lundi 31 mai 2010

Kaiser Permanente and their "Giant" Genome project

Sunday, May 30, 2010

Many members of Kaiser have been asked if they want to participate in this study, and the results of which are going to be used for genomic research. The information when all culminated will contain information without any personal data included. Actually the request for donations started back in 2008. This is to be the largest study of it’s type.

All patients had to do to participate was to spit into a container sent to them by mail and return it to Kaiser. As the article states though, participants will not have the ability to see their results as again this is being done to allow scientific analysis and not necessarily for patient treatment at this point. Kaiser was given a grant of $25 million from the NIH to conduct the project as part of a stimulus package.

Additional members will be asked to contribute later as they intend to build a repository for blood samples, in other words when patients come in to have blood word done, they will be asked if they want to participate and give a DNA sample at that time. The processing of the DNA has all be set up to be “robotically” processed and it further states here that 2500 samples can be tested per week, pretty amazing number. As mentioned here too their biggest fear is a power failure as the cost per each individual analyzed is around $10,000.

This month, researchers at Kaiser Permanente in Oakland and the University of California, San Francisco began the highly automated, large-scale process of analyzing that DNA, which is being extracted from tens of thousands of saliva samples donated by Kaiser members in Northern California since 2008.

Each sample of ordinary spit is laden with cells containing the volunteer’s entire set of genes, their genomes, which carry in sequences of DNA the coded instructions for building and maintaining life. The hope for this so-called genome-wide association study is that, when the genes of people with diseases like cancer and multiple sclerosis are compared with the genes of those in good health, computer analysis will pinpoint genes responsible for the illnesses.

Following instructions found in a kit mailed to her Oakland home, Mrs. Young deposited the requested spit into a special plastic cup. She sealed it with a blue lid fitted with a built-in preservative and sent it back to Kaiser. Along with her saliva, the samples from the other 130,000 people began arriving in Kaiser’s mailbox.

However, the study has begun just as some scientists have started to question the value of these experiments, and when private ventures, like 23andMe, are struggling to find a consumer market for gene tests.

David B. Goldstein, a Duke University researcher, said he believed “interesting and valuable information” would come from the Kaiser study, but he questioned whether it was the most efficient way to gather information about the genetic links to disease. “It’s an awfully expensive study,” Dr. Goldstein said in an e-mail message.

In the coming years, 400,000 more members will be asked to contribute their DNA to the project when they come in for routine blood work. Kaiser is spending $9 million to build a repository for the blood samples.

At the Kaiser research lab, a production line of robotic equipment has been set up to process the 130,000 cups of saliva that have been mailed by patients and stored, at room temperature, in racks of cardboard “pizza boxes,” 50 cups to a box. Here, the robots draw out a sample of spit, and chemically process it to extract the donor’s DNA.

At Dr. Kwok’s ninth-floor lab, three sets of robots prepare the DNA samples shipped from Oakland. The full complement of DNA from each volunteer is washed over a custom-designed silicon chip about this size of small fingernail. Microscopic wells etched into the chip are each engineered to pluck out one of 675,000 possible gene variants.

“Our biggest fear is a power-failure,” said Dr. Kwok. Each array, filled with 96 processed DNA samples, costs $10,000.

From Californians’ DNA, a Giant Genome Project -

Technorati Tags: DNA, Kaiser Permente, genomics, University of California, San Francisco, Oakland, patients, tests, automation, technology, arrray

jeudi 20 mai 2010

DNA As Crystal Ball: Buyer Beware

by Sharon Begley, Newsweek, May 18, 2010

When it comes to predicting risk of disease, Alzheimer's genes—and others—strike out.

When James Watson, codiscoverer of the double helix, had his genome fully sequenced in 2008, there was one piece of DNA he insisted the lab not tell him about: whether he had a genetic variant that significantly increases the chance of developing Alzheimer’s disease. Called apoE, the gene comes in three variants, of which APOE4 increases the risk of Alzheimer's between 10- and 30-fold. Different people have different feelings about learning what lies in their medical future, especially if it is something for which there is neither cure nor treatment. (House got good mileage out of this dilemma when Thirteen, played by Olivia Wilde, decided to find out whether she carries the gene for the inevitably fatal, incurable Huntington's disease. She does.) If studies coming out over the last few months are any indication, however, most of us can postpone making this difficult decision: the revolution in using DNA to read people's medical future is turning out to be more hype than hope.

