Future Treatment of cancer Genetics or target drugs

[nec207]

After reading this news page today on Dr. Timothy Ley it seems Future Treatment of cancer will be Genetics or target drugs:p




ST. LOUIS — Genetics researchers at Washington University (http://topics.nytimes.com/top/reference/timestopics/organizations/w/washington_university/index.html?inline=nyt-org), one of the world’s leading centers for work on the human genome, were devastated. Dr. Lukas Wartman, a young, talented and beloved colleague, had the very cancer (http://health.nytimes.com/health/guides/disease/cancer/overview.html?inline=nyt-classifier) he had devoted his career to studying. He was deteriorating fast. No known treatment could save him. And no one, to their knowledge, had ever investigated the complete genetic makeup of a cancer like his.


So one day last July, Dr. Timothy Ley, associate director of the university’s genome institute, summoned his team. Why not throw everything we have at seeing if we can find a rogue gene spurring Dr. Wartman’s cancer, adult acute lymphoblastic leukemia, he asked? “It’s now or never,” he recalled telling them. “We will only get one shot.”
Dr. Ley’s team tried a type of analysis that they had never done before. They fully sequenced the genes of both his cancer cells and healthy cells for comparison, and at the same time analyzed his RNA, a close chemical cousin to DNA, for clues to what his genes were doing.

The researchers on the project put other work aside for weeks, running one of the university’s 26 sequencing machines and supercomputer around the clock. And they found a culprit — a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.


Read more here http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?pagewanted=all

[Redblade20XX]

I applaud them for finding the gene.

The problem with this is that in essence what they did was just a brute force attack. The way they did it was inefficient. It took them weeks to find the gene. Imagine how long it would take if it were several hundred of patients with several different genes linked to the same form of cancer.

They need to figure out if there are any links that could cut down the time of processing the patient.

- Red

[Paqman]

The way they did it was inefficient. It took them weeks to find the gene

I don't know much about this kind of biotech, but it seems to me that's going to be influenced by the amount of compute power they have available. Just look at the increase in sequencing pace over the time of the human genome project.

The approach could become valid with just a few doublings of processing power. Following Moor'es Law an 8 week wait would drop to under 2 days in about 9 years, which is about the fastest something is likely to move from research to the field.

[nec207]

I don't know much about this kind of biotech, but it seems to me that's going to be influenced by the amount of compute power they have available. Just look at the increase in sequencing pace over the time of the human genome project.

The approach could become valid with just a few doublings of processing power. Following Moor'es Law an 8 week wait would drop to under 2 days in about 9 years, which is about the fastest something is likely to move from research to the field.


Drugs that target genes or cancer type seems to be the future where biotech is going.The survivor rate is much higher than what they where doing before.

[Redblade20XX]

The approach could become valid with just a few doublings of processing power. Following Moor'es Law an 8 week wait would drop to under 2 days in about 9 years, which is about the fastest something is likely to move from research to the field.

It would be like that if Moore's law holds true (which I really doubt.) :)


Drugs that target genes or cancer type seems to be the future where biotech is going.The survivor rate is much higher than what they where doing before.

It's good that they are using targeting drugs to deal with the mutated genes rather than radiation treatment. It's a positive that survival rate is increasing but they need to address the time it takes to detect the genes.

- Red

[nec207]

The approach could become valid with just a few doublings of processing power. Following Moor'es Law an 8 week wait would drop to under 2 days in about 9 years, which is about the fastest something is likely to move from research to the field.

What do you mean can you elaborate

[Paqman]

What do you mean can you elaborate

Gene sequencing is very demanding computationally. The rate at which you can sequence genes is directly linked to the computing power of your big gene sequencing machine.

Moore's Law (http://en.wikipedia.org/wiki/Moores_law) (very) roughly means that for the same price, the speed of a computer doubles every 18 months. So in 3 years, computers will be four times as fast, and in four and half years, they'll be 8 times as fast.

