2011 September 17 Saturday
Families That Sequence Together Get Better Results

Want more accurate DNA sequence results? Get your whole family sequenced at once. The family that sequences together stays healthy together? An article in MIT's Technology Review reports on a family that got their 4 genomes sequenced to learn more about their DNA.

In November 2009, the West family embarked on an unusual family project. Parents John and Judy and teenagers Anne and Paul each had their genomes sequenced, and enlisted a team of scientists at Stanford University to interpret the meaning of the combined 24 billion letters of DNA in those genomes.

Since the technology used to do DNA sequencing makes errors the errors are easier to detect if different copies of the same chromosome carried by siblings and parents get sequenced and compared.

By comparing intergenerational genomes, scientists can identify likely errors by looking for spots where the child's genome differs from the parents'. Last year, Leroy Hood and collaborators sequenced a family of four in an attempt to identify the genetic variations underlying a rare condition called Miller syndrome, inherited by the two children. They estimated that errors are 1,000 times more prevalent than true mutations.

Your cost per genome is going to be below $10000 and falling. In 2012 expect to pay below $5k per genome. Want to start at a lower cost? For a couple hundred dollars per person you can get about a million genetic variants tested and get interpretation reports for a year. I'm about ready to finally take the plunge on the DNA testing option.

By Randall Parker    2011 September 17 11:15 AM   Entry Permalink | Comments (2)
2011 August 19 Friday
Web Genetic Study Confirms Genetic Associations

Direct-to-consumer genetic testing company 23andMe used customer data and volunteered health information from customers to confirm over 180 known genetic associations with diseases and human characteristics. As the number of people who have gotten themselves genetically tested goes up by orders of magnitude so too will the ability of genetic testing services provides to find more associations between genes and assorted diseases and attributes of humans.

MOUNTAIN VIEW, CA – (August 17, 2011) – 23andMe, Inc., a leading personal genetics company has replicated over 180 genetic associations from a list of associations curated by the National Human Genome Research Institute’s Office of Population Genomics ("GWAS Catalog") demonstrating that self-reported medical data is effective and reliable to validate known genetic associations. The results, available online in the journal PLoS ONE, establish 23andMe's methodology as a significant research platform in a new era of genetic research.

"In this paper we confirm that self reported data from our customers has the potential to yield data of comparable quality as data gathered using traditional research methods," stated 23andMe Chief Business Officer Ashley Dombkowski. "As the 23andMe platform has been clearly shown to replicate known genetic associations as well as discover new ones, we have established our research platform as an innovative model for genetic research which has the power to move scientific research forward faster and more cost effectively working in collaboration with academic and commercial researchers," continued Dombkowski.

I think we are going to reach a stage where most research on identifying functional significance of human genetic variations will be done as a result of people donating their genetic test results and health and other information to researchers. The cost of genetic testing has fallen so far that most genetic testing will be funded by individuals just wanting to get their own personal genetic information. The only thing that could stop this better future? A clamp-down on direct-to-consumer genetic testing by US Food and Drug Administration. The FDA should be encouraged to stay out of the way of progress. Tell your Congress critters.

By Randall Parker    2011 August 19 10:30 AM   Entry Permalink | Comments (2)
2011 February 06 Sunday
Belgian Malinois Detects Cancer Too

A female black lab named "Marine" who excelled at using her nose to detect bowel cancer is not alone. A Belgian Malinois in Paris shows a knack for detecting prostate cancer by sniffing urine. Given that dogs are going to sniff urine anyway might as well as make this instinctive desire useful.

Arnhem, The Netherlands, 7 February 2011 -- In the February 2011 issue of European Urology, Jean-Nicolas Cornu and colleagues reported the evaluation of the efficacy of prostate cancer (PCa) detection by trained dogs on human urine samples.

A reminder on why this matters: Dogs show the potential to detect cancers at earlier stages. If cancer can be caught before metastasis then the odds of death go way down.

In their article, the researchers affirm that volatiles organic compounds (VOCs) in urine have been proposed as cancer biomarkers. In the study, a Belgian Malinois shepherd was trained by the clicker training method (operant conditioning) to scent and recognize urine of people having PCa. All urine samples were frozen for preservation and heated to the same temperature for all tests. After a learning phase and a training period of 24 months, the dog's ability to discriminate PCa and control urine was tested in a double-blind procedure.

The dog turned out to be right that one of the controls really had undetected cancer. Good doggy!