The latest research to throw cold water on the crystal-ball powers of DNA is a paper in the current issue of the Journal of the AmericanMedical Association. It starts out as a standard genomewide association study (GWAS) in which scientists sequence genomes of people with and without particular diseases and identify genetic variants associated with those illnesses. In this case, Monique Breteler of the University Medical Center in Rotterdam and her colleagues analyzed the genomes of just over 35,000 people, some healthy and some with Alzheimer's, and found that four DNA misspellings (or, in the vernacular, single-nucleotide polymorphisms) were connected to Alzheimer's in that they were common to people with the disease but were not found in healthy people.

Until recently, that would have been that: a rigorous, thorough analysis—just over 35,000 genomes—leading to headlines about newly discovered genes linked to this dreaded disease. (Two of the four identified misspellings were previously known, and two are new.) But to their credit, Breteler's team took the next step. They used the four misspellings, along with individuals' age and sex and whether or not they carried the apoE4 genetic variant that so frightened Watson. The results were not pretty. Adding the newly discovered genes "did not improve the ability of a model that included age, sex, and apoE to predict" whether someone would develop Alzheimer's. The genes, concluded the scientists, were "not clinically useful."

In a phone interview, Breteler went further. "Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction" of whether someone will develop Alzheimer's, she told me. "Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction." Identifying risk genes isn't pointless, however: they can identify new causes of the disease, and therefore new ways to treat it.

The finding that adding Alzheimer's-risk genes to plain old age, sex, and apoE status does not improve the accuracy of disease prediction seems to defy everything the public is being told about the dawn of a new era of personalized medicine, in which knowing our genomes will tip us off about what diseases we are most at risk for. Such genome-based forecasting is deemed vastly superior to such antediluvian methods as family history. And it is the basis for the explosion in consumer-based genome testing, such as that offered by 23andme, Navigenics, and Pathway Genomics, whose plan to sell its saliva-swab DNA collection kits at Walgreens stores was shot down by the FDA last week.

Yet, as the JAMA study shows, there are serious doubts about how useful genomic information is going to be, outside of a few rare applications such as the ability of a child with leukemia to metabolize chemotherapy, one of the earliest attempts to pair genomics with medicine. Just last year, a study in JAMA concluded that determining whether a patient carries genes that affect the risk of blood clots (venous thromboembolisms) does not necessarily prevent blood clots. In a related setback last year, Medicare concluded that genetic tests that indicate how well patients metabolize the clot-buster warfarin does not meaningfully help doctors determine the safe dose; the agency therefore declined to pay for the tests. This year, another JAMA study, of 19,313 women, found that using multiple genetic markers to assess someone's risk of cardiovascular disease produces no better a risk assessment than old-fashioned tests such as cholesterol level, blood pressure, and family history. And this was a study that used 101 genetic variants. Not to pile on, but let me mention one more, on assessing a woman's risk of breast cancer. A study of almost 12,000 women by scientists at the National Cancer Institute, published in TheNew England Journal of Medicine in March, found that supplementing traditional risk factors (whether first-degree relatives such as a mother or sister developed breast cancer; reproductive history) with 10 genetic variants associated with breast cancer did no better at predicting whether a woman would get the disease than the traditional factors alone.

How can knowing whether or not someone has genes associated with a disease not be helpful in predicting whether that disease will strike? No one knows for sure. But it must reflect the fact that the effect of a gene depends on a person's "genetic background"—all the other genes he or she has. And it also reflects a person's environment. In some environments a gene does lead to disease; in others, it doesn't.

