Is There A Doctor in The House? Physician-Mediated DTC Genetic Testing

23andMe has received a lot of attention as well as significant criticism from the medical community for their ever-expanding direct to consumer (DTC) genetic test offerings. While I share many concerns about 23andMe, it is worth noting that of the hundreds of tests that are directly available to consumers these days, 23andMe is the only lab that has received marketing authorization by the FDA for DTC testing. The only one.

These days anyone can easily order testing online directly from a number of companies, for themselves or their children – from pharmacogenomic testing to whole genome sequencing. How is it possible that so many labs are offering testing when only 23andMe has been given the green light by the FDA to offer DTC health risks tests?

One answer is so called ‘Consumer-Initiated, Physician-Mediated’ testing. With this flavor of DTC testing, laboratories can offer testing directly to consumers and bypass the need for FDA approval. So long as a qualified healthcare provider is involved in ordering the test, the FDA will continue to exercise their enforcement discretion and not get involved.

“As a matter of policy, the FDA generally does not review some types of tests, called laboratory developed tests (LDTs), that are created and performed in a single laboratory, if they are offered to patients only when prescribed by a health care provider. These tests typically do not have the FDA’s independent assurance of the analytical validity, clinical validity, or clear communication of test results.” FDA Website Updated 12-20-2019

I gotta’ say that I am baffled that consumer-initiated, physician-mediated testing is expanding so rapidly without any regulatory checks or balances. It seems like every other day there is a press release about a new partnership that enables labs to offer complex genetic tests, direct to consumer, with a physician’s order.

The biggest DTC genetic testing lab in the world by the number of samples, Ancestry.com (more than 15 million samples tested according to their website), recently announced that they are entering the health testing space and will be providing customers with some results related to hereditary risk for cancer, cardiovascular disease and more. And with their partner, Quest Diagnostics, Ancestry.com plans to release full exome data to customers later this year. However, unlike their main competitor, 23andMe, they are not offering this testing DTC with blessing from the FDA. Instead they have partnered with PWNHealth, LLC, so that their tests will be “physician-ordered” and thus escape the regulatory authority of the FDA. With this model, a test is selected and paid for online by the consumer, and then the lab requests a  physician at PWNHealth to authorize the test order.  

Ancestry.com isn’t alone in the decision to market complex medical tests directly to the public; PWNHealth also counts Invitae, Flugent, Sema4, Lineagen, Pathway Genomics, OneOme, Color Genomics, Ambry Genetics, and others as their partners. Just this past year, mega labs Quest Diagnostics and LabCorp launched new patient-initiated, physician-mediated lab testing, both partnering with PWNHealth. While PWNHealth seems to be a major player in this area of physician-mediated testing, the physicians working for PWNHealth aren’t the only ones signing test orders for consumer-initiated tests.

I know this from my personal experience of initiating one of these genetic health risk tests for myself. It was remarkably easy to order an extensive genetic test for hereditary cancer susceptibility. Ordering the test did not require me to provide health or family history information that would allow a physician to determine if this test was medically appropriate for me. In fact, all that was required for the test order was my credit card number and mailing address so that the lab could ship me a test kit. I returned my DNA-containing spittle never having talked about it with my own doctor, or any other doctor for that matter. Several weeks later, I received my results with a physician’s name and address on the report listed as the “Ordering Physician,” which Google Maps shows me is a UPS Store in a strip mall in Colorado (1,400 miles from my home state of Washington). This doctor was not a name I recognized from ordering the test, and I had no communication with him prior to, or in the time since my testing. Interestingly, I was able to find him LinkedIn where under Experience he lists: “PHYSICIAN OF RECORD (POR) services provided for DIRECT-TO-CLIENT laboratory testing.”

Consistent with this, while recently tuned into a webinar hosted by a lab offering a new consumer-initiated genetic testing product, a representative of one of the companies that provides physician “oversight”  stated that the physicians signing off on these genetic test orders do not have any expertise in genetics and at the company, “genetic counselors are considered the experts and the physicians approve or reject orders based on the genetic counselor recommendations.”

My sense is that the companies promoting and selling these consumer-initiated tests are getting a free pass for now because they provide genetic counseling along with the test results. Advocates of these consumer-initiated tests say that any pathway that allows people access to their own health information is a positive, and physicians that sign off these orders as well as the genetic counselors involved may feel that they are doing more good than harm by improving access to this information.

But the idea that a physician will, in exchange for payment, sign off on test orders for people who are not under their care is quite troubling to me. If these labs were billing CMS, such arrangements, which essentially pay physicians a fee in exchange for referral to the laboratory, may be seen as illegal kick-backs. In fact, the regulatory gaps that allow for consumer-initiated, physician-mediated genetic testing are the same ones that allowed one of the biggest Medicare fraud schemes of all time to take place.

What does the movement towards a growing number of these types of DTC testing options mean for the field of medical genetics?

Perhaps people will have greater access to genetic testing. But will the information received through these tests improve people’s health? Or will they lead to people receiving inaccurate, incomplete or misunderstood information? What are the downstream costs to our healthcare system to follow-up these results for tests that were never indicated in the first place?