Urine was obtained from 66 patients referred to an urologist for elevated prostate-specific antigen or abnormal digital rectal examination. All patients underwent prostate biopsy and two groups were considered: 33 patients with cancer and 33 controls presenting negative biopsies. The dog completed all the runs and correctly designated the cancer samples in 30 of 33 cases. Of the three cases wrongly classified as cancer, one patient was re-biopsied and a PCa was diagnosed. The sensitivity and specificity were both 91%.

This study shows that dogs can be trained to detect PCa by smelling urine with a significant success rate. It also suggests that PCa gives an odor signature to urine. Identification of the VOCs involved could lead to a potentially useful screening tool for PCa.

This is the journal published version of the preliminary report.

What's needed: a heavily automated training program for a large number of dogs.

By Randall Parker    2011 February 06 10:44 PM   Entry Permalink | Comments (5)
2011 January 11 Tuesday
Medicine 2.0: Ordering Your Own Medical Tests

A Wall Street Journal article reports on direct-to-consumer medical tests you can order from the web.

Cheryl Lassiter likes to keep a close eye on her cholesterol levels, but with a high-deductible insurance plan, she doesn't want to pay the fees for repeated checkups by her doctor. So a few times a year, she orders up a lab test herself, using an online service that charges about $40.

"You cut out the middleman," says Ms. Lassiter, 56, a writer who lives in Hampton, N.H.

Want to try different diets and exercise regimens and monitor your progress in improving your blood cholesterol, lipids, and other indicators? Ordering your own blood tests is one way to do it. This article has useful links to sites for interpreting blood test results such as vitamin D blood tests, liver enzyme tests (drinking too much?), blood lipids, and thyroid-stimulating hormone.

While the online genetic testing services such as 23AndMe get a fair amount of press multiple online general medical testing services offering direct-to-consumer testing are doing business with less notice. Well, my advice: notice them!

The online testing services, which include companies such as Direct Laboratory Services Inc., Health One Inc., PrivateMD Labs LLC and Personalabs LLC, typically don't own labs themselves. Instead, they allow consumers to order tests online, then direct them to a lab that contracts with the firm, such as Laboratory Corp. of America Holdings. The lab draws the patient's blood and performs the actual test. To meet state requirements, the Web firms generally have doctors on staff who sign the orders without seeing the patients.

I like the idea of direct lower cost services. You can opt for a high deductible medical insurance policy for lower cost and direct your own routine care. Or if you live in a country with government-provided but rationed care you can try to work around it by ordering your own tests. You can even buy your own home CardioChek cholesterol meter. Still a long way from Dr. McCoy's medical tricorder. But a step in that direction.

In a previous post about lengthening medical care queues commenter Jake describes medical tests he orders for himself, his costs, and how he uses the results. He calls this practicing Medicine 2.0. Next we need online expert systems to help us sort thru our symptoms and advise us on our health needs. Beware that some government agencies question our ability to handle the truth and get our own testing done.

By Randall Parker    2011 January 11 09:59 PM   Entry Permalink | Comments (7)
2010 December 21 Tuesday
Chip To Sequence Genome In Minutes?

A small chip will some day sequence your entire genetic sequence in minutes. Of course, small and fast also means very cheap too.

Scientists from Imperial College London are developing technology that could ultimately sequence a person’s genome in mere minutes, at a fraction of the cost of current commercial techniques.

Couples on dates or sizing up each other in bars will some day surreptitiously take DNA samples of each other and do sequencing to find out if their romantic interest has desired attributes. How smart? How likely to be faithful? How driven? Genetic sequences will provide clues.

The researchers have patented an early prototype technology that they believe could lead to an ultrafast commercial DNA sequencing tool within ten years. Their work is described in a study published this month in the journal Nano Letters and it is supported by the Wellcome Trust Translational Award and the Corrigan Foundation.

The research suggests that scientists could eventually sequence an entire genome in a single lab procedure, whereas at present it can only be sequenced after being broken into pieces in a highly complex and time-consuming process.

With the prices dropping I expect most of us will know at least some of our our genetic differences from genetic testing in the next 5 years. Right now 23andMe is running a DNA testing sale of $99. It strike me that this would make a novel Christmas gift. Got to see if a certain family member wants this as a gift.

In the 10-15 year time line full genome sequencing will become common. I'll be surprised if most of us do not know our our full genome sequence by 2025. Costs are falling so rapidly that 15 years seems sufficient to make genome sequencing very cheap.