Individuals can differ in whether or not they even want to know their risk of Alzheimer's. Some prefer not knowing; others believe it will help them plan, financially and personally. One in every five of us who reaches age 65 will develop Alzheimer's disease. But at minimum, believers in personalized medicine should not be selling the public a bill of goods. I spent a week at Harvard Medical School last year, meeting with scientists, and one of my most surprising conversations was with geneticist David Altschuler, who to all appearances should be a cheerleader for genome-based personalized medicine. (He was a leader of the HapMap project to link large swaths of genetic variation to disease.) Yet he told me that using an individual's genome to assess the risk of disease is "overhyped." He continued, "If you ask what percentage of diagnostic tests in the history of medicine have been helpful, the answer is very few. There is a long history of new technologies being applied broadly beyond their utility." He echoes Breteler's view that the greatest benefit of GWAS and similar studies of genes and disease will be to illuminate the mechanisms that cause disease, and thus offer ways to intervene in those mechanisms to prevent or treat an illness.

Personalized medicine has many high-profile partisans, such as Francis Collins, director of the National Institutes of Health, who made the case for the field in his recent book. Nevertheless, second thoughts are clearly setting in as a result of studies like those I outlined above. Last year, geneticist Steve Jones of University College London wrote in The Daily Telegraphthat despite the billions of dollars that governments, industry, and foundations have poured into genomics and personalized medicine, "the mountain has labored and brought forth a mouse," one that will have little effect on how medicine is practiced, let alone predicting someone's risk of disease.

mardi 11 mai 2010

Genetic tests on shelves - Usefulness of consumer screenings questioned

Tuesday, May 11, 2010 at 12:02 a.m.

Consumer interest in genetic testing could receive a major boost this week when kits from Pathway Genomics of San Diego hit the shelves of Walgreens drugstores nationwide, even as some scientists question the usefulness of the screenings.

Pathway and the three other big companies that make genetic-testing products, sold mainly on the Internet or through doctors’ offices, have attracted relatively few customers since debuting the items less than three years ago.

Estimates put total sales at 50,000 to 100,000 tests.

Prices have been part of the problem. The cost ranges from about $400 to $2,000 for a comprehensive genetic-marker test that seeks to identify risks for adverse drug reactions, passing on mutations to children or developing certain diseases and health conditions.

Pathway’s kit will sell for about $20 in Walgreens stores. The buyer spits into a specialized container and then ships the saliva to the company for an analysis that costs $79 to $249, depending on the tests requested.

On Pathway’s website, the company offers a single testing package for $399.

“We are really doing this to increase consumer awareness, not just for us but for the entire genetic-testing industry,” said Jim Woodman, vice president of corporate strategy for Pathway.

The move represents a big step for the privately owned company, which launched its service in September. About 50 people work at Pathway’s laboratory and headquarters in the Sorrento Valley area of San Diego.

Interest in genomics has soared as the pace of research in the field has accelerated. Scientists are regularly uncovering new mutations in human DNA sequences that are tied to cancers, chronic health conditions, Alzheimer’s disease and illnesses that run in families.

More than 60 prescription drugs, including the anti-blood-clotting medications Plavix and Warfarin, have been associated with genetic markers indicating that a patient might have trouble taking them.

Not everyone welcomes the services of Pathway and its counterparts.

Officials for the American Medical Association said genetic tests shouldn’t be done without direct supervision of a doctor who can help interpret the results and recommend care based on the findings.

Consumers can easily misunderstand the test results if left on their own, said Dr. Eric Topol, a cardiologist and geneticist who serves as chief academic officer for San Diego-based Scripps Health.

Several states have banned direct sales of genetic tests to consumers.

In California, companies that offer such services must obtain a laboratory license from the Department of Public Health. The state has issued licenses to all of the major genetic-testing businesses — Pathway, 23andMe of Mountain View, Navigenics of Forest City and DECODE Genetics of Reykjavik, Iceland.

For the past year, Palomar Pomerado Health has sold 23andMe test kits at its “expresscare” retail clinics inside Albertsons grocery stores in Escondido and Rancho Peñasquitos.

The Federal Trade Commission, which oversees labeling for the tests, is the only federal agency that regulates the industry.

One concern about the retail genetic testing involves what isn’t covered.

