Egypt joins Geneva negotiations on Global Plastics Treaty, calls for urgent agreement    Egypt delivers over 30 million health services through public hospitals in H1 2025    Madinet Masr in talks for three land plots in Riyadh as part of Saudi expansion    Egypt's PM tells Palestinian PM that Rafah crossing is working 24/7 for aid    Egypt, Japan discuss economic ties, preparations for TICAD conference    Real Estate Developers urge flexible land pricing, streamlined licensing, and dollar-based transactions    Egypt's Sisi pledges full state support for telecoms, tech investment    EGP inches down vs. USD at Sunday's trading close    EGX launches 1st phone app    Escalation in Gaza, West Bank as Israeli strikes continue amid mounting international criticism    Egypt recovers collection of ancient artefacts from Netherlands    Egypt, UNDP discuss outcomes of joint projects, future environmental cooperation    Egypt harvests 315,000 cubic metres of rainwater in Sinai as part of flash flood protection measures    After Putin summit, Trump says peace deal is best way to end Ukraine war    Egypt, Namibia explore closer pharmaceutical cooperation    Jordan condemns Israeli PM remarks on 'Greater Israel'    Renowned Egyptian novelist Sonallah Ibrahim dies at 88    Egyptian, Ugandan Presidents open business forum to boost trade    Al-Sisi says any party thinking Egypt will neglect water rights is 'completely mistaken'    Egypt's Sisi warns against unilateral Nile measures, reaffirms Egypt's water security stance    Egypt's Sisi, Uganda's Museveni discuss boosting ties    Egypt, Huawei explore healthcare digital transformation cooperation    Egypt's Sisi, Sudan's Idris discuss strategic ties, stability    Egypt's govt. issues licensing controls for used cooking oil activities    Egypt to inaugurate Grand Egyptian Museum on 1 November    Egypt's Sisi: Egypt is gateway for aid to Gaza, not displacement    Greco-Roman rock-cut tombs unearthed in Egypt's Aswan    Egypt reveals heritage e-training portal    Sisi launches new support initiative for families of war, terrorism victims    Egypt expands e-ticketing to 110 heritage sites, adds self-service kiosks at Saqqara    Palm Hills Squash Open debuts with 48 international stars, $250,000 prize pool    On Sport to broadcast Pan Arab Golf Championship for Juniors and Ladies in Egypt    Golf Festival in Cairo to mark Arab Golf Federation's 50th anniversary    Germany among EU's priciest labour markets – official data    Paris Olympic gold '24 medals hit record value    A minute of silence for Egyptian sports    Russia says it's in sync with US, China, Pakistan on Taliban    It's a bit frustrating to draw at home: Real Madrid keeper after Villarreal game    Shoukry reviews with Guterres Egypt's efforts to achieve SDGs, promote human rights    Sudan says countries must cooperate on vaccines    Johnson & Johnson: Second shot boosts antibodies and protection against COVID-19    Egypt to tax bloggers, YouTubers    Egypt's FM asserts importance of stability in Libya, holding elections as scheduled    We mustn't lose touch: Muller after Bayern win in Bundesliga    Egypt records 36 new deaths from Covid-19, highest since mid June    Egypt sells $3 bln US-dollar dominated eurobonds    Gamal Hanafy's ceramic exhibition at Gezira Arts Centre is a must go    Italian Institute Director Davide Scalmani presents activities of the Cairo Institute for ITALIANA.IT platform    







Thank you for reporting!
This image will be automatically disabled when it gets reported by several people.



