Tag Archives: genomics

TOP TEN STORIES IN GENETICS, 2016: An Adolescent Science Meets the Big World

Clinical genetics is a young science, not yet come of age – a new discipline. It’s early days, say the small group of clinicians and researchers who have watched over its formative years, dreaming like proud parents of a future where genetics and genomics are integral to clinical medicine. And as for many parents, it may sometimes have seemed that the all-consuming, semi-hermetic little laboratory of childhood would go on forever.

But guess what, people? I believe we have entered the teenage years.  I believe baby has borrowed the car keys and taken it out for a spin.  I see a field boasting a few real accomplishments, and on the cusp of so many changes, from therapies for genetic disease and cancer to a suddenly burgeoning DTC marketplace. And like all parents, geneticists are poised to discover the limits of our ability to control what we have nurtured. That’s exciting, more than a little bit scary, and the theme of this year’s top ten.

  1. FDA CANCELS PLANS TO REGULATE LDT’s

Over the past two decades, a single technological advancement has revolutionized the way we practice medicine.

I am talking, of course, about overnight delivery of packages.

Years ago, laboratory testing services were divided into large companies that sold test kits and devices nationwide, and the small labs in hospitals and other clinical settings providing services to their local providers. With limited resources, government regulators focused on the tests that affected more people, and agreed by convention that ‘laboratory-developed tests’ would not be subject to the same scrutiny. Today these distinctions are virtually meaningless, as giant companies like LabCorp and Quest perform tests ‘in-house’ on samples gathered worldwide, tossed in a box and sent overnight. Still laboratory-developed tests (or LDT’s) – a category that includes virtually all genetic tests – remain in regulatory limbo.

In 2010, the FDA announced its intention to address this loophole. In July 2014, they issued draft guidance detailing their plan for a regulatory structure that divided the LDT universe into high, low and medium risk tests. While some professional organizations disputed the FDA’s right to have a role in regulation of LDT’s and threatened legal action, others approved the framework in principle but disagreed on specifics, including how to handle the thorny new territory of exome and genome sequencing. A dialogue ensued with representatives of labs, clinicians and patients that has lasted two years and included multiple workshops and public meetings. That process, it was widely assumed, was nearing its end, with the resulting draft guidance expected to be sent to Congress for approval in the near term.

And then came November 8th and the election of Donald J. Trump, ushering in an executive opposed to regulation on principle, to join a similarly inclined House and Senate. Ten days later, the FDA ran up the white flag, announcing that the agency would not take steps to finalize its existing plan and would instead reopen the discussion with a new administration and a new Congress. What this means precisely is a matter of some interesting speculation, but in general it suggests that an industry that has been struggling for years to avoid too much regulation will have to consider the consequences of living with none at all.

 

  1. IS THIS THE FUTURE? CRISPR EXPERIMENT ADDS RARE PROTECTIVE VARIANTS TO HUMAN EMBRYOS

The second experimental use of CRISPR technology to alter human embryos was reported in May of 2016, again by a group out of China. Again, the embryos used were not viable, and no attempt was made to transfer them for reproductive purposes. While this experiment did not produce the same ethical firestorm as the first, it was in several ways a more significant indicator of both the potential and the peril of human germline engineering using CRISPR.

In the first experiment investigators attempted to alter a gene variant responsible for causing hemoglobinopathy, with limited success – proof in principle that it could be done, but nothing to assure worried observers that it could be done safely. In version 2.0 there were fewer off target effects, but researchers were not able to consistently control the content of changes introduced in place of the edited DNA. This is not inconsistent with what we know so far about CRISPR: if we envision it as a word processing search-and-replace function, it is good at the finding and erasing part, but hit or miss when it comes to  putting in a replacement.

What stands out about the second experiment is that the goal was not to eliminate a disease-causing gene, but to insert a rare and protective one – in this case, the CCR5Δ32 allele that offers the bearer reduced susceptibility to AIDS. Gene editing is often envisioned as a way that individuals whose children are at risk can avoid or change genes that cause disease, but in the vast majority of these cases there are simpler and better established tools such as PGD if the goal is to obtain embryos that do not carry a specific variant associated with some catastrophic risk. Why use technology to substitute out a pathogenic BRCA variant or a double dose of the sickle cell genes when the parents are perfectly capable of producing a healthy embryo themselves? What CRISPR and related technologies can do that is not available through other means is to introduce a gene that neither parent carries. That is a powerful new option, and it is both exciting and scary in the manner of all things powerful and new.