Some scientists believe accurate measurements of each person’s disease risk aren’t possible without looking at all 3 billion DNA base pairs that make up that individual’s genome. That process costs more than $10,000 and requires the work of supercomputers.

Instead, the companies offering consumer genetic testing isolate only several hundred thousand genetic variations for review.

The results can be misleading, Topol said.

For example, a test could indicate that a person has a 30 percent risk of developing a particular type of cancer while the average risk is half that amount. The difference might seem alarming, but it may not matter if the likelihood of getting the cancer is more strongly driven by rare genetic variances occurring in particular family lines, Topol said.

In another case, a person might take false comfort in test results showing genetic markers for lower-than-average risk of a heart attack. The patient might push aside the more important fact that numerous relatives going back several generations have suffered congestive heart failure.

“Our ability to look at an individual’s DNA sequence and tell them their risk for these types of health conditions is low,” said Kelly Frazer, chief of genome information sciences for the department of pediatrics at the University of California San Diego’s School of Medicine.

The main businesses offering retail genetic testing said they’ve been careful to market their products as educational information rather than medical advice or a diagnosis.

“We make it very clear that this doesn’t mean (customers) are going to get a condition, but it’s something they should be aware of, and here are things they can do to mitigate that risk,” Woodman said.

But even among these companies, there often is wide variation in how genetic results are explained.

Francis Collins, director of the National Institutes of Health, reported in an October article in The New England Journal of Medicine that he sent his personal DNA sample to the three leading genetic-testing companies.

“They were not consistent in how they interpreted the results,” said Collins, a geneticist who helped guide the Human Genome Project. “I think all the companies probably overrepresented the degree to which we already can predict people’s future risk of illness and underrepresented how much of heritability has yet to be discovered.”

Keith Darcé: (619) 293-1020;

DNA testing at Walgreens

Pathway Genomics with have genetic testing kits selling at Walgreens Pharmacy.
Walgreen will start offering the kits in about 6000 stores (It will not be available in New York because of a state law)

Walgreen plans to offer Pathway's Insight Saliva Collection Kit at retail from $20 to $30. The saliva test, which will be done at Pathway's labs, will cost between $79 and $249. Genetic tests typically cost about $300.



mercredi 5 mai 2010

GET10 conference: Mapping the Personal Genomics Landscape, Posted by Dan Vorhaus on May 4, 2010

Last week saw the first annual Genomes, Environments, Traits (GET) Conference, in Cambridge, Massachusetts. Timed to coincide with DNA Day 2010, the conference marked one decade since the publication of the draft consensus human genome sequence. The GET Conference was billed as “the last chance in history to collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.” Not quite everyone with a public personal genome sequence attended – Craig Venter, Desmond Tutu, Glenn Close were all unavailable – but a majority of the genomic pioneers were in attendance and the GET Conference was a one-of-a-kind event.

For those who missed the GET Conference, several high quality recaps are available. The most detailed is A Day Among Genomes, by Carl Zimmer of Discover’s blog The Loom. More targeted reflections on the conference and related events come from Emily Singer of Technology Review summarzing key trends highlighted by the genome pioneers (Singer also has a related piece on the difficulties of understanding human genomes), David Dobbs of Neuron Culture on genomes, cool conferences, and what the hell to tell people about behavioral genes, and Turna Ray of Pharmacogenomics Reporter on the recent Myriad Genetics decision, and its impact on the business of patenting genes. If you’d like even more detail, the Twitter community provided real-time play-by-play.

While there’s no need for a further summary, the GET Conference does provide an occasion to look at the evolving personal genomics landscape in a more holistic fashion.

Genomes GET Personal. Personal genomics refers to the generation and delivery of an individual’s genomic or genetic information. The data itself ranges from testing a single base (referred to as a single nucleotide polymorphism, or SNP) to attempting to sequence each of the approximately six billion bases that make up a human genome. Data generation occurs on a variety of platforms, but it takes more than data to make genomics personal. We must move beyond merely inexpensive genomics to truly personal genomics. That requires analysis of the data, linking it to the life of the individual donor, and, ultimately, using the data in some fashion.

