It’s a far more complex field than genomics, studying how proteins
are structured and expressed, how they change and communicate. When you
tie genome sequencing to proteome sequencing, it adds billions of data
points across millions of patients. That’s both good and bad.
With a fire hose of information that big, you can develop better
drugs and look for better biomarkers: anything in a patient’s blood,
urine or saliva—from proteins to enzymes to red-cell count—that
indicates the presence of a disease. But fire hoses are hard to handle,
and that’s where Big Data comes in.
The combination of massive computer power and sophisticated
algorithms that can manage staggeringly complex problems—from predicting
precisely where a tornado will touch down to making your Web search
more efficient—is the next great wave of data processing. Companies like
Roche, Illumina, Life Technologies, Pronota and Proteome Sciences are
expanding their bioinformatics platforms to develop new diagnostics and
new drugs based on them. Sometimes a diagnostic and a drug are developed
in tandem, a model known as Dx/Rx. These new proteomic-derived agents
are designed to target everything from sepsis to Alzheimer’s disease to
cancer and offer the opportunity to deliver bespoke medicine, tailored
to your molecular structure. It’s Savile Row biology.
Archaeologists announced Feb. 4 that bones excavated from underneath a parking lot in Leicester, "beyond reasonable doubt," belong to the medieval king. Archaeologists announced the discovery of the skeleton in September. They suspected then they might have Richard III on their hands because the skeleton showed signs of the spinal disorder scoliosis, which Richard III likely had, and because battle wounds on the bones matched accounts of Richard III's death in the War of the Roses.
To confirm the hunch, however, researchers at the University of Leicester conducted a series of tests, including extracting DNA from the teeth and a bone for comparison with Michael Ibsen, a modern-day descendant of Richard III's sister Anne of York.
Indeed, the researchers found the genetics matched up between Ibsen and that from the skeleton. "The DNA remains points to these being the remains of Richard III," University of Leicester genetics expert Turi King said during a press briefing.
(Caroline Wilkinson, professor of craniofacial identification at the University of Dundee) used a scientific approach to determine the king's facial features from his skull. She then created a model using 3D printing technology.
The model was painted and completed by Janice Aitken, a lecturer at the University of Dundee's Duncan of Jordanstone College of Art & Design, who said she drew on her experience in portrait painting.
The mapping of the human genome, completed in 2003, cost $2.7 billion. Now the cost for an individual's whole-genome sequencing (WGS) is $7,500 and falling fast. One day WGS could be as easy to get as a pregnancy test at the drugstore. To do the testing, lab technicians need less than a teaspoon of blood, which is chemically treated to burst open the cells so the DNA inside them can be collected. Those microscopic strands are then fed into sophisticated machines that read each of the 3 billion bits of information, called base pairs, that make up a person's genetic alphabet. Computers scan the data for the equivalent of spelling mistakes. Some mistakes cause disease; others don't. And in between is a vast gray area where scientists just don't know what the changes mean.
In an ideal world, genetic analysis could save money by catching diseases early, offering targeted treatments and identifying the most effective preventive measures. Dr. Katrina Armstrong, a professor at the University of Pennsylvania School of Medicine, notes that testing 21 genes could reveal which breast-cancer patients are unlikely to benefit from a particular chemotherapy--knowledge that could spare women the treatment and save $400 million each year. "If genomics can help us understand who will get the most benefit and who will get little or no benefit from an intervention," Armstrong says, "it will take us a long way toward improving patient outcomes and saving money.
“The University of Washington’s ENCODE project stands for “ENCyclopedia Of DNA Elements.” The on/off switches controlling genes were encrypted within the remaining genome. Without these switches, named “regulatory DNA,” genes are inert. (In the past, this was trivialized as “junk DNA”)”
“ENCODE combined the efforts of 442 scientists in 32 labs in the UK, US, Spain, Singapore and Japan. They generated and analyzed over 15 trillion bytes of raw data – all of which is now publicly available. The study used around 300 years’ worth of computer time studying 147 tissue types to determine what turns specific genes on and off, and how that ‘switch’ differs between cell types.”
Dr Ewan Birney, a Cambridge scientist who helped lead the project, was quoted in the UK Telegraph: “This idea of junk DNA – we always knew must be something more than protein coding genes, things that switch them on and off. But I really was not expecting this number and density of switches. It feels like a jungle out there. It is not a neat orderly place. It is absolutely full of life.”
Margaret and I went to see the thriller last night. She was really keen on it. I wanted a mindless comedy at the end of the week. I was going to see the first few minutes and switch theatres but I stayed for the whole movie. Glad I did. Amazing amount of use (and abuse) of science and technology on display.
The movie revolves around “gene doping” to create “super spies”. More precisely the director, Tony Gilroy calls it “chromosomal gene doping through a synthetic virus”. So there are plenty of blue, green, yellow pills “chems” and action scenes in labs and pharma shop floors. Of course, there is also plenty of drones and sensors and rifles and passport counterfeiting technology.
One of the most fascinating sequences is when Aaron Cross (the main character) performs self-surgery to fish out a homing sensor (shaped like a pill) embedded in his abdomen, and manages to feed it to an attacking wolf in a vicious fight. The wolf then becomes the target of a drone-fired missile while Aaron buys some time with the illusion that the missile had killed him. Bourne movies stand out for their up -close action sequences. This one has plenty of those but also stunning aerial sequences, especially in the Alaskan snowy, hilly terrains, including the wolf sequence above and in the many Philippines islands.
There is plenty of jargon and science/tech talk through out the movie. In many ways, I felt like I was in the movie “Inception”. So here is a heretic suggestion. Read up on the movie before you go. Or plan to see it twice to enjoy the nuances.
One final note of satisfaction. Director Gilroy wrote (adapted from the Ludlum novels the first 3 Bourne movies). In addition to doing plenty of research for this movie, It is good to see him transition to a bigger role!
As DNA technology continues to rapidly evolve, the Innocence Project, made up of several prominent lawyers and artists (including John Grisham who has written many a legal bestseller) have helped free 290 prisoners across the US wrongly sentenced.
“Two years ago, the commercialization of DNA by 23andme and others seemed to stun geneticists and the medical research community, despite years of scientists downloading genetic discoveries on public databases.
Leading geneticists called the information too preliminary to be relevant to individuals, while some worried that it might frighten patients who tested positive for a given disease and didn't understand that these tests provided risk factors, not a definitive yes or no. Ethicists and the American Civil Liberties Union fretted about the privacy questions inherent in companies holding this data.”
“Other major consumer genetics sites include deCODEme of Iceland; Navigenics of Foster City, Calif.; and newcomer Pathway Genomics in San Diego.”
"It currently costs roughly $60,000 to sequence a human genome, and a
handful of research groups are hoping to achieve a $1,000 genome within
the next three years. But two companies, Complete Genomics and BioNanomatrix,
are collaborating to create a novel approach that would sequence your
genome for less than the price of a nice pair of jeans--and the
technology could read the complete genome in a single workday."