 

8. GENETIC DISCRIMINATION MAKES A CAMEO

Many wise observers have noted that for all our deeply felt concerns about genetic discrimination, to date the examples are few, far between, and usually more clumsy than systemic (looking at you, Burlington Northern Santa Fe Railroad). These arguments, redux, were on display in 2016 as Canada debated and ultimately passed its own national genetic discrimination law. Yes, Globe and Mail Guy, there is little evidence of a big problem, and a look at law suits filed between 2010 and 2015 under GINA, America’s genetic discrimination law, proves the point. But one real unanswered question remains: is the absence of institutionalized discrimination a sign that it is destined to be a bit player in the big picture of genomics, or is it only too soon to tell? Big companies, whether they are offering insurance or providing employment, may not have had an incentive to weather a PR shitstorm in order to use genetic information to limit their exposure to risk when not that many people have been tested, and the reliability of the data is debatable – which it has been in these early days. Genetic discrimination, in other words, may be making an appearance in Act II.

Two stories got some attention in 2016; whether they are one off events or signs of the future – well, that’s crystal ball territory. Are they important? They are something to which we should be paying attention. Attention should be paid.

In January, Stephanie Lee at Buzzfeed published an account of a boy named Colman Chadam who was asked to leave his Palo Alto, CA school because he carried two mutations commonly associated with cystic fibrosis, although he did not have any signs or symptoms of the disease. The results of genetic testing, inappropriately revealed by a teacher at the school, were taken, also inappropriately, as diagnostic. The reason this got him thrown out of school was to avoid contact with another student who did have CF. The emphasis on keeping children with CF apart, which sounds weird if you don’t know much about the disease, was about the only appropriate thing that happened, because individuals with CF are at risk of passing one another dangerous and life-limiting infections.

Although Colman did not have to leave the school, and the Chadam’s lawsuit against the school district has settled, the case continues to raise issues about how genotype as distinct from phenotype can be used under the law. In addition, it may signal the need for measures to protect personal privacy (no such thing, I know, I know) in an age when genetic testing is commonplace.

Three weeks later, Christina Farr wrote an article for Fast Company about a woman who was turned down for life insurance because she had a risk-conferring BRCA1 variant. Unlike the Chadam case, this is not a result of genetic illiteracy, and it is not a violation of any law: GINA does not cover insurance for life or long-term care. It is, in fact, exactly the kind of genetic discrimination that ethicists and patients thinking about genetic testing have worried about over the years, and if systemic, would certainly be an important point for genetic counselors to raise in pretest counseling (if pretest counseling is still something we do, which is an issue unto itself…but related). According to the article, genetic testing for cancer susceptibility is not required by any insurance company, although nothing stops them from doing that, but companies are starting to request to see test results when they exist. Failure to answer questions honestly can invalidate policies if you are caught.

If this becomes the status quo, it may affect uptake of genetic testing. If it is curbed through regulation, genetic testing may change the way the insurance industry operates. Act II is going to be interesting! I am having a couple of stiff drinks and heading back to my seat.

 

7. TYPE II DIABETES: RESISTANT TO INSULIN AND EASY ANSWERS

Genome wide association studies (GWAS), a way of looking at common variants in the gene pool to identify genetic susceptibility to common diseases, have been unable to explain the degree to which liability to these common diseases is inherited, although it clearly is. If you are in genetics and this is news to you, you have not been paying attention.

Many reasons for this have been proposed, and many are likely a part of the answer. One thought was that individually rare variants might be collectively common enough to play a big role in generating risk, which would not be picked up by GWAS, as it traditionally looked only at variants carried by at least 5% of the population (“the population,” as though there was only one!). Looking at rare variants takes a village, but that is what a googleplex of Type II Diabetes researchers did to produce an epic July 2016 paper in Nature.

Okay 300 authors on the paper so close enough.