By Randall Parker    2010 December 21 12:38 AM   Entry Permalink | Comments (4)
2010 November 25 Thursday
Cheap DNA Testing Deal

Razib Khan and Ray Sawhill both alerted me to a special personal DNA testing deal from 23andme.com for $99 plus $60 for a year of data analysis updates (where new research tells more about the half million DNA letters they test). Razib says to get the discount the discount codes are LOYALFAN, HHY6P4, GIZMODO99.

23andme does what is called SNP testing. SNP stands for single nucleotide polymorphism. Sounds fancy, right? Not really. SNPs are places in your 2.9 billion DNA letters where people differ from each other. The half million that 23andme test are so far known to be more interesting from a medical or genealogical standpoint than some millions of other known SNPs.

So do they offer practical useful information? For some people, yes. For example, they check some SNPs that are associated with higher risk of side effects from cholesterol-lowering statins and blood thinners such as Warfarin. I think DNA testing for drug side effects will provide a big boon because not only can we use DNA tests to avoid side effects from existing drugs but also when drugs cause dangerous side effects during drug development fewer drugs will need to be dropped from development if a subset of at-risk people can be identified. With genetic tests that identify those at risk everyone else will be able to still use these drugs which otherwise would never make it to market.

I would like to see the genetic testing services provided by companies like 23andme to be used more routinely with medical research studies on humans. For example, I recently reported on how some people get little or no benefit from exercise. If the people who did that study had also used 23andme's testing service on their study subjects they might already have clues as to which SNPs might contribute to those findings.

I expect genetic testing will eventually tell us lots of insights useful for our daily lives. For example, do we benefit from exercise, what kinds, and what kinds to avoid? What about fat versus protein versus carbohydrates or types of fats? Nutrigenomics will provide some answers which will allow us to customize our diets. Also, which drugs to avoid or take? Both the long and short term benefits and risks of drugs depend at least partly on our genetic makeup.

By Randall Parker    2010 November 25 09:47 AM   Entry Permalink | Comments (1)
2009 January 11 Sunday
Genetic Assays About Ourselves

Noted Harvard psychologist and author Steven Pinker has an article in the New York Times Magazine entitled My Genome, My Self. He explores the relationship between your DNA sequence and your personal identity.

Last fall I submitted to the latest high-tech way to bare your soul. I had my genome sequenced and am allowing it to be posted on the Internet, along with my medical history. The opportunity arose when the biologist George Church sought 10 volunteers to kick off his audacious Personal Genome Project. The P.G.P. has created a public database that will contain the genomes and traits of 100,000 people. Tapping the magic of crowd sourcing that gave us Wikipedia and Google rankings, the project seeks to engage geneticists in a worldwide effort to sift through the genetic and environmental predictors of medical, physical and behavioral traits.

Parenthetically, I think the Personal Genome Project is an excellent idea. DNA sequence information is becoming so cheap so far that our biggest problem is how to compare the genetic data of a large number of people against many characteristics about them. Lots of genetic variations make only small contributions to traits. So picking out those influences is very difficult. A large sample size of people is needed to give scientists decent odds of picking up on which genetic variants make a difference in which trait.

The Personal Genome Project is an initiative in basic research, not personal discovery. Yet the technological advance making it possible — the plunging cost of genome sequencing — will soon give people an unprecedented opportunity to contemplate their own biological and even psychological makeups. We have entered the era of consumer genetics. At one end of the price range you can get a complete sequence and analysis of your genome from Knome (often pronounced “know me”) for $99,500. At the other you can get a sample of traits, disease risks and ancestry data from 23andMe for $399. The science journal Nature listed “Personal Genomics Goes Mainstream” as a top news story of 2008.

The $99,500 service doesn't offer utility commensurate to the money at this point because we do not know the functional significance of the vast bulk of the locations in the genome that differ from one person to the next. Still, if you are rich why not get the full picture? You'll find out more quickly for each new genetic discovery whether it matters to you.

In order to keep costs down the 23andMe folks do not check for as many genetic differences. They focus more on telling you about genetic variants suspected or known to be useful or at least revealing. Their disease risk info might spur you to get tested more often for some form of cancer for which you have higher risk (early detection being great for raising the chance of a cure). Or you might look at your test results and resolve to try harder to make lifestyle and diet choices to reduce your risk of heart disease. I also think their ancestry analysis could be especially interesting for adopted people and others who do not know much about where their ancestors came from.

