What comes after genome sequencing?

by Dr. Hsien-Hsien Lei
Posted September 14, 2007 in DNA in General

It’s been just over a week since we were all in a tizzy over the sequencing of Craig Venter’s diploid genome and already people are asking, “What next?” And the answer would be: systems biology.

According to Dr. Leroy Hood, president of the the Institute of Systems Biology, systems biology is “the science of discovering, modeling, understanding and ultimately engineering at the molecular level the dynamic relationships between the biological molecules that define living organisms.” And over at new DNA Network member blog, The Seven Stones, Dr. George Church takes the leap from the “Jimome & Craigome” to systems biology. In The Personal Genome Project published in Molecular Systems Biology, Dr. Church said we need the following:

• Focused population association studies
• Animal models
• Functional genomics on the cells from the subjects

As an epidemiologst, I’m particularly interested in population association studies for which many study participants would be recruited to give a sample of their DNA, submit to a lifestyle survey, and commit to follow-ups. The UK Biobank and CARTaGEne in Quebec, Canada are two such examples (please see previous Eye on DNA post).

In parallel with genome mapping and sequencing, researchers in Europe believe it’s time to start working on a proteome map to delineate which specific genes are producing which specific proteins. Mapping the proteome is considerably more difficult than dealing with the genome because some proteins are present in almost undetectable amounts. It’s also very difficult to know if all proteins have been found if certain genes happen to be inactive at the time of assay.

Professor Rudolf Aebersold from the Institute of Molecular Systems Biology in Switzerland:

The idea would be that if we could map out the whole proteome, we could develop a toolbox structure enabling assays (for detecting proteins) to be done faster and more cheaply.

As you can see, the work fun doesn’t stop with whole genome sequencing. In fact, it’s just begun.

Photo: Proteomics - protein separation from Wellcome Images under Creative Commons

Tags: genetics, genes, dna, systems biology, genome, sequencing, proteomics, proteins

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5 Comments »

Comment by DNA News

2007-09-14 18:46:10

Our ability to generate vast amounts of DNA sequences is clearly going well beyond our ability to analyse it, perhaps at a exponential vs linear ratio. Systems biology is still a fuzzy subject, but it needs lots of support if we want to be able to take full advantage of the enormous quantity of information we are gathering through genome projects

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Comment by Hsien-Hsien Lei, PhD

2007-09-16 10:46:02

DNA News, Thanks for the comment. Couldn’t agree with you more.

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Comment by Thomas

2007-09-14 23:59:28

Many thanks, Hsien-Hsien, for this post and for highlighting George Church’s post on The Seven Stones.

I find the concept of personal functional genomics applied to (personal) stem cells an absolutely fascinating perspective.

When will these technologies be applied to the scale required for molecular epidemiology? Time will tell. But it is clear that new technologies will be needed that are adapted to the large scale phenotyping (at the biochemical/molecular level) of human populations. In this sense, the field of metabonomics might be a promising avenue and may in fact extend the application of systems biology to personalized medicine and molecular epidemiology beyond the fields of genomics and genetics (Global systems biology, personalized medicine and molecular epidemiology, Nicholson, 2006).

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Comment by Hsien-Hsien Lei, PhD

2007-09-16 10:48:00

Thanks for the useful links, Thomas! I still remember when I first across the term metabonomics. Here’s an excerpt of something I wrote back in May 2006:

Today’s new word is pharmaco-metabonomics - personalized medicine that takes into account how environmental factors interact with the unique way each person metabolizes drugs. Metabonomics is also known as metabolomics (both are impossible to pronounce). The combination of pharmaco-metabonomics and pharmacogenomics should make it possible to develop the ultimate personalized medicine.

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2007-10-10 00:45:35

[...] death sentence”: As epidemiologist Dr. Hsien-Hsien Lei writes today in regard to systems biology, which considered the “overall picture of how genes interact with each other and with the [...]

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