The report by first author Christian Fuchsberger showed that MEGA*GWAS produced the most GWAS-y result possible: intellectually interesting, informative and ultimately inadequate. Using exome and whole genome data to capture a broader range of variation, the study found significant association to a handful of previously unknown common variants, and then failed to replicate a good chunk of what we thought we knew. Uncommon variation? The researchers found 23 loci that appeared significant, which was meaningful, but nowhere near enough to validate the rare variant hypothesis as the smoking gun in the Mystery of the Missing Heritability. “A comprehensive and extremely well written paper,” said Dan Koboldt at MassGenomics, and you can almost hear him sigh.

 

6. DATABASES: IT’S NOT JUST FOR WHITE PEOPLE ANYMORE

We don’t have enough diversity in our databases. It’s not exactly news, and yet publication of an article called “Genetic Misdiagnoses and the Potential for Health Disparities” in the August issue of the New England Journal of Medicine felt like a slap in the face.

The methodology was not complex. For hypertrophic cardiomyopathy patients, doctors use genotyping to identify individuals and family members at risk for sudden and catastrophic cardiac events. Identification as ‘at risk’ is a traumatic and often life changing event, requiring ongoing medical screening and behavioral modifications. For these families, a lot rides on whether or not a variant is considered pathogenic. One bioinformatics tool is to look at databases, because there are limits on how bad a variant can be if it shows up regularly in healthy individuals. The study checked variants labeled pathogenic against an increasing wealth of exome data available in public databases and found that a number were common in the African-American population. Result: reclassification from pathogenic to benign of multiple variants affecting primarily African-American families.

“Simulations,” said the authors, “showed that the inclusion of even small numbers of black Americans in control cohorts probably would have prevented these misclassifications.

 

5. IMMUNOTHERAPY: A NEW STAR BURNS BRIGHT AND HOT

Earlier this week, my sister-in-law was telling me about a friend with a cancer deemed treatable but not curable. “But if they get it in remission,” she said, “and he has more time, maybe there will be something new.” There it was – the cancer prayer. May There Be Something New. And I thought, has there ever been a moment when those words felt more hopeful than right now?

Hopes have been raised before, by promises that money would bring answers, and we wandered down blind alleys and into mazes waving cash as though the scent of it would draw the answers to us, but this time, progress is lighting the way like street lamps, and money follows hope instead of the other way round. Immunotherapy – engineered cells meant to light the bodies own defenses into a controlled burn that destroys cancer cells and leaves the rest untouched – has burst onto the scene since 2015. Cancer researchers report on progress in Hemingway stories, terse narratives of a few more days, an extra month or two, and that’s a win, but suddenly we are getting Gabriel Garcia-Marquez fables of magic beans and people rising from their deathbed.

So which story is more 2016: Sean Parker’s 250 million dollar cancer institute, connecting Silicon Valley money with Car-T cells that he describes as “little computers,” and presenting to the NIH in comic sans? Or the unexpected lethal immune response that shut down a Car-T trial by Juno Therapeutics in November, after four people died of cerebral edema?

It’s the two in conjunction that tell the tale. Immunotherapy is truly a candle in the wilderness, but it’s a candle that burns rocket fuel. Or perhaps I should say, in the spirit of the season: catch a falling star and put it in your pocket – bet it burns a hole in your ass.

 

4. A NEW DTC GENETICS EMERGES WITH HELIX

In October, Helix announced the first fruit of its partnership with DNA-lifestyle start-up Exploragen and it’s grapes: Vinome, a company that promises to sell you wine tailored to your genetic profile for something like fifty bucks a bottle. I’m not a wine drinker and that sounds like a lot of money but, hey, you do you.

For Helix, the Illumina spinoff that debuted in 2015, this was one of a series of 2016 announcements giving us a more concrete vision of their plans for a sequence-once-access-often platform for DTC genomics. The structure of it is like Apple, if your IPhone didn’t even pretend to be a phone, and existed entirely as a vehicle for apps. With your first purchase, Helix will underwrite the cost of sequencing and storing your entire exome, and then sell it back to you bit by bit in the guise of applications created by partners.