Pinker says we can make use of genetic information without going crazy about it (my phrasing, not his).

Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture. Today it is the humane democracies of Scandinavia that are hotbeds of research in behavioral genetics, and two of the groups who were historically most victimized by racial pseudoscience — Jews and African-Americans — are among the most avid consumers of information about their genes.

I think we are going to find lots of ways to use genetic information and this will fragment into different industries. Lots of people will write software to analyze genetic data for different purposes. For example, there'll be a mini-industry on genes and diet. There'll be another on ancestry tracing. There'll be still another on genetics and sports. Is there a way to compensate for your genes with drugs to make you perform just as well as someone who has better genes for swimming or tennis? Companies will look for ways.

DNA won't just get translated into static information to ponder. You will ask how best to interact with your DNA. That'll involve drug development, diet, exercise, and perhaps creation of environments that complement your genetic profile.

Of course, some answers from genome sequencing will not be pretty. Pinker has decided not to be told whether he carries a variant of the apolipoprotein E gene (APOE) that increases risk of Alzheimer's disease. It is understandable to not want to know about something that you can't do anything about. But as the decades go by and more effective treatments get developed for a long list of diseases some of the highly undesirable genetic variants will get matched up with useful treatments. So learning about your worst genetic variants won't carry as much a sense of futility and loss as is the case today. There is one case where genetic knowledge can be used today: testing before pregnancy. Turns out, there's a new company which specializes in pre-pregnancy genetic testing. They ask on their web site "Thinking about starting a family?".

The genes analyzed by a new company called Counsyl are more actionable, as they say in the trade. Their “universal carrier screen” is meant to tell prospective parents whether they carry genes that put their potential children at risk for more than a hundred serious diseases like cystic fibrosis and alpha thalassemia. If both parents have a copy of a recessive disease gene, there is a one-in-four chance that any child they conceive will develop the disease. With this knowledge they can choose to adopt a child instead or to undergo in-vitro fertilization and screen the embryos for the dangerous genes. It’s a scaled-up version of the Tay-Sachs test that Ashkenazi Jews have undergone for decades.

How does this work? First a couple gets tested. If they do not have any of the problematic genetic variations which this company screens for then they can start a pregnancy the old fashioned way. If they do have variations which could cause genetic diseases in offspring they then have some choices to make. But the point is they really do have choices they can make. As Pinker says, this is actionable information.

As biotechnology and biomedical science advance we will find many more ways in which we can respond to genetic knowledge about ourselves and take useful decisions. But already today we can make decisions about reproduction based on genetic tests. Granted, those tests do not cover every way that genes can affect health or other qualities of offspring. But a genetic screen for known well characterized genetic diseases is a good start.

I wonder whether small Amish populations that have high rates of a few genetic diseases would be willing to do matchmaking based on genetic data. They might not be willing to use IVF and pre-implantation genetic diagnosis (PGD) for embryo selection. But for those mutations which are only harmful when there are two copies then matchmaking could be used to avoid marriages between pairs who carry the same harmful genetic variant. Something like the Counsyl test could help to reduce the frequent of genetic diseases in the Amish or other populations that have higher frequencies of genetic diseases.

By Randall Parker    2009 January 11 11:54 PM   Entry Permalink | Comments (3)
2007 March 10 Saturday
MIT Barcoded Nanoparticles For Cheap Medical Testing

Computers that cost tens of millions of dollars in the 1970s were much slower that computers of today that cost a few hundred dollars in hand-held personal digital assistants (PDAs). That pattern is going to repeat over the next two decades with biotechnology as cheap mass-manufactured microfluidic "labs on a chip" and nanoparticles replace big expensive medical testing equipment and make medical testing doable by anyone. Picture a cheap device that can test for millions of different biomolecules in a single sample of tissue or blood.

CAMBRIDGE, Mass.--MIT researchers have created an inexpensive method to screen for millions of different biomolecules (DNA, proteins, etc.) in a single sample-a technology that could make possible the development of low-cost clinical bedside diagnostics.

The work, based on tiny customizable particles, could also be used for disease monitoring, drug discovery or genetic profiling. Even though the particles are thinner than the width of a human hair, each is equipped with a barcoded ID and one or more probe regions that turn fluorescent when they detect specific targets in a test sample.

