genome that he didn't want to know the test's prediction for Alzheimer's. "There's nothing you can do to prevent it, so why would you want to know?" Watson said.

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Your Verdict On Getting A Genome Test? Bring It On

Whole genome sequencing has become an essential tool for researchers. But slow speeds and high costs have helped keep the technology from becoming a routine diagnostic test for doctors.

But that's starting to change. And results from two studies published this week suggest that in-depth personalized genome sequencing could be inching closer to clinical reality.

Sick babies in intensive care might be among the first to benefit from clinical whole genome sequencing, says a recent study in Science Translational Medicine. Researchers at Children's Mercy Hospital in Kansas City, Mo., streamlined the sequencing and analysis of an entire genome. The process that once took several months. They did it in a few days.

Time is an important factor in the NICU, says Stephen Kingsmore an author of the study and director of the Center for Pediatric Genomic Medicine at Children's Mercy Hospitals and Clinics. "If a physician has an acutely ill baby, and they're trying to figure out immediately which of those 3,500 [known genetic] diseases it might be, and so today it's just not possible for them to make a definitive diagnosis, that is, which gene is mutated," he says. "Either the baby dies, or the baby gets better and goes home before that's known."

Researchers were able to rapidly sequence the infants' genomes using the latest sequencing technology. The results were analyzed with software that allowed doctors to enter the baby's symptoms, characterize mutations in the genome, then screen for over 500 genetic diseases that affect infants.

Treatment is available for many of these diseases, but an early diagnosis is key, Kingsmore told Shots. "You can't start a treatment for a specific disease until you've made a definitive diagnosis," he said. "The goal is to get the right diagnosis as quickly as possible, and then start the right treatment as quickly as possible."

If there are no treatments, the tests can help physicians refer parents to genetic counseling services.

Though the results of the study could someday change infant care, the technology still has limitations. Each infant screening cost about $13,500 in the study, so only the sickest babies can receive the pricey test, said Kingsmore in a Web conference on Tuesday. Another potential roadblock is location. Unless each hospital invests in state-of-the-art sequencing equipment, shipping samples for remote testing and analysis adds diagnostic delays.

Though rapid sequencing in the NICU is limited to diagnoses of a few hundred genetic disorders, another study, published this week in the New England Journal of Medicine, focuses on identifying unique genetic mutations that may not even yet be associated with disease.

Researchers from Radboud University Nijmegen Medical Center in the Netherlands sequenced the protein-coding DNA, or exomes, of 100 patients, most of them young people, affected by severe intellectual disabilities with unknown causes. The researchers then compared the patient genomes with those of their unaffected parents to search for mutations that could be the cause of intellectual disability.

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In-Depth Genome Analysis Moves Toward The Hospital Bed

From the day she was born, the baby girl had seizure after seizure as doctors at Children's Mercy Hospital in Kansas City, Mo., frantically tried to keep her alive. Finally, her family decided to let their baby go, and the medical devices were withdrawn. She was 5 weeks old.

Her doctors suspected a genetic disorder, and as it happened, the hospital had just begun a study of a new technique for quickly analyzing the DNA of newborns, zeroing in on mutations that can cause disease.

This new method, published Wednesday in the magazine Science Translational Medicine, is a proof of concept a demonstration that it is possible to quickly scan a baby's entire DNA and pinpoint a disease-causing mutation in a couple of days instead of the more typical weeks or months.

For the study, researchers at Children's Mercy Hospital mapped the DNA of five children. The study's investigators said the test could be one of the first practical fruits of the revolution in sequencing an individual's entire DNA.

For the baby with seizures, her doctors provided a sample of her blood. The analysis took only 50 hours and provided an answer: The baby had a mortal gene mutation so rare that it had only been reported once before.

If only the test could have been done within days of the baby's birth, said Dr. Joshua Petrikin, one of the baby's doctors.

"There was no treatment, there was not anything that could have changed the outcome," Petrikin said. "But we could have more appropriately counseled the family and bypassed what had to have been intense suffering."