Effectively, the Helix model lowers the barrier of entry for any product based on DNA testing, by spreading out the cost over a myriad of marketing opportunities. Some current players in the DTC universe have signaled their interest in playing in Helix’s playground; Geno 2.0, National Geographic’s version of ancestry testing, is already available on the Helix website. Others may take their toys and stay at home. Daniel MacArthur of the Broad Institute once penned an April Fool’s Day account of a company named Helix Health’s plans for a hostile takeover of 23andMe using Somali pirates, but for real the entry of an Illumina-backed company into the DTC space must have some Mountain View observers concerned that the current industry thought leader might end up the Blockbuster Video of the genomics world.

The uncorking of Vinome raises a few questions that existing partnerships with, say, the Mayo Clinic or the Icahn School of Medicine at Mt Sinai do not. One role that Helix could potentially play is to provide the vetting service much needed in the consumer genomics world, with its mishmash of pharmacogenetics and Warrior Gene testing and supplements designed just for your DNA.

As for Vinome, the eminently quotable Jim Evans called it “silly” in an article by Rebecca Robbins in STAT. “Their motto of ‘A little science and a lot of fun’ would be more accurately put as ‘No science and a lot of fun,’” said Evans — which I guess is true, if paying fifty dollars for a bottle of wine is your idea of fun. But like Apple, Helix is going to have to make some hard decisions about how much it takes responsibility for the quality of the partners it allows to come play in its sandbox.

 

3. GENOMES OF MASS DESTRUCTION

In February, for the first time but probably not the last, the U.S. Director of National Intelligence’s assessment of worldwide threats included genome editing as a weapon of mass destruction. Congratulations, genetics: we’ve made the big time.

The report pointed to the widespread use of new genetic technologies like CRISPR in countries with different regulatory and ethical standards, its low cost and the rapid pace of change as pre-conditions that might lead to intentional or unintentional misuse, though it was vague as to what form they thought the threat might take. More specific concerns were articulated later in the year by the Pentagon’s Defense Advanced Research Projects Agency (called DARPA of course, because…government) in announcing a program called Safe Genes intended to establish a military response to of dangerous uses engineered genes. DARPA, which Scientific American reports has been a major funder of synthetic biology, will support projects that look at ways to remove engineered genes from a variety of habitats and in a variety of circumstances, including those spread through gene drive.

 

2. A BREAKTHROUGH DEFIES CONVENTION AND GEOGRAPHY

On April 6, 2016, a baby was born after the transfer of his mother’s nuclear DNA into an enucleated donor egg in an effort to avoid the mitochondrial disease that killed the couple’s two previous children. The success of mitochondrial transfer therapy itself was not a shock, since earlier experiments had demonstrated good outcomes in animal models and in in vitro human embryos. The circumstances, however, were startling: the procedure was done in Mexico, for Jordanian parents, with the help of a New York-based fertility doctor with no known expertise in mitochondrial disease.

Some have argued that mitochondrial transfer therapy represents a violation of international norms forbidding any germline genetic change, which were meant to provide a clear dividing line between somatic changes associated with gene therapy and genetic engineering with the potential to impact future generations. Pretty clear in theory, but all of these divisions are less clear in reality – there are no guarantees that gene therapy doesn’t affect eggs or sperm, and mitochondrial DNA itself challenges any simple equivalence between the molecular structure of DNA and the intellectual concept of our ‘germline’.

Mitochondrial transfer is illegal in the United States but permitted in Great Britain under a 2015 law, and applications for clinical use have been approved for 2017. Its apparent success – independent sources confirm that the baby appears to have traces of maternal mt DNA associated with Leigh syndrome but no sign of disease – is a cause for celebration for the families whose children are at risk. The step forward is a milestone, but so is the way in which it occurred, which demonstrates the extent to which geography and national laws are no match for money and access in determining what is possible.

Personal note: on my wish list for 2017, can we PLEASE stop cheapening the concept of parenthood by using the term ‘3-parent babies’? If I donated a kidney, that person would have some of my DNA, but it wouldn’t make me their momma.

 

1. WHITE SUPREMACISTS LOVE GENETICS, BUT GENETICS DOES NOT LOVE THEM BACK

Nothing about the year 2016 was more disturbing than the empowerment of the alt right, an all-purpose term for the angry souls that crept out from under rocks to preach hate and division. Here at home and all around the world, narratives of race and ancestry emerged as powerful drivers in political and social movements based on appeals to base and tribal instincts – fear mongering about immigrants, Islamaphobia, white supremacy. In October, Elspeth Reeve at Vice ran a story about white supremacists posting their 23andMe results to prove their whiteness.