For those of us who frequently read and think about such topics, it’s easy to develop a slightly myopic view of the significance of personal genomics. For example, as Carl Zimmer noted in his review of the GET Conference, it was a challenge to evaluate personal genomics critically “in front of an audience made up of genome scientists, people from the biotech sector, venture capital folks, and other assorted people who are, shall we say, already in the genomic tank.”

The reality is that, to date, personal genomics has been the province of a comparative few. Academic researchers, a fraction of healthcare patients supported by too few providers conversant in clinical genetics, and a handful of companies, entrepreneurs and early adopters striving to deliver genetic information to consumers outside of the clinical setting. But the rest of the world – including a majority of consumers, patients, healthcare providers and payors – is waiting in the wings.

With the cost of generating genomic data dropping, and their possible uses expanding, personal genomics is poised to enter the mainstream. When that happens, certainly by the end of this decade, and possibly far sooner, what will the personal genomics landscape look like? To put it another way, what are the channels or pathways through which ordinary individuals – those of us who are not geneticists or early adopters – will explore their own genomes?

Personal Genomics Pathways. The first step in answering that question is to sketch the personal genomics landscape as it exists today – to understand the pathways through which individuals are currently entering personal genomics.

The following sections outline four different categories of personal genomics: clinical, consumer, research and unintended. Delineating these categoris is not an easy task, and there are frequent examples of companies or technologies that reside in more than one of these four categories. Nevertheless, as the field continues to evolve, mapping the “big picture” can facilitate more precise dialogue, regulatory actions and commercial predictions.

Research. Genomic research is distinguished from the categories described below by its intended use (to improve our understanding of the genetic bases for complex human diseases and traits). But it is important to note that not all genomic research is personal genomic research. This is due to the fact that, in most research settings, genomic information flows in only one direction: from the individual to the researcher. Even aggregate research findings, let alone individualized data, are rarely returned to volunteer participants. Thus, despite the explosion over the past five years of genome-wide association studies (GWAS) and, more recently, the construction of large-scale genomic databases (including the UK Biobank and the Kaiser Permanente Research Program on Genes, Environment, & Health), the vast majority of genomic research does not qualify as personal genomic research.

This is partly due to a timing delay. The proliferation of individual-level genomic research data is a relatively new phenomenon, and research norms have been slow to adapt to a growing body of evidence suggesting that people are interested in learning the results of research carried out using their DNA, and that it is ethical for researchers to return such results. It also reflects some legal uncertainty, specifically whether research conducted (in the United States) in non-CLIA environments can be returned directly to participants without violating federal law. Driven by increasingly vocal calls from both research participants and researchers themselves – including several commentators in the GLR’s What ELSI is New? series – the government agencies that supply the bulk of the funding for genomic research are continuing to examine the issue of genomic data-sharing in the research context.

For the moment, the number of individuals participating in personal genomic research is on the rise. At the GET Conference, George Church provided an update on the Personal Genome Project, which is using unique informed consent protocols to build a research cohort of 100,000 individuals who will have the opportunity to actively participate in personal genomic research, and who will have direct access to their individualized genomic sequence information. The first ten participants (the “PGP-10”) have already made their data available online.

There have also been attempts to develop DTC genomic research initiatives and, while the yields so far have been modest, the model is an intriguing one that promises to involve increasing numbers of individuals in the research aspect of personal genomics.

Clinical. One of the key drivers of the personalized medicine movement is clinical personal genomics. It is defined by its application of genomic data (to clinical care) and its mode of delivering that data to the individual (through a licensed healthcare provider). Extremely wide-ranging, clinical personal genomics has the potential to integrate individualized genetic or genomic information into nearly every aspect of patient care.