The idea behind the test is to take advantage of what is known about disease symptoms to narrow the search for genetic aberrations. And that, said Dr. Joe Gray, an expert in genome analysis at Oregon Health and Science University, "is a good step in the right direction."

"It's a big genome," said Gray, who was not involved with the study. "How do you know what part of it to search?"

The method is expensive, costing about $13,500. It is not yet covered by insurance.

The rest is here:
Fast genome test could help sick newborns

In its fourth and last segment of its '$1,000 Genome' series, NPR's health blog, Shots, asks what people can expect to learn from their own genome sequence, and why they might not want to learn everything.

Beau Gunderson, a Silicon Valley startup employee, recently had his exome sequenced and found out that he did not inherit an Alzheimer's gene variants and shares some genes with Olympic sprinters, NPR's Rob Stein reports. But Gunderson still wonders what his genome could tell him about diseases he might get.

Others think that sequencing could open a Pandora's Box. "There are also people walking around out there who carry mutations that create an extraordinarily high probability that they will develop a horrendous, untreatable, unpreventable disease by age 50, 60 years old," says James Evans of the University of North Carolina, Chapel Hill. "That isn't necessarily information that everybody wants."

Furthermore, there could be genetic discrimination for life and disability insurance, and in the future, thugs might plant someone's DNA at a crime scene.

But proponents argue the potential benefits of sequencing "far outweigh" any risks, and that people "just have a right to have their genome," Stein writes.

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The Genome — a Pandora's Box?

By Jeff Hansel The Post-Bulletin, Rochester MN

Speakers at Mayo Clinic'sIndividualizing Medicine conferenceoffered impressive examples of real-world genome-based treatment, and called for more research.

Michael Snyder, director for the Center for Genomics and Personalized Medicine at Stanford University, said Stanford researchers chose to study Snyder's own genome rather than recruit a test subject.

Speaking during this week's conference at Mayo Civic Center,Snyder said his entire genome has been sequenced. Whenever he gets a cold, he gets tested to see how the virus affects his genome and it does.

"Our health situation is really a product of our genome (a person's entire genetic makeup) as well as the food we eat, the various things we're exposed to in our environment," Snyder said.

Getting a full-genome sequence costs about $3,000 half the cost of buying a new hot tub, he said. That does not include $10,000 or so for scientists to make sense of results.

Still, genome-testing cost is decreasing rapidly and Snyder expects much of the population will soon be able to get a whole-genome analysis if desired.

Lots of ethical issues come up, such as how much of the information learned should be shared with the patient. If there's no cure for a disease and it's unclear how soon or if the patient will get it, should the patient be told he's at higher risk?

Mutations often do not impact a person's health directly. But some, such as combinations that increase the risk for Type 2 diabetes, might trigger disease when a person's body is exposed to disruption.

Stanford researchers, for example, demonstrated Snyder was at increased risk for Type 2 diabetes. He thought that odd, since he's not overweight and exercised a little.

Continue reading here:
Would you get your genome tested?

By Jeff Hansel The Post-Bulletin, Austin MN

Speakers at Mayo Clinic'sIndividualizing Medicine conferenceoffered impressive examples of real-world genome-based treatment, and called for more research.

Michael Snyder, director for the Center for Genomics and Personalized Medicine at Stanford University, said Stanford researchers chose to study Snyder's own genome rather than recruit a test subject.

Speaking during this week's conference at Mayo Civic Center,Snyder said his entire genome has been sequenced. Whenever he gets a cold, he gets tested to see how the virus affects his genome and it does.

"Our health situation is really a product of our genome (a person's entire genetic makeup) as well as the food we eat, the various things we're exposed to in our environment," Snyder said.

Getting a full-genome sequence costs about $3,000 half the cost of buying a new hot tub, he said. That does not include $10,000 or so for scientists to make sense of results.

Still, genome-testing cost is decreasing rapidly and Snyder expects much of the population will soon be able to get a whole-genome analysis if desired.