The Language of Genomics
Published in Daily News Egypt on 01 - 10 - 2009

DALIAN, China: Last month, a company called Complete Genomics announced 10 new customers for its genome-sequencing service. The price was not specified, but the company said its goal is to offer the service for $5,000 within a year.
What struck me was not the announcement itself, but the name of the CEO: Cliff Reid, the CEO when I knew him in the 1980s of a text-search company called Verity. The connection hit me almost immediately. Genes are, in a sense, the instruction language for building humans (or any other living thing). And language is symbols that interact to build meaning. And, yes, of course, it was the same Cliff Reid I knew back in the late 1980s.
What Complete Genomics is doing with the $91 million it has raised so far is exciting. It has built a genome-sequencing factory and plans to build several more over the next few years. Many academic and commercial research facilities want one, as do several countries.
What I find interesting are the implications. Right now, a genome is akin to a novel written in an unknown language. There is a huge amount of information in there, but we can't understand it. Imagine getting a copy of Tolstoi's War and Peace in Russian and (assuming you can't read Russian) trying to figure out the story. Impossible. That's pretty much the situation of natural-language understanding at the time Reid joined Verity.
On the other hand, we have started recognizing some words - specific genetic variants - that seem to correspond to certain incidents in history. In the case of genetics, those incidents are diseases and conditions. And just as it usually takes several individuals to cause an incident, so it often takes several genetic variations, plus ambient factors, to cause a disease. Genes often work together, sometimes aided by factors such as a person's diet or behavior, to cause a condition.
There are two key challenges in genomics. One is simply detecting the genes, alone or in combination, that seem to lead to certain diseases. That alone can be useful. With enough data, we can then figure out that the same "disease is in fact a variety of different disorders, some susceptible to particular known treatments and some susceptible to others or simply incurable.
For this, mere correlation is sufficient. People with BRCA-derived breast cancer benefit from treatment with herceptin, whereas those with other kinds of breast cancer do not. We don't know why, but the correlation is clear. The second challenge is to understand how the genes interact among themselves or with other factors to produce the condition, which should enable the development of new preventive measures or treatments based on the details of how the condition begins and how it progresses. That, of course, is much more interesting - and harder to do. In a sense, it's the difference between matching words and understanding a piece of text.
So, it is no surprise that Reid has found a role in this new marketplace. Complete Genomics and its competitors are about to create huge amounts of data. CGI's edge is not just sequencing the genomes cheaply, but also refining the data into lists of variations. In other words, for most research the questions revolve not around an entire genome, but around the relevant differences of any individual's genome from the norm.
There are common differences, like the differences between blue eyes and brown eyes, or even between people likely to have Crohn's disease and those who are unlikely to have it. Then there are differences that result simply from a "broken gene, which is not a variant but simply a mistake. Most of these are harmless; the really harmful ones don't survive long enough to show up anywhere.
The researchers' task is to find meaning from all this data. We're just at the beginning of this process, which will take many years. While some researchers are looking for statistical correlations, others are studying how the individual genes interact.
For all of them, access to genome sequences is important. But the genomes mean little without the corresponding medical records, just as the Russian novel - in any language - means little without a corresponding knowledge of Russian history.
Obtaining that history requires consent from the individuals whose genomes are sequenced. It also requires a lot of data processing to make the records usable. Much of the information is simply not recorded. And much is still on paper, or in scanned images, insurance company records, and pharmacy transactions. There is a standard language for representing diseases, but in many cases the records containing this language might as well be hidden in mattresses.
The current movement in many developed countries towards electronic medical records will improve health care directly, but it will also lead to much improved information liquidity to help genetic and other medical research.
We now have the ability to sequence genomes at increasingly lower costs, and we are slowly making the corresponding health information computer-readable. Companies such as Complete Genomics are developing software that can process the information.
There is, of course, still a huge amount of data to collect and process, and huge amounts of research and discovery to happen. But it is hard not to be optimistic about our increasing medical knowledge. The challenge five years from now will be to turn all that knowledge into practice through better preventive measures, better drugs, and better care.
Esther Dyson, chairman of EDventure Holdings, is an active investor in a variety of start-ups around the world. Her interests include information technology, health care and private aviation and space travel. This commentary is published by Daily News Egypt in collaboration with Project Syndicate, (www.project-syndicate.org).


Clic here to read the story from its source.