This embrace of a science that does not love them back is evident even without a deep dive into the world of Stormfront and 4chan.  Twitter trolls talk about ‘founder effects’ and ‘genetic drift’. A Breitbart tech editor, now barred from twitter, writes gleefully about associations between race, behavior and intelligence, mocking disbelievers as prisoners of an “all-consuming cult of equality.”  The L.A. Times describes the alt-right as “young, web-savvy racists who are trying to intellectualize and mainstream bigotry.”   These viewpoints aren’t mainstream, but their proponents can no longer be dismissed as fringe, with Breitbart’s founder about to be ensconced in the White House as chief strategist, and reports suggesting that the presumptive next National Security Advisor Michael Flynn taking meetings with the head of an Austrian political party founded by former Nazis.

The connection between white nationalism and population genetics is proof once again that genetics as a field is uniquely susceptible to misuse by agenda-driven movements intent on the subjugation of others. Donald Trump ran against political correctness, but his rise has proven the importance of language. As Michelle Obama says, “words matter.” Push back against the misuse of genetics to fuel ‘racialist’ theory. Ancestry sites should think very hard about the manner in which they present their findings, which stress differences without acknowledging the greater than 99% of DNA that we all share. Scientists need to address and refute the ways in which their work can be misconstrued to reinforce prejudice and unsubstantiated visions of racial differences. We all have to be careful not to promote explanations of genetic effects that oversell the determinative power of genes.

Genetics is a science of the future. Let’s not let it be used to drag us back into a tribal past. Peace out, Genetics, and here’s to a better year in 2017.

 

 

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What Genetic Counselors are Talking About

Last week, I attended the National Society of Genetic Counselors (NSGC) Annual Education Conference in Boston. Although I attended talks on a variety of subjects, where possible I chose sessions focused on new genomics technologies and associated issues. There were some common threads tying these discussions together beyond ‘genomics’ itself. Here’s a quick summary of some of the things I observed and learned.

1. Secondary, Ancillary, Incidental – Oh my!

It is no surprise that discussions around the use of Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) universally include the question of what to do with the “extra” data—those pieces of information we weren’t looking for, but happened to find. What was surprising are the differences in the terminology we use to describe these extra pieces of data. Jessica Everett, a GC from the University of Michigan Mi-OncoSeq project explained that confusion over this terminology lead her team to decide that they would universally refer to an incidental finding as an unintended piece of information that “falls into your lap” and a secondary finding is extra information you end up finding out, but have to look for.

There are likely some official definitions and designations that already exist here. But it is apparent that we as a GC community currently don’t have a consensus on the nomenclature around this issue.

2. GCs don’t need new skills, but rather need to apply our skills in new ways.

This type of thinking is music to my ears—I love the challenge of applying our skills in new and unique ways. The GC role in pharmacogenomic testing specifically was a sub-theme here. I heard multiple genetic counselors who work in the realm of pharmacogenomic testing say that while they initially believed their role with patients undergoing testing for pharmacogenomic purposes would be minimal, the applicability of our traditional skills and opportunity to provide value to both patients and physicians was far greater than they anticipated. 

3. “Scalability” of the Genomic counseling session

The sheer volume of information and amount of time required to consent patients for WES/WGS technologies was routinely cited as a barrier to genetic counseling in the genomic era. In some cases, GCs plan for a 2+ hour pre-test counseling session, and in most cases there are multiple visits or contacts before testing is initiated. There was also alot of discussion about how best to inform patients about the various types of information that can be learned through genome sequencing technologies. Bioethicist Scott Kim (also from the Mi-OncoSeq project) made a good case for a ‘flexible default’ model for informed consent in these situations.

Consistently GCs commented that when asked ‘do you want to know everything?’ patients and research participants will almost always reply ‘yes– of course I want to know everything!’ However, the use of specific scenarios or examples seems to be required in order to elicit a more meaningful discussion about potential results, and what information patients will decide to opt out of receiving. (This is a topic I’ve previously written about.)

