Sep 22, 2009

Flu symptoms self-assessment: Do you have seasonal or swine flu (H1N1)?

Influenza is a viral infection that attacks your respiratory system, including your nose, throat, bronchial tubes and lungs.

If you're generally healthy and you catch influenza — commonly called the flu — you're likely to feel rotten for a few days, but you probably won't develop complications or need hospital care. If you have a weakened immune system or chronic illness, though, influenza can be fatal.

For those at high risk of influenza, the first line of defense is an annual flu shot. This year, in addition to a regular flu shot, you may need a different flu shot for protection against novel H1N1 swine flu, a new type of influenza identified earlier this year. The first doses of swine flu vaccine will be available later this fall, after seasonal flu immunization begins.

Initially, the flu may seem like a common cold with a runny nose, sneezing and sore throat. But colds usually develop slowly, whereas the flu tends to come on suddenly. And although a cold can be a nuisance, you usually feel much worse with the flu.

Common signs and symptoms of the flu include:

  • Fever over 101 F (38 C) in adults, and often as high as 103 to 105 F (39.5 C to 40.5 C) in children
  • Chills and sweats
  • Headache
  • Dry cough
  • Muscular aches and pains, especially in your back, arms and legs
  • Fatigue and weakness
  • Nasal congestion
  • Loss of appetite
  • Diarrhea and vomiting in children

When to see a doctor
If you have flu symptoms and are at risk of complications, see your doctor right away. Taking antiviral drugs within the first 48 hours after you first notice symptoms may reduce the length of your illness by a day or two and may help prevent more serious problems. Seek immediate medical care if you have signs and symptoms of pneumonia. These include a severe cough that brings up phlegm, a high fever and a sharp pain when you breathe deeply. If you have bacterial pneumonia, you'll need treatment with antibiotics.

Flu viruses travel through the air in droplets when someone with the infection coughs, sneezes or talks. You can inhale the droplets directly, or you can pick up the germs from an object, such as a telephone or computer keyboard, and then transfer them to your eyes, nose or mouth.

The flu is caused by three types (strains) of viruses — influenza A, B and C. Type A can be responsible for the deadly influenza pandemics (worldwide epidemics) that strike every 10 to 40 years. Type B can lead to smaller, more localized outbreaks. And either types A or B can cause the flu that circulates almost every winter. Type C has never been connected with a large epidemic.

Type C is a fairly stable virus, but types A and B are constantly changing, with new strains appearing regularly. Once you've had the flu, you develop antibodies to the strain that caused it, but those antibodies won't protect you from new strains. That's why doctors recommend getting a flu shot every year.

You're at increased risk of influenza or its complications if you:

  • Are an infant or young child
  • Are over age 50
  • Are a resident of a nursing home or other long term care facility
  • Have a chronic disorder, such as diabetes or heart, kidney or lung disease
  • Have a weakened immune system, such as from medications or HIV infection
  • Will be pregnant during flu season
  • Work in a health care facility where you're more likely to be exposed to the flu virus
  • Are in regular, close contact with infants or young children

Children on long-term aspirin therapy also may be at greater risk.

The flu vaccine is safe for children 6 months and older. If your child isn't at risk of the flu but lives with someone who is, you still may want to have your child vaccinated. That way, your child is less likely to infect others. The more people immunized, the less likely it is that the flu will spread through a community.

Sep 11, 2009

Get Your Entire Genome From Complete Genomics For $5000

It’s getting progressively cheaper to sequence your entire genome. Earlier in June, Illuminaannounced it would provide sequencing for close to $50k, half of their original price. Not to be outdone, Complete Genomics just released on Monday that it had gathered $45 million dollars in funding. The Silicon Valley based company is planning to use that money to further develop their streamline sequencing operations so that they can offer a complete genome for just $5000 by next year. CG’s goal is to finish 10,000 sequences by years end 2010. Even though that’s later than we had hoped, it’s still a whole lot of DNA and at the cheapest price for a whole genome seen so far. The question is, can they really pull it off?

We’ve been looking for a company, any company really, to break the $1000 price mark for a complete genome sequencing sometime in the next few years. That’s about the point where retail sales of the service will explode. With their exponentially decreasing price tag, Complete Genomics might be on that path. However, we know of at least one company that is trying to reach that goal by the end of this year. Stay tuned for that story in the next few weeks.

If you’ve never heard of Complete Genomics, read our first and second story to catch up. Basically they use a common form of short read sequencing and throw in a ton of computer power to sequence a human genome. Interest in personal genomics is escalating as genetic links to diseases are discovered. 23andMe already offers some testing for such diseases and is hoping to gather samples for further clinical trials. By providing the entire genome for perusal on the cheap, CG could make it economically feasible to expand that research into many more illnesses. Already, we’ve shown you how some facilities are erroneously promising to predict a child’s aptitudebased on genetic sampling. Perhaps with the cheap sequencing CG could provide, scientific research will match pace with the growing demand for such testing.

