$100 human genome in sight

Last Updated: Wed, Feb 25, 2009 07:19 hrs

Chennai: Imagine if a physician could conduct a biopsy on a cancer patient’s tumour and prescribe treatment at a cost less than for a chest x-ray. A nano fluidic chip that not only cuts time on DNA sequencing but dramatically reduces costs, promises to do just that, says a release.

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Han Cao, founder of BioNanomatrix, has designed a nanofluidic chip that could lower DNA sequencing costs dramatically to $100, reports the inaugural issue of the Indian edition of Technology Review, MIT’s magazine of innovation, which will hit the stands in the country next week.

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BioNanomatrix, a startup that runs the lab, is pursuing what many believe to be the key to personalised medicine: DNA sequencing technology so fast and cheap that an entire human genome can be read in eight hours for $100 or less. With the aid of such a powerful tool, medical treatment could be tailored to a patient’s distinct genetic profile.

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For example, the doctor could determine the particular genetic changes in the tumour cells of lung cancer, and order the chemotherapy best suited to that variant.

If this is an example of a technology that will revolutionise medical treatment, then at EmTech 2009, the emerging technologies conference at Delhi next week, many other such life altering technologies will be showcased. The conference will unveil 10 technologies with the greatest potential to impact the way we live and do business. These revolutionary innovations promise fundamental shifts in areas from energy to health care, computing to communications, says Jason Pontin, Editor-in -Chief of Technology Review.

Despite scepticism from some quarters, BioNanomatrix believes it can reach the $100 target in five years. The reason for its optimism: Han Cao has created a chip that uses nanofluidics and a series of branching, ever-narrowing channels to allow researchers to isolate and image very long strands of individual DNA molecules for the first time. Cao’s chip, which neatly aligns DNA, is essential to cheaper sequencing because double-stranded DNA, when left to its own devices, winds itself up into tight balls that are impossible to analyze.

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To sequence even the smallest chromosomes, researchers have had to chop the DNA up into millions of smaller pieces, anywhere from 100 to 1,000 base pairs long. These shorter strands can be sequenced easily, but the data must be pieced back together like a jigsaw puzzle. The approach is expensive and time consuming as the human genome consists of about three billion pairs of nucleotides. Even with the most elegant algorithms, some pieces get counted multiple times, while others are omitted completely. The resulting sequence may not include the data most relevant to a particular disease.

In contrast, Cao’s chip untangles stretches of delicate double-stranded DNA molecules up to 1,000,000 base pairs long—a feat that researchers had previously thought impossible. The series of branching channels gently prompts the molecules to relax a bit more at each fork, while also acting as a floodgate to help distribute them evenly. A mild electrical charge drives them through the chip, ultimately coaxing them into spaces that are less than 100 nanometers wide. With tens of thousands of channels side by side, the chip allows an entire human genome to flow through in about 10 minutes.

The data must still be pieced together, but the puzzle is much smaller (imagine a jigsaw puzzle of roughly 100 pieces versus 10,000), leaving far less room for error.

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Because the chips can process long pieces of DNA, the molecules retain information about gene location; they can thus be used to quickly identify new viruses or bacteria causing an outbreak, or to map new genes linked to specific diseases. And as researchers learn more about the genetic variations implicated in different diseases, it might be possible to biopsy tissue and sequence only those genes with variants known to cause disease, says Colin Collins, a professor at the Prostate Center at Vancouver General Hospital.

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