4. Collaboration

Although this may be the least exciting or surprising underlying theme, it is likely the most important. Almost every lecture concluded with a slide highlighting the importance of a collaborative and multidisciplinary approach to genomic testing.

As always, I’d love to hear about others’ reactions and impressions from this year’s AEC. Please feel free to share, below.

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On The Old Saw: That Personalized Medicine Will Cost Money In Theory But Will Be A Money-Saver In Practice*

June, 2011 marked the 10th anniversary of the great ‘Mission Accomplished’ moment of the Human Genome Project, when President Clinton, with no regard whatsoever for his own personal safety, stood directly in between Francis Collins and Craig Venter to announce the completion of “the most important, most wondrous map ever produced by humankind.”  In November, in honor of the occasion, the American Museum of Natural History, in partnership with the Council for Responsible Genetics, hosted a panel discussion entitled “The Human Genome and Human Health – Will the Promise Be Fulfilled?”  This was an opportunity for four very smart people to recap the discussion of everything that hasn’t happened as predicted in the last 10 years (Oh, the missing heredity!  Oh, the shortcomings of personal genomics!) and why, in retrospect, this was all entirely predictable, as things generally are in retrospect.  And then the two scientists on the panel predicted that we are on the cusp of great things and the two social scientists on the panel warned that great things come at a steep price and we all agreed, and why not?  After all, we almost always are, and they almost always do.

The thing about making predictions is that it is hard to get it wrong if you go with generalities (it’s always something!) and even harder to get it right, if you are going after specifics.  Thousands of people will have a heart attack this year.  The guy sitting in front of you with the ten pounds of jelly donut hanging over his belt buckle?  Hard to say.  So we in the prognostication business cling to certain reliable, gospel truths.  Technology will get faster and cheaper every year!  Understanding pathophysiology will lead to cures!  You will meet a tall, dark, handsome stranger!  No – sorry, that one isn’t us.  New studies will illuminate the relationship between genotype and phenotype!  Hallelujah.

Here’s another one: personalized medicine will save us money!  Can I get an amen?  It’s something we hear all the time, in medical journals and newspapers and political speeches.  “The savings from personalized medicine,” said a man in the audience at the panel discussion, nodding his head with conviction, “how soon we will see that?”

“Well,” said Dr. Robert Green, renowned neurogeneticist from Beantown (Hah-vard, of course) “I am not convinced that it will save us money.  I think it might cost us money.”  You could almost hear the band stop playing.

Is he right?  The Personalized Medicine Coalition cites savings as one of the intrinsic advantages:  “The cost of health care in the United States is on an unsustainable upward climb. Incorporating personalized medicine into the fabric of the health care system can help resolve many embedded inefficiencies, such as trial-and-error dosing, hospitalizations due to adverse drug reactions, late diagnoses, and reactive treatments.” (The Case For Personalized Medcicine, 3rd Edition.)

But think about it.  Someone comes into your office carrying their personal genomic printout from 23andMe or Navigenics or whoever comes next.  They have an increased risk of Condition X.  What do you suggest?  Step 1: increased screening and testing.  Well maybe the testing modalities are not that good.  Too bad.  You suggest them anyway, because it is downright cruel to tell a person they have an increased risk of the dreaded Condition X and that THERE IS NOTHING TO DO ABOUT IT.  Why do we send people who are BRCA 1 or 2 positive for bi-annual screening of their ovaries?  Because it is a great screening test?  Noooo.  Because it is all we have to offer?  Bingo.

And remember, that printout is going to contain multiple increased risks.  So, step 2: return to step 1, and repeat.

Now, conversely, someone comes into your office with a paper saying that they have a decreased risk of Condition Y.  Do you tell them to stop doing screening?  Skip their annual physical?  Start smoking cigarettes?  Noooo.  Because you know perfectly well that SOMEONE with exactly this genotype is going to get Condition Y, and you don’t want to be responsible if it turns out to be THIS GUY (see Paragraph 2 on the challenges of prognostication).

We are forgetting the medical equivalent of Moore’s Law: that visits to the doctor result inevitably in EXPONENTIALLY MORE VISITS TO THE DOCTOR.  Call it Dr. Moore’s Law: Medical Care Generates Additional Medical Care at a Rate that is Exponential.