Lots of ethical issues come up, such as how much of the information learned should be shared with the patient. If there's no cure for a disease and it's unclear how soon or if the patient will get it, should the patient be told he's at higher risk?

Mutations often do not affect a person's health directly, but some, such as combinations that increase the risk for Type 2 diabetes, might trigger disease when a person's body is exposed to disruption.

Stanford researchers, for example, demonstrated Snyder was at increased risk for Type 2 diabetes. He thought that odd, since he's not overweight and exercised a little.

Read the original here:
Genome testing could help individualize treatments

Enlarge Courtesy of Beau Gunderson

Beau Gunderson's $999 genome test showed that he didn't inherit the gene for Alzheimer's, but he carries genes found in Olympic sprinters.

Beau Gunderson's $999 genome test showed that he didn't inherit the gene for Alzheimer's, but he carries genes found in Olympic sprinters.

Beau Gunderson's fascinated by what he might learn from his DNA.

"I'm curious about what makes me tick, essentially," says Gunderson, 29, who writes code for a Silicon Valley startup.

So Gunderson has signed up for every genetic test he's been able to afford. And he can't wait for the price of getting his entire genetic code his genome to drop to about $1,000, as many are predicting is imminent.

"Yeah, if the price does drop to a thousand bucks for example I might pay that. That's a good personal price point for me," Gunderson said.

So-called whole genome sequencing is already available for between about $4,000 and $10,000.

"The early adopters that are getting this done now are those who have this incredible curiosity about their genetic makeup, about their potential genetic destiny," said Jay Flatley, who heads Illumina Inc., of San Diego.

Illumina even recently started offering an iPad app that people can use to learn more about whole genome sequencing and their own genomes. In September, the company announced a new service that could deliver a genome in two weeks.

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Will Low-Cost Genome Sequencing Open 'Pandora's Box'?

CALGARY, Oct. 2, 2012 /CNW/ - Genome Alberta is pleased to be one of the sponsors of the Canadian Science Policy Conference 2012 which is coming to the West for the first time this November 5th - 7th. In particular we want to be the first to thank the Hon. Gary Goodyear, Minister of State for Science and Technology who will give the opening keynote address on Monday, November 5th at 8:45a, and the Hon. Stephen Khan, Alberta Minister of Enterprise and Advanced Education who will give the keynote luncheon speech on Tuesday, November 6th.

CSPC 2012 has lined up an impressive program with more than 90 speakers from industry, academia, the media and government. These include:

The keynote session: "Pulling Together: What is the appropriate division of labour between business, government, and the academy in advancing science-based innovation in Canada?" will feature a panel discussion with 3 leading Albertans who are also Honourary Co-Chairs of the National Science Policy Conference:

There will be 21 sessions during the conference, reflecting the four conference themes, submitted from across the country and internationally, including:

For the complete agenda please go tohttp://www.cspc2012.ca/glance.php and for descriptions of all the panel discussions see http://www.cspc2012.ca/paneldescriptions.php .

Genome Alberta is a strong supporter of the Canadian Science Policy Conference and of a strong provincial and national science policy that can produce the best in basic and applied research for the benefit of everyone. Canada was in the top 10 of the Scientific American Global Science Scorecard published this month, and a healthy discussion of science policy will ensure we maintain our strong ranking and be competitive on a global scale.

About Genome Alberta

Genome Alberta is apublicly funded organization that initiates, funds, and manages genomics research and partnerships. We are based in Calgary but lead projects around the province and participate in a variety of projects across the country. We are one of Canada's six Genome Centres and work closely with these centres to advance the science and application of genomics, metabolomics, and many other related 'omics'

You can find out more about Genome Alberta at http://genomealberta.ca , learn more about genomics on our blog pages at http://genomealberta.ca/blogs, follow us on Twitter as @GenomeAlberta, and check out our unique made-in-Alberta Genomics News site at http://GenOmicsNews.ca

SOURCE: Genome Alberta

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Genome Alberta Welcomes Alberta Minister of Enterprise and Advanced Education, Stephen Khan and Federal Minister of ...