What does it mean when the very same doctors are signing off on genetic tests that provide information such as results of pathogenic variants in genes for which we have proven interventions to improve health outcomes (e.g. BRCA and Lynch syndrome) are also signing orders for tests that make such evidence-less claims such as to design a DNA-based weight loss plan or to personalize your cannabis experience? Could this blending of evidence-based applications of genetics with snake oil damage trust in all of the work that we genetic counselors do? 

We are at an important crossroads where regulation and policy are needed to ensure responsible implementation of genetics in medicine. With this quickly evolving field there is an urgent need to address regulatory shortcomings with regards to genetic testing to reduce fraud and to ensure that people have access to high quality genetic tests and information. If medical tests are to be available directly to consumers, we need mechanisms to ensure that such tests have a high analytical and clinical validity and results must be comprehensible by those receiving them. Given the FDA’s current enforcement discretion of LDTs, we have no regulatory body accountable to see that this is the case. 

If the FDA continues to turn a blind eye to physician-mediated DTC lab testing, individual states may need to exercise their regulatory authority over the physicians who inappropriately order medical tests for people not under their care. In 2017, healthcare attorney and physician, Kimberly Lovett Rockwell, MD, JD  suggested in a JAMA Viewpoint article that state medical boards should consider sanctions against practitioners who work for DTC testing companies and order testing for any consumer without a medical history or examination, regardless of testing utility. Imagine all of the Medicare fraud that could have been prevented had such actions been taken a couple of years ago!

Lastly, one of the most important actions that will improve access to quality genetic healthcare and reduce inappropriate genetic testing would be CMS recognizing genetic counselors as healthcare providers (#supportH.R.3235 – Access to Genetic Counselor Services Act of 2019). Such recognition would allow reimbursement for genetic counseling services that are not tied to selling genetic testing products. Lack of fair reimbursement for independent genetic counseling has contributed tremendously to the shift of genetic services out of the traditional healthcare setting and into the consumer marketplace. CMS recognition would ensure the public that genetic counselors are subject to the same fraud, waste, and abuse laws and regulations as other healthcare providers and thus less likely to be unwitting parties to supporting DTC test schemes.

It is sadly ironic  that genetic counselors are faced with opposition to CMS recognition given the opinion by some that ordering and interpreting genetic tests is engaging in the “practice of medicine”, and should only be performed by licensed physicians. Yet at the same time, so many genetic tests are being ordered by licensed physicians outside of what is considered the standard and accepted “practice of medicine”.

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What Can I Say?

I like doing crossword puzzles with their mix of trivia and clever word play. I will never win any contests, but I am a competent puzzler (I prefer the term puzzler to it’s more high falutin’ cousins, cruciverbalist and engimatologist). Sometimes a devilish clue will stump me because it leads my mind to a very narrow interpretation of it. I have found a helpful strategy to solving the clue is to give it some benign neglect. If I let my mind stray to other things and then come back to 23-Down, the cobwebs will have fallen and in a slap-the-forehead moment the answer pops into my head. One way of distracting myself is to let my eyes wander across the newspaper page. As it happens, crossword puzzles are often on or near the same page as Advice Columnists and I find myself reading those letters from people seeking help with their woeful life situations. I am usually impressed by the counseling and psychological insights offered by the columnists and often find myself wondering what my response would be to the letter-writers (and I find myself singing the lyrics to John Prine’s wry song “Dear Abby“).

Last Saturday when I was stuck on trying to remember the city where Aga Khan’s mausoleum is located, I turned to reading “Ask Amy,” Amy Dickinson’s advice column. Although Amy did not supply me with the answer to the puzzle clue (Aswan, along the Nile in Egypt, for those of you who are also puzzlers), my attention was grabbed by a letter to Amy from – a genetic counselor. The counselor, who has chosen not to have children, asked Amy how best to respond to clients’ questions about whether the counselor has children and what decision she would make for her own child. The counselor also related a story about a recent couple who believed that the quality of care provided by their physician was compromised by that provider being childless.

My first thought was “Such questions play on our professional and personal insecurities. This genetic counselor might have been better served by peer or one-on-one supervision.” Supervision is an important part of professional growth. Although there are a few genetic counseling supervision groups, they are not particularly common, perhaps because there is no strong genetic counselor cultural tradition for them or professional requirements to participate in one. To some extent, the NSGC sponsored listservs – or Forums, as they are now called – sometimes serve that role but it’s not exactly the same thing.

My second reaction was I guess that’s a question a chatbot wouldn’t have to deal with. As Siri might say, “I am not sure that I understand that question.”

My third thought was “What would I say to that counselor if she posed the question to me?” If you are in a clinical position, no doubt you have encountered similar questions about your personal life. Before I was married, I remember the not uncommon occurrence of counseling a single parent pregnant woman who came to the session with her mother and afterwards the mother asking me on the sly “You’re such a nice a young man. Are you married?”

It is impossible for us to mirror all of our clients’ characteristics, experiences, and life situations. We can’t be all things to all people.  In fact, one might argue that being too similar to our clients can result in counter-transference issues that can negatively affect the quality of our counseling. A counselor can be too empathic; sometimes the ways that we are different from our