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How to sequence an entire genome from a single cell | KurzweilAI

How to sequence an entire genome from a single cell | KurzweilAI | Longevity science | Scoop.it

The notion that police can identify a suspect based on the tiniest drop of blood or trace of tissue has long been a staple of TV dramas, but scientists at Harvard have now taken the idea a step further. Using just a single human cell, they can reproduce an individual’s entire genome.

 

The researchers developed a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.

 

 

Ray and Terry's 's insight:

As reported by KurzweilAI.net, this technique could lead to more nimble cancer treatments and enhanced prenatal screening.

 

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X Prize to Sequence Genomes of World’s Oldest People. Hopes To Unlock Secrets of Longevity

X Prize to Sequence Genomes of World’s Oldest People.  Hopes To Unlock Secrets of Longevity | Longevity science | Scoop.it

Toni Balcean turned 101 in September. How’d she beat a century? Simple. “Clean living and good Italian wine.” Case closed! Unless, of course, you like science. A retooled Archon Genomics X PRIZE aims to help scientists better understand healthy aging by sequencing 100 healthy centenarian genomes—in a month, with an accuracy of one error per million base pairs, and for under $1,000 per genome.

 

All this may sound eerily familiar. In fact, the Archon Genomics X PRIZE was first proposed back in 2006. Singularity Hub covered it in 2008 when the goal was to sequence 100 human genomes in 10 days for less than $10,000 per genome.

 

Grant Campany, Senior Director of the Archon Genomics X PRIZE, recently told Singularity Hub, “From 2006 to 2009, competitors registered for the Archon Genomics X PRIZE with the best of intentions, but over the past few years the industry has fragmented significantly, so we needed to restructure the competition to be more inclusive of the emerging and established sequencing platforms.”

 

So, in October 2011, the X PRIZE announced a new set of criteria. The payout remains $10 million; however, the Foundation upped the sequencing period to 30 days and made the target cost $1,000 to reflect rapidly declining sequencing prices.

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Rapid genomic deep-sequencing testing pinpoints newborns' genetic diseases in a few days

Rapid genomic deep-sequencing testing pinpoints newborns' genetic diseases in a few days | Longevity science | Scoop.it

A faster DNA sequencing machine and streamlined analysis of the results can diagnose genetic disorders in days rather than weeks. 

 

Up to a third of the babies admitted to neonatal intensive care units have a genetic disease. Although symptoms may be severe, the genetic cause can be hard to pin down. Thousands of genetic diseases have been described, but relatively few tests are available, and even these may detect only the most common mutations.

 

Whole-genome sequencing could test for many diseases at once, but its cost, the complexity of the results and the turnaround time are prohibitive. In what they hope will be a prototype for other hospitals, a research team led by Stephen Kingsmore at Children’s Mercy Hospital in Kansas City, Missouri, has implemented a much faster, simpler system for finding relevant mutations in whole-genome sequences that is designed for physicians without specialized genetic training.

 

These kinds of innovation will help more hospitals bring sequencing into clinical care, says Richard Gibbs, director of the human genome sequencing centre at Baylor College of Medicine in Houston, Texas. “A lot of people are going to realize from this that the future is now.”

 

Sequencing has been used before to pinpoint the cause of mysterious diseases. In 2011, Gibbs led a team that sequenced 14-year-old twins with a neurological movement disorder and found a way to improve their treatment2. In another instance, whole-genome sequencing suggested that a mysterious case of severe inflammatory bowel disease had a genetic cause and could be relieved through a bone marrow transplant3. But both these examples required several weeks and a team of experts to resolve. The Children’s Mercy Hospital plans to offer routine sequencing in the neonatal intensive care unit by the end of the year.

 

To order a test, physicians will choose terms from pull-down boxes to describe the infant's symptoms. Software then compiles a list of potential suspect genes. After the genome is sequenced, the software hunts for and analyses mutations in only those genes, which allows it to compile a list of possible causative mutations more quickly. The team had early access to a new DNA sequencing machine from sequencing company Illumina, based in San DIego, California, that could generate a whole genome within 25 hours. The entire process, from obtaining consent to preliminary diagnosis, took 50 hours, not counting the time taken to ship DNA samples and computer hard drives between Illumina's lab in the UK, where the DNA sequencing was carried out, and the hospital, where analysis was conducted. Kingsmore estimates that the cost of sequence and analysis is $13,500 per child, including costs to verify variants in a laboratory certified to perform clinical tests.

 

Fast sequencing cannot diagnose all genetic diseases. Current sequencing technology tend to overlook mutations such as duplicated genes, for example. Nonetheless, deep sequencing will be able to provide diagnoses for many cases that would otherwise remain harrowing mysteries.


Via Dr. Stefan Gruenwald
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Battle of the Next-Generation DNA Sequencers Heating Up | Singularity Hub

Battle of the Next-Generation DNA Sequencers Heating Up | Singularity Hub | Longevity science | Scoop.it

Today’s standard sequencing method uses an indirect approach to DNA sequencing based on fluorescently-tagged nucleotides, the building blocks of DNA. However, Ion Torrent has developed a simple, yet ingenious way to detect the sequence of nucleotides in a sample of DNA. Exploiting the fact that a hydrogen ion is released whenever a nucleotide attaches to a strand of DNA, sensors in Ion Torrent’s microchip have been designed to detect this chemical signature.

 

Equality in gene sequencing ahead?

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Whole-Genome Sequencing Trials Suggest Time Has Come to Bring Personalized Medicine to Cancer Field

Whole-Genome Sequencing Trials Suggest Time Has Come to Bring Personalized Medicine to Cancer Field | Longevity science | Scoop.it
Pathologists take note! Human whole-genome sequencing of tumors was the source of information for making treatment decisions in a recently published study.

Via Brian Shields
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Faster, cheaper gene sequencing points to greater cancer understanding

A common mutation in a tumor-suppressing gene could explain why blacks are more likely to get early breast and colon cancer, researchers at Georgia Health Sciences University said.The ability to more quickly and cheaply ...

Via Brian Shields
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4-Year-Old’s Missing Gene Discovered Through Crowdfunded Sequencing | Singularity Hub

4-Year-Old’s Missing Gene Discovered Through Crowdfunded Sequencing | Singularity Hub | Longevity science | Scoop.it

Crowdfunding is starting to accomplish some pretty impressive feats beyond video game reboots and smartphone-linked watches on Kickstarter.

 

In mid-July, the nonprofit organization Rare Genomics Institute (RGI), which sequences genomes of children with rare genetic diseases, announced that it had identified a previously unknown gene variant...

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