Clinical personal genomics includes genetic testing for autosomal dominant genetic traits (e.g., Huntington’s disease), diagnostic testing to predict the likelihood of the development or recurrence of a disease with a known genetic component (e.g., breast cancer) and carrier testing for prospective parents concerned about passing on genetic traits (e.g., cystic fibrosis) to their children. (Arguably, reproductive personal genomics – including carrier testing and other reproductive technologies, such as prenatal testing and pre-implantation genetic diagnosis (PGD) deserve their own category but, since such services are typically offered under the supervision of healthcare providers, they are considered clinical personal genomics in this post.) Clinical personal genomics also involves testing for genetic variants that influence whether and how certain therapeutics will behave in an individual patient, often referred to as pharmacogenetics.

Providers of clinical personal genomics include numerous laboratories offering either FDA-approved genetic testing “kits” or laboratory developed tests (LDTs) (which are not currently regulated by the FDA) targeted at specific genes (as well as at other biomarkers). In addition to the companies that supply the tests or kits, clinical personal genomics also requires genetic counselors, clinical geneticists and other healthcare providers capable of helping patients to understand and act on their genomic data.

A pair of recent announcements by CVS Caremark (acquiring a majority stake in Generation Health) and Medco (acquiring DNA Direct), the country’s two largest pharmacy benefit managers (PBMs), suggest that personal genomics is primed to play an increasingly prominent role in the delivery of medical care. However, there is broad-based concern that there are insufficient numbers of trained healthcare professionals, especially genetic counselors and primary care providers with an adequate understanding of genetics, to handle the expected increase in patients seeking, or needing, clinical personal genomics services.

Consumer. Also referred to as direct-to-consumer (DTC) genomics, the distinguishing features of consumer personal genomics are its intended use (informational, educational or recreational, but not clinical) and its mode of delivery (directly to the consumer, without the requirement of a licensed intermediary).

Consumer genomic services run the gamut from genealogy (, to paternity (Paternity Experts) to genetic matchmaking (Scientific Match), and everything in between. While some consumer personal genomics services are both popular and uncontroversial (ancestry testing) or are clearly niche products (, others have straddled the line between consumer and clinical personal genomics, creating confusion for consumers, healthcare professionals and regulators alike.

As an example, 23andMe tests more than half a million SNPs and reports back information relevant to more than 130 traits and conditions, many of which appear unambiguously aimed at influencing their customers’ clinical or medical decision-making. 23andMe also offers a popular genetic genealogy service, and has repeatedly expressed an interest in using its customers as the basis for a personal genomics research platform. What results is a single company with multiple overlapping products that could easily be viewed as a hybrid of the clinical, consumer and research personal genomics types.

What keeps companies like 23andMe in the consumer personal genomics category, at least for the time being, is an insistence on direct-to-consumer access. With a few important exceptions (e.g., New York and Germany), individuals worldwide can purchase and use these services without the involvement of a healthcare provider.

With the list of DTC providers growing rapidly, it can be difficult to keep track of everything that is out there. At present, the only publicly accessible registries of DTC providers are maintained by private entities, including AccessDNA, DNA Test Index, and the Genetics & Public Policy Center (pdf) at Johns Hopkins University.

Recently, however, the NIH launched a new genetic testing registry (GTR) which has the potential to serve as a more comprehensive resource for tracking DTC genomics services. The GTR, which will include providers of both clinical and consumer personal genomics services, is not yet operational. Listing in the GTR is also voluntary so, even once it is in place, it is unlikely to serve as a comprehensive directory of all consumer personal genomics services. There are reports, however, that Representative Patrick Kennedy is attempting to revive the Genomics and Personalized Medicine Act in a form that would include a mandatory genetic testing registry.

Of all of the personal genomics categories listed here, consumer services is the one most likely to rapidly splinter into multiple categories. At the moment, there are few regulations that deal directly with DTC genomics companies and the services they provide. As the generation of genomic data becomes increasingly inexpensive and commonplace, the spectrum of consumer services will expand considerably. As was true of the development of personal genomic research norms, regulatory activity in this area has lagged commercial and scientific development. At some point, however, additional regulations will arrive, helping to further define this category. For instance, it is possible that the GTR will serve as a precursor to a more comprehensive system of regulation for genetic testing. Additional regulation, whatever its impetus, would likely produce further fragmentation within this category, with some companies sliding into defined regulatory boxes and others changing their offerings to avoid regulatory control (and expense).