Using a new, extremely versatile technique, the researchers can produce a "virtually unlimited" array of particles to test for DNA, RNA, proteins and other biomolecules, said Daniel Pregibon, a graduate student in chemical engineering at MIT.

Pregibon is the lead author of a paper on the work that will appear in the March 9 issue of Science.

He and co-author Patrick Doyle, the Doherty Associate Professor of Chemical Engineering, believe their particles could become an effective and inexpensive way to perform medical diagnostic tests at a patient's bedside.

Current testing methods are cost-prohibitive for bedside use, Pregibon said. The MIT particles are inexpensive to manufacture, and their results are as accurate, if not more so, than the results from more expensive systems, he said.

Cheap biomedical testing equipment won't just get used at bedsides in hospitals. The far bigger use of cheap, small, and highly automated test equipment will be in homes. Bedstands will have sensors that check for signs of disease in exhaled breath. Sensors in sinks will check spit. Toilets will contain sensors that analyze urine and feces. Bathroom mirrors will contain safe low power lasers that'll briefly scan your mouth and eyeballs and skin for signs of diseases.

Just living in a house will put you in an effortless but very detailed and constant medical testing regimen. There'll be no need for a Star Trek medical tricorder because the scanning equipment will be built into houses and cars and even watches and jewelry. Medical testing won't require a trip to a doctor. Testing and even most diagnosis will happen in home computers running medical expert systems.

But back to this latest step toward cheap and ubiquitous medical testing technology: When a particle binds to a target molecule that activates flourescent barcode pattern.

One end of each particle is a fluorescent "dot-pattern" barcode that reveals what the target molecule of the particle is, and the other end is loaded with a probe and only turns fluorescent if the target molecule is present. The particles can also be designed to each test for multiple targets, by adding several unique regions.

"We can make the particles, encode them and add functionality all in a single step," said Pregibon.

Small stuff can get made cheaply. This is small stuff. Some day it'll be dirt cheap.

After exposure to a sample (e.g. some blood serum) the particles flow through a microfluidic device and read to see if they bound to anything in he sample.

To rapidly "read" the particles, the researchers designed a custom "flow cytometer" using a microfluidic device and standard microscope. In this flow-through system, the oblong, disk-like shape of the particles ensures that they are precisely aligned for accurate scanning. Each time a particle flows past a detector, its barcode is read and the corresponding target is quantified.

The microparticles are inexpensive because they can be produced efficiently in a single step. The design of the particles also makes the scanning devices cheaper. With multiple distinct regions, the barcode can be read and the target quantified using a single fluorescent color, which greatly simplifies detection.

Again, biotechnology is going the way of computer technology. Biotechnology manufacturing will use much of the same materials, equipment, and processes used to make semiconductor computer chips. Microfluidic devices for biomedical testing will be mass produced for cheap mass market personal medical test equipment. Most medical testing will not get done in hospitals and doctor's offices. Most diagnosis will get done by expert systems before you ever step foot in a doctor's office.

Then will come the nanobots that'll do repairs.

By Randall Parker    2007 March 10 11:05 AM   Entry Permalink | Comments (0)
2002 October 01 Tuesday
The Coming Era of Nutritional Genomics

Some experts dispute whether we know enough about how various genetic variants work to start dispensing dietary advice based on the results of genetic tests. However, companies are starting offer such services. The NY Times has published an article which is mostly on this field known as nutritional genomics or nutrigenomics (free registration required):

Sciona, a British company, is selling customized dietary advice for about $200. The company tests for 19 variations in nine genes. Six genes are involved in removing toxins from the bodies. Consumers who have variations that the company says slow this process are advised, for instance, to avoid well-done red meats, which have higher levels of certain toxins.

Another test is for the gene that produces Mthfr, an enzyme involved in using folic acid, an important vitamin. People with a less efficient version of this gene are told to eat more liver, broccoli and other foods rich in the vitamin.

Personal genetic profiles will allow individualized advice about diet, exercise, drug choices, and medical testing regimens. People who have poor toxin processing enzymes will know what toxins to avoid exposure to and even what drugs to take to enhance toxin processing. Eventually it is likely that such people will even opt for gene therapy or liver replacement. Said liver will be grown from one's own stem cells after those stem cells have been genetically engineered to enhance their toxin processing. One can even imagine diet books written for different genetic groups.

By Randall Parker    2002 October 01 01:32 PM   Entry Permalink | Comments (0)
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