Now, please, don’t get me wrong.  I realize that, at times, personalized medicine is going to save us money.  Pharmacogenetics improving the use of medication will save time, money, and lives.  Preventing certain forms of chronic disease like diabetes, if we find a way to intervene for those most at risk, will save a fortune.  But right now, the savings are much more speculative than the costs.  A reflexive adherence to the dogma that personalized medicine saves money creates a hype that can only lead to disappointment.  Making medicine better is a huge goal: making medicine solvent is too much to ask of any fledgling field.  Feeding the hype is tempting, because it generates the sort of excitement that brings in attention and funding.  But ultimately, propagating a dogma that generates unrealistic expectations will snatch defeat from the jaws of victory, as our real-life success stories are weighed against the myths of our own making.

*Gratuitous Kant reference.  Philosophy students: please enjoy.

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Genomics and the Social Web: A Timeline

(As posted on www.hernaturehisnurture.com)

I thought I’d share this timeline that I put together recently for a presentation on the social asepcts of genomics. Although clearly not an exhaustive list of events, I still find it interesting to see the major milestones in genomics side-by-side the evolution of the social web.  Not only does this provide a potential explanation for why the genomics industry has developed the way that it has, but it helps to illustrate the relationship between genomics and social media: openness, connectivity, patient autonomy and citizen science.

 

(click on image for larger view)

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Digesting the Scripps DTC Study Results

Last week preliminary data from a Scripps Health study, looking at effects of DTC genomewide testing, were published in the New England Journal of Medicine (link to pdf article). The study represents the first published data of this kind. Up until this point, the dialogue surrounding the potential benefits and harms of DTC testing has been mostly anecdotal guess-work. So, needless to say, these results are important. Media outlets were quick to report that ‘consumers can handle the truth’ and that testing has no impact on health behaviour.   But, beyond snappy headlines, these results warrant a closer look. I thought I’d give a quick run-down of my reaction here, in the hopes of getting a good discussion going.

In full disclosure, I recently joined The Medcan Clinic in Toronto as a genetic counsellor. We offer personal genome testing using the Navigenics platform in the context of a comprehensive genetics assessment (see ‘Putting GC into DTC’ guest post from last year for details on this model.)  As you can imagine, I am particularly interested in these findings.

Some important things regarding study design:

  • Study subjects participated in health assessments (assessing dietary fat intake, exercise behaviour, anxiety symptoms and uptake of screening tests) using an electronic survey tool. No physical exam or blood work was taken into account in assessing baseline or follow-up parameters here.
  • These results represent data from the baseline assessment and a 3-month follow-up. This is a 20-year longitudinal study, so essentially this data is the tip of the iceberg.
  • The study protocol used the Navigenics Health Compass testing, but Navigenics did not provide any financial support for the study, nor were they part of the study design, analysis of data or manuscript preparation.

The most interesting points (as I see it):

  • At 3-month follow-up, there were no significant health behavior changes made by study participants measured by amount of fat intake and exercise behavior, except for in the 26.5% of participants who reported sharing their results with their doctor. These participants did have lower fat intake and increased exercise activity.
  • Those who shared their results with a Navigenics genetic counselor only (10%) did not show any significant behavior change.
  • At 3-month follow-up, there was no significantly increased anxiety or test related distress. Whether or not an individual had genetic counseling did not affect this parameter.

What I take from this:

  • Sharing results with a physician is more likely to impact health behavior. This lends evidence against the direct-to-consumer model.
  • As genetic counselors, maybe we need to be more focused on the potential for us to add value to consumers of genome wide testing, and less focussed on the potential psychological harms of the testing.
  • We all know these tests do not take into account family history. There is a role of GCs to help consumers understand their risks in the context of their family history, to assist consumers in sharing this information with their doctors, and to work with general practitioners to help integrate this information into their practice.

What I can’t wait to see:

  • More long term data! This is predisposition testing combined with 3-month follow-up info. I am curious to see whether more subjects decide to share this information with physicians down the road (presumably many did not have doctor’s visits scheduled in the months immediately following receipt of their results). I’m also curious about whether consumers or physicians will use this information to guide future investigations, when these subjects experience an issue requiring attention.

There are obviously a huge number of issues beyond those I’ve highlighted here. Please share your thoughts and reactions below.