Predicting precisely which consumer services will be offered and how, if at all, they will be regulated, is impossible. All we know is that personal genomics consumers ten years from now are certain to have many, many more options than they do today.

Unintended. This final category is a catch-all, characterized by a single shared feature: these individuals did not intentionally confront their personal genomic information. At the Genomics Law Report, we have discussed a variety of ways in which an individual might receive an unintended, and possibly unwanted, introduction to personal genomics. Paternity identification, surreptitious testing, genetic testing of a first-degree relative, forensic activity and the re-identification of previously de-identified genetic information all have the capacity to introduce unsuspecting individuals to their genetic information. It’s also possible that individuals who have agreed to share or to explore only certain aspects of their genetic information will be unexpectedly presented with personalized genetic information beyond the originally intended scope of their agreement. No doubt there are other means of unintended exposure as well.

While not every unintended exposure to personal genomic information will be undesirable, such occurrences should clearly be minimized. Although the GET Conference featured a self-selecting audience largely enamored of personal genomics, not every individual shares the desire to peer deeply, or at all, into his or her own genome. An introduction to personal genomics, no matter the context, should be expected, if not always desired (e.g., certain clinical testing), with ample opportunity afforded for pre-test education and, where necessary, informed consent.

Unfortunately, as the cost of generating individualized genomic data declines, more and more such data will be generated. The proliferation of personal genomic data, and the increasing array of valuable applications of such data, is likely to increase the incidence of unintended personal genomics exposures. A combination of public education and policy and legal reforms will be needed to minimize the number of such events and mitigate their impact when they invariably occur.

The Future of Personal Genomics. The categories described above are roughly drawn, and they may well be incomplete. There is no question that they are neither exclusive nor exhaustive. All we really know is this: to the extent that they accurately reflect the current personal genomics landscape, they will not do so for long.

Genomic researchers with novel questions will continue to require novel, and increasingly participatory, research models. Clinical practice will grow and is likely to become simultaneously more specialized (e.g., increasing availability of genetic diagnostic tests) and more generalized (e.g., incorporation of whole-genome sequences into medical records as a default). Consumer personal genomics will go wherever the entrepreneurial imagination can take it and regulatory bodies permit it, leading to splintering and further blurring between its boundaries with other categories.

The 2010 GET Conference closed with the personal genomics company Knome awarding a free exome sequence to the most original audience-supplied idea applying personal genomics. The winning proposal, submitted by Jonathan Eisen, would supplement understanding of our ancestors by sequencing current and ancestral microbiomes. A sampling of the submissions that didn’t win – including sequencing of millions of sperm from an individual to understand germ line variation, replacing newborn blood-spot testing with genomic sequencing, using real-time genetic testing to identify and prevent allergic reactions, constructing encryption keys from an individual’s genomic code and the development of new commercial models to expand access to and participation in personal genomics – provides a glimpse at the untapped applications for personal genomics.

Where will personal genomics head from here? I, for one, am already looking forward to the 2011 version of the GET Conference by which time, if recent history is any guide, this roadmap will already be out of date. And that, without question, is the most exciting thing about personal genomics as we close the book on the 2010 GET Conference.

Filed under: Direct-to-Consumer Services, General Interest, Genetic Testing/Screening, Genomic Sequencing, Genomics & Society, Industry News, Pending Regulation
Tags: 23andMe, AccessDNA DNA Test Index, Carl Zimmer, carrier screening, CLIA, Craig Venter, CVS Caremark, David Dobbs, de-identification, Desmond Tutu, DNA Day, DNA Direct, DTC genomics, DTC research, DTC testing, Emily Singer, exome sequence, forensic DNA, Generation Health, genetic genealogy, genetic testing, Genetic Testing Registry, Genetics & Public Policy Center, GET Conference, Glenn Close, informed consent, Jonathan Eisen, Kaiser Permanente, Knome, laboratory developed tests, LDT, MedCo, NIH, Personal Genome Project, personal genomics, reproductive genetics, Turna Ray, UK Biobank