Daniel MacArthur of Genetic Future was able to pry CG head Cliff Reid to provide some details in how they hope to achieve their goals. First, Reid disclosed that the test won’t be offered directly to consumers, but rather through retail providers such as Knome and 23andMe. That means the price you or I will see could be considerably higher than $5k. Whatever the retail price, Reid promises 120 billion base pairs sequenced, 98% of the genome, with just one error in 10,000. That’s considerably better stats than what CG offered in February (92% of genome, about one error in 1,000).

Between now and year’s end 2009, Complete Genomics will focus on its dozens of customers currently in the line up. These include the Broad Institute out of MIT and Harvard which announced it was purchasing at least 5 genomes from CG in March. The Broad Institute reportedly paid $20k for each of their genomes which might be taken as the current baseline price for CG customers. If so, that’s a factor of four that the company has to make up between now and next year.

But scaling is no problem for genome sequencing. Remember that it took 15 years to sequence the first human genome, but the next 6 were done in 24 months. Now we’re talking about doing thousands a year. That’s just nuts and one of the amazing parts about sequencing that I love. Exponential growth is sexy science. And it’s supposed to be one of CG’s strengths. They just finished their first genome in the summer of 2008, and are now on schedule to finish 100 by the end of 2009. Current estimates of finishing 1000 by mid 2010, and 9000 more by the end of that year fit within the exponential growth curve. As MacArthur points out, most of these sequencing services will likely be purchased by researchers in genomic and cancer studies. So the demand is also there.

How can CG scale so quickly? By remaining inflexible but efficient. Their process doesn’t rely on making huge improvements in sequencing technology. Or finding a new sequencing technique. It comes down to streamlining the process. Stick to one task, human genome sequencing, miniaturize whenever possible, fewer reagents means lower costs, and build build build. You can bet a huge portion of that $45 million is going to expanding their facilities in Mountain View.

Who provides the cheap genomes is probably less important than the change it will create. While scientific research will undoubtedly benefit first, the public at large will likely become a dominant consumer. Genetic information is on the journey to becoming one of the most important sets of data someone can know about themselves, with insights into disease, aptitudes, and longevity. Give us the chance for cheap access to that info and you’ll never run out of customers. Just a little while longer, it’s bound to happen.

Sep 8, 2009

New Genetic Variation Linked To Diabetes

Researchers say they have identified a genetic variation in people with type 2 diabetes that affects how the body's muscle cells respond to the hormone insulin. Previous studies have identified several genetic variations in people with type 2 diabetes that affect how insulin is produced in the pancreas. Today's study shows for the first time a genetic variation that seems to impair the ability of the body's muscle cells to use insulin to help them make energy.
People with type 2 diabetes can have problems with the body not producing enough insulin and with cells in the muscles, liver and fat becoming resistant to it. Without sufficient insulin, or if cells cannot use insulin properly, cells are unable to take glucose from the blood and turn it into energy. Until now, scientists had not been able to identify the genetic factors contributing to insulin resistance in type 2 diabetes. In the new research published in Nature Genetics, scientists from international institutions including Imperial College London, McGill University, Canada, CNRS, France, and the University of Copenhagen, Denmark, looked for genetic markers in over 14,000 people and identified four variations associated with type 2 diabetes. One of these was located near a gene called IRS1, which makes a protein that tells the cell to start taking in glucose from the blood when it is activated by insulin. The researchers believe that the variant they have identified interrupts this process, impairing the cells' ability to make energy from glucose. The researchers hope that scientists will be able to target this process to produce new treatments for type 2 diabetes. "It is now clear that several drugs should be used together to control this disease. Our new study provides scientists developing treatments with a straightforward target for a new drug to treat type 2 diabetes," said Froguel. The most significant of these variations was located near the insulin receptor substrate 1, or IRS1, gene.

Article: "A multistage genome-wide association study detects a new risk locus near IRS1 for type 2 diabetes, insulin resistance and hyperinsulinemia", Nature Genetics, 6 September 2009.

Sep 4, 2009

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Sep 2, 2009

Whole-Genome Sequencing: Any Useful Data?

ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of disease, implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analyzing, and displaying sequence data.

In the initial phase of ClinSeq, we are enrolling roughly 1,000 participants; the evaluation of each includes obtaining a detailed family and medical history as well as a clinical evaluation. The participants are being consented broadly for research on many traits and for whole-genome sequencing. Initially, Sanger-based sequencing of 300-400 genes thought to be relevant to atherosclerosis is being performed, with the resulting data analyzed for rare, high-penetrance variants associated with specific clinical traits.

He also mentioned the 1000$ genome project and the unofficial estimation is that now it’s possible to sequence a person’s genome for under 5000$ and the 1000$ aim can become a reality at the end of this year.