Technically Moore's Law actually refers to component counts in a device of a fixed size, but this has been closely linked to processor power over the years. We keep expecting the correlation to break down as one physical blocker or another looms on the horizon, but so far human ingenuity has been able to overcome them all. Moore's Law will break down at some point, but not necessarily any time soon.

[drmrgd]

Gene sequencing is very demanding computationally. The rate at which you can sequence genes is directly linked to the computing power of your big gene sequencing machine.

Moore's Law (http://en.wikipedia.org/wiki/Moores_law) (very) roughly means that for the same price, the speed of a computer doubles every 18 months. So in 3 years, computers will be four times as fast, and in four and half years, they'll be 8 times as fast.

Technically Moore's Law actually refers to component counts in a device of a fixed size, but this has been closely linked to processor power over the years. We keep expecting the correlation to break down as one physical blocker or another looms on the horizon, but so far human ingenuity has been able to overcome them all. Moore's Law will break down at some point, but not necessarily any time soon.

There will still be a limit that goes beyond the computer when it comes to sequencing. You'll always be limited by the chemistry and detection (i.e. the enzyme's ability to incorporate the next nucleotide and machines ability to determine whether the next nucleotide that was flowed was actually incorporated into the strand).

The computation power needed to run whole genomes - not to mention storage space (a terabyte really isn't all that big anymore!) - is pretty astounding. On top of that, though, the ability to accurately determine the probability of a variant occurring at a single position is still a long way off, and this field of computational biology, computational statistics, and bioinformatics really need to grow - and grow fast!

This is in fact the future of cancer treatment, though. The goal will be more of a 1 shot 1 kill, where a doctor will take a tumor biopsy, send it to a lab for a DNA prep and sequencing, and based on the genetic profile pick a drug that will work the first time. There will no longer be the need to just keep trying drugs until a patient starts to respond. In addition, it will be easier to monitor for circulating tumor cells, as well as, go beyond the tumor driver mutations to make sure that the cancer is gone once and for all.

[nec207]

On top of that, though, the ability to accurately determine the probability of a variant occurring at a single position is still a long way off, and this field of computational biology, computational statistics, and bioinformatics really need to grow - and grow fast !

I don't really understand what you mean by this.

[drmrgd]

I don't really understand what you mean by this.

Well, in the old days, you'd take a piece of DNA and submit it to the sequencer. The output would be 1 sequence read, and you could easily view it by eye to determine whether or not each nucleotide was what it was supposed to be, or if there was a variant in there.

In the Next Generation sequencing space, you might now have thousands of sequence reads for that same piece of DNA. It would be really, really tedious and difficult to read each one by eye (especially given that the technology lends itself to multiple pieces of DNA in each sequencing run, which could add up to millions of reads!). So, there are various computational methods to align sequence reads to a reference and then determine at every single position whether or not the nucleotide is correct or incorrect, and if incorrect, whether it's a true variant or incorrect due to some systematic problem.

[nec207]

Gene sequencing is very demanding computationally. The rate at which you can sequence genes is directly linked to the computing power of your big gene sequencing machine.

Moore's Law (http://en.wikipedia.org/wiki/Moores_law) (very) roughly means that for the same price, the speed of a computer doubles every 18 months. So in 3 years, computers will be four times as fast, and in four and half years, they'll be 8 times as fast.

Technically Moore's Law actually refers to component counts in a device of a fixed size, but this has been closely linked to processor power over the years. We keep expecting the correlation to break down as one physical blocker or another looms on the horizon, but so far human ingenuity has been able to overcome them all. Moore's Law will break down at some point, but not necessarily any time soon.


There is a quite accurate rule of thumb that a processor is twice as powerful than the equivalent ranking processor from two years ago. Therefore a processor from 2012 is twice as powerful than a processor from 2010 and a processor from 2010 is twice as powerful than a processor from 2008. Since 2x2=4 a processor from 2012 is four times more powerful than a processor from 2008.


However most people misunderstand the rule and just assume that they should add two every two years. This is wrong. It really means that it doubles every two years. So in 2012 a processor is eight times more powerful than one from 2006, not six times more as 2x2x2=8.