DNA Sequencing the Promise of Future

DNA has been considered the code of life and the language of creation. Deciphering it completely will, no doubt, lead to dramatic changes to our lives. New and improved medicine will be created; genetic diseases will be spotted and corrected early on in life; micro organisms will be engineered to create new and improved sources of energy. The list goes on, but it suffices to say that our future will be completely changed with new breakthroughs in DNA analysis. No wonder then that most researchers are painstakingly working on understanding DNA better by creating new method of sequencing.dna1

One of the biggest research projects on DNA was, of course, the human genome project. This project was to find out the exact order of nucleotide (A, G,T,C), or DNA sequencing.  It was a big success as it achieved its primary objective of sequencing entire genome. In process we also  discovered 20,000-25,000 genes .

Despite all this research we still haven’t been able to translate this research to something  visibly useful for mankind. We haven’t found dramatic new cures for diseases or anything similar.

Lack of Progress -Cost

So why haven’t we made more progress? The answer is simple, currently we have only about 20 people’s who’s complete DNA is sequenced. We need more data to make useful conclusions.

Naturally the next question we should ask is why only about 20 people? The answer lie in cost of sequencing. It cost about $10000 to sequence a DNA.

The Promise of Future, Low Cost?

Therefore, if we need to sequence entire genome of more people, we need to bring down the cost. To bring down the cost we need to figure out new and innovative ways to sequence DNA. Luckly,  companies like Complete Genomics and Pacific Bio Science has made some very exciting progress. Complete Genomics is claiming that they will sequence DNA for only $5000 and Pacific BioScience is aiming to bring down the cost even further down to under $100.

Complete Genomics

Complete Genomics is indicating that in five years they will sequence one million genomes. Compare to about 20 we have now that is an astounding number. Imagine the usefulness of data when you go from 20 to a 1 million big data set. Furthermore, according to their February 6 press release the company planned to sequence 1000 genomes this year and about 20000 by 2010.

To store this much data they need not tera but petabytes of storage. So they will be building a data center that by 2010 will have the capacity for 30 petabyte.

How does it work?

Here is high level description of their system:

  1. First a long piece of DNA is compacted into a ball of DNA Nano-ball (DNB) by inserting it into a circular template DNA with adaptors (synthetic DNA) and enzyme which makes hundreds of copies of the DNA.
  2. The DNB (DNA Nano-ball ) is poured onto a slide that captures the DNBs.
  3. Sequence the DNA with fluorescent markers that bind to each one of DNA letters (C,A,T,G) – each letter will bind to  one of the four colors green, blue, red, yellow.
  4. Picture of the entire sequence is taken.
  5. Computationally generate the entire sequence.

dna-sequencing-complete-genomics-system

Pacific Bio Science?

The promise of Pacific Bio Science is indeed a very exciting one. They promised to bring the cost to under $100 by producing the entire sequenced genome in minutes.

They devised a very simple, to understand, and ingenious approach that takes advantage of natural process of DNA replication. In fact, they use the enzyme responsible for replicating DNA – the DNA polymerase, to sequence the DNA.

Their technology is called SMRT (Single Moleculre Real Time, pronounced as Smart) . SMRT  works by eavesdrops on the actual process of DNA replication by DNA polymerase. The eavesdropping is done through two new technologies:

1.      Phosopholinked Nucleotides:

Different color florescent label is attached to each nucleotide (e.g: Green to A, Yellow G, Orange to C, and Pink to T). This florescent label is attached to the terminal phosphate molecule, and hence during the DNA replication by DNA polymerase the florescent label is ejected.

2.      Zero Mode Waveguide (ZMW)

This is a nanophotnic visualization chamber that will allow detection of ejected florescent labels. Because DNA polymerase take couple millisecond to incorporate a nucleotide, ZMW can detect the floresecent label of the currently incorporated nucletod. Hence capturing a sequence of DNA.

Progress in developing cheap ways of sequencing DNA seems to be very promising. Soon we will have a very cheap way to sequence DNA. Time will tell what this progress will actually translate too, but I hope that we make use of this technology in fighting diseases. Specifically, let’s hope for the future that will have targeted personalized drugs that will help us better our lives.

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One Response to “DNA Sequencing the Promise of Future”

  1. phproxy says:

    Unfortunately, for most cloud computing platforms the vehicle example you provide doesn’t calculate. If you notice a car as a means to an end, and all of you cherish is getting there, then you need an application platform like Google’s AppEngine. Here you simply add an app, and it will be dealt with. If on the other hand you run ec2, you’re no longer stressing about computer hardware, but still about instances and virtual servers. Every one of them run OS’s that need to be maintained; it’s like taking taxi’s but still having to know everything about the taxi’s engines. I predict that at some point we’ll move towards AppEngine like models or ‘managed clouds’.

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