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Learning from the Naturopathic Model

I recently sat down with Jill Davies, a genetic counselor who is doing some really interesting work with genomics and preventive medicine in the primary care setting.  I won’t get into the details here, as I am hoping Jill will describe her role in her own words on DNA Exchange in the next little while. But our meeting has my wheels turning and has given me some new found inspiration about future career possibilities.

Coincidentally, the evening before my meeting with Jill, I attended my first naturopathic medicine appointment. My new family doctor has a patient share with an in-house Naturopathic Doctor (ND), in which my electronically stored medical records can easily be shared between the two. I’ve always been a little curious about naturopathy, and the pure ease of this system provided the added boost to follow through and try it.

During my hour and a half appointment with the ND we discussed in detail my medical history, family history, health concerns and general health goals. My main reasons for seeking naturopathic services are:

  1. the prevention of disease
  2. optimizing my health

As I discussed these goals with the ND it struck me that these very same objectives could drive me to seek personal genome services. I’ve always thought about personal genomics from an academic perspective, and to my surprise, never really put myself in role of the consumer. I’ve certainly thought about the consumers, but always as some abstract group of people most commonly referred to “early adopters.” So for the first time I could envision these services not just as a DTC internet purchase or as a function of specialty medicine, but as part of the primary care setting.

It is not my intention here to debate the efficacy of nutrigenomic products (such as Carolyn’s The DNA Diet, for example) or even the use of genomics in naturopathic medicine, but instead present the current model of naturopathic medicine as a potential model for personal genome services.

Consider this:

People seek naturopathic medicine services for a number of personal reasons. They meet with a professional with specific training in naturopathic medicine, and discuss their concerns. The naturopathic doctor then uses whatever “tools” they feel are most useful to address those concerns. Sometimes the knowledge gained from this service will be used to compliment the patient’s primary medical care, and sometimes not. In settings with a patient-share system with a family doctor, any test results can be easily shared between the two providers to enhance patient care. Generally, the patient can claim at least part of the cost of naturopathic medicine services from their private health insurance plan.

If you read the paragraph above again and substitute “personal genome” for “naturopathic medicine” and “genetic counselor/geneticist” for “naturopathic doctor,” does this seem incredibly plausible to you? It sure does to me.

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(initially posted on herNaturehisNurture)

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Communication in the Genomic Era

Last month the Genomics Law Report, a blog about the “intersection of genomics, personalized medicine and the law,” launched a series called “What ELSI is New?” They invited guest commentaries from various disciplines to provide a short post on what they felt was the most important ELSI issue facing the fields of genomics and personalized medicine. If you haven’t had a chance to peruse the series of commentaries, I’d definitely recommend it. I love the idea of looking at an issue from 360 degrees.

In full disclosure, I was very excited to be invited to contribute to this series. And you can find contributions from familiar players such as the NSGC Board of directors and Sharon Terry of the Genetic Alliance here and here. In considering the series in it’s entirety, I was struck by how many submissions centered on communication: between scientists, physicians, patients, the public. Below are a couple of excerpts I found particularly relevant to the field of genetic counseling.

From Chris Gunter of the HudsonAlpha Institute for Biotechnology:

I am struck by the absolute hunger of the public to understand genomics and personalized medicine… I propose our field engage in our own form of personalization: using education and media in all forms to convert the energy of the public into an army for science…

From Mathew Harper of Forbes:

…if genomics is really going to impact medicine, we’re going to have to start bridging the gap between the companies and scientists doing this early work and the traditional medical establishment…23andMe’s big contribution has been to start this conversation, but we’re still a long way from figuring out how genomics will fit into medical culture, no less into the regulatory framework.

From Zoe Mitchell and Dr. Gavin Harper of Oxford Nanopore Technologies:

As we enter an era of personalized, genomic medicine, the understanding and communication of probabilities is likely to be a stumbling block, not only for the public but for clinicians too…How to provide context, interpretation and counselling around these complex sets of probabilities is a new challenge in statistics, ethics and psychology.

I realize that the importance of communication isn’t news to anyone in the genetic counseling world. However, I like that it seems to be a focal point for the early thought leaders in the genomic era. This, in turn, will hopefully make our job of ensuring that our voice is heard in this discussion, just a little bit easier.

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