Genetic entrepreneur to compete in Genomics X Prize

[ScienceRocks]

Genetic entrepreneur to compete in Genomics X Prize

By Helen Briggs BBC News

Genetic make-up contributes to longevity
Continue reading the main story Related Stories

• $10m prize for super genetic test
• Analysis: Human genome hype or reality?

A race to unlock genetic clues behind living to 100 is set to begin next year, after a US team announced it will compete for the $10m Genomics X Prize.
Genetic entrepreneur Dr Jonathan Rothberg is entering the challenge to identify genes linked to a long, healthy life.
His team - and any other contenders - will be given 30 days to work out the full DNA code of 100 centenarians at a cost of no more than $1,000 per genome.
The race will start in September 2013.
Under the rules of the Archon Genomics X Prize, teams have until next May to register for the competition.
Dr Rothberg's team from Life Technologies Corporation in California is the first to formally enter the race.
Continue reading the main story[/URL

] Dr Jonathan Rothberg

• • Pioneer of DNA sequencing
  • His latest business venture, Ion Torrent, makes the Personal Genome Machine and the Ion Proton sequencer
  • Rothberg claims his machines can sequence DNA more quickly and cheaply than ever thought possible
  • The Ion Proton sequencer will be used for the challenge

  Being able to sequence the full human genome at a cost of $1,000 or less is regarded as a milestone in science.
  It is seen as the threshold at which DNA sequencing technology becomes cheap enough to be used widely in medicine, helping in diagnosis and in matching drugs to a patient's genetic make-up.
  [URL="http://www.bbc.co.uk/news/science-environment-18876478#story_continues_3"]Continue reading the main story

• “Start Quote
  
  

  If they can do a human genome in two hours with one little machine, it's just stunning. We have come a long way.”
  ​

  End Quote Dr Craig Venter Genetic entrepreneur
  One hundred people aged 100 have donated their DNA for the project.
  Scientists believe people who reach a very old age may have certain rare changes in their genes which protect against common diseases of later life, such as heart disease and cancer.
  If these genes can be identified by analysing the DNA codes of centenarians, it will help scientists search for new medical treatments and perhaps ways to prolong life.
  However, many sample DNA sequences will be needed in order to get the accuracy needed to pinpoint changes on the scale of a few genetic letters among the three billion in the human genome.
  Continue reading the main story

  Dr Craig Venter

• • One of the scientists behind the effort to decode the first human genome sequence
  • Venter and his team built the genome of a bacterium from scratch and put it into a cell to make a synthetic life form
  • He has had his own DNA sequence decoded

  Dr Jonathan Rothberg, a geneticist and entrepreneur, said the DNA of 100 centenarians is a good start towards finding "the fountains of youth".

BBC News - Genetic entrepreneur to compete in Genomics X Prize

 

[waltky]

Fast sequencing of baby DNA offers hope for ill infants...

Gene machines used to find cause of baby illnesses
Fri, Oct 05, 2012 - US scientists have sequenced the entire genetic code of four gravely ill newborns and identified genetic diseases in three of them in two days, quick enough to help doctors make treatment decisions.

Doctors behind the preliminary study released on Wednesday say it demonstrates a practical use for whole genome sequencing, in which researchers analyze all 3.2 billion chemical “bases” or “letters” that make up the human genetic code. “It is now feasible to decode an entire genome and provide interim results back to the physician in two days,” said Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy medical center in Kansas City, Missouri, whose study was published in the journal Science Translational Medicine. The study tested two software programs developed at Children’s Mercy that were used in conjunction with a high-speed gene sequencer from Illumina called HiSeq 2500, which can sequence an entire genome in about 25 hours. The company helped pay for the study and company researchers took part in it.

Next-generation gene sequencing machines have driven down the cost of whole genome sequencing, but making practical use of the data has been more challenging, largely because of the time it takes to analyze. As many as a third of babies admitted to a neonatal intensive care unit in the US have some form of genetic disease. Treatments are currently available for more than 500 diseases, but identifying them quickly has been a problem. Typically, genetic testing on newborns using conventional methods takes four to six weeks, long enough that the infant has either died or been sent home. Neil Miller, director of informatics at Children’s Mercy, said the software helps doctors identify which genes to test, and analyze the data quickly.

One of these programs, called SSAGA, allows doctors to order this test based on the child’s symptoms, without having to know in advance which genes to test for. The software only maps genes associated with the child’s symptoms. SSAGA does this for nearly 600 diseases, but the team is expanding this to include all 3,500 known disease genes, Miller told the briefing. The team developed a second software program called Runes that helps determine which of the suspected genes was most likely to be the cause of the child’s illness.

Even though the study did not provide cures for the babies, she said, it could give parents more information about the cause of their child’s illness. The test is projected to cost US$13,500, but the team believes that may be worth it given the high cost of care in a neonatal intensive care unit, which runs roughly US$8,000 per night. The next move is to broaden the test to include 100 or more babies to determine the benefits, costs and potential problems linked with the testing. Because the Illumina machine was not available in the US, the team had to discount the time it took to ship the blood samples to Britain, where the actual sequencing was done. However, Kingsmore said the hospital expects to receive its own HiSeq 2500 machine next month.

Gene machines used to find cause of baby illnesses - Taipei Times

See also:

'50-hour genome' test for babies with genetic diseases
4 October 2012 - Faster results mean sick babies can be given the correct medication

Doctors in the US say they have taken a big step forward in the speed of analysing the DNA of seriously ill babies with genetic diseases. The whole of a baby's genetic code - genome - was sequenced, analysed and the results given to doctors within 50 hours in intensive care units at Children's Mercy Hospital, Kansas City. The process would normally take at least a month, they said. Experts in the UK said it was an "impressive" technical achievement.

US doctors say up to a third of babies admitted to neonatal intensive care units are there because of genetic diseases caused by mutations in their DNA. However, there are more than 3,500 different genetic diseases meaning many are rare and difficult to diagnose. The first copy of the blueprint of human life - the Human Genome Project - took years to accomplish and an incredible amount of money. Since then both the time and the cost have fallen dramatically. Children's Mercy Hospital has been testing a new way of reading the genetic code which takes 50 hours from the moment a blood sample is taken. They were able to make a diagnosis in three out of the four babies they tested, according to a study published in Science Translational Medicine.

Costly business

Dr Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at the hospital, said: "We can now consider whole genome sequencing to be relevant for hospital medicine. "It is now feasible to decode an entire genome and provide interim results back to the physician in two days. "We think this is going to transform the world of neonataology." The results could help doctors provide the best treatment and counsel families. However, at a cost of about £8,400 ($13,500) it is still expensive.

Prof David Bonthron, from the University of Leeds, said: "It's pretty impressive technically, they're pushing the envelope of how fast you can turn this stuff around - two days is pretty fast." He said speed was also vital in analysing the genes of a foetus still in the womb if abnormalities have been identified. However, he added: "The speed issue is maybe a bit restricted in its applicability as other areas are not that time pressured. In outpatients a few days is not that important."

BBC News - '50-hour genome' test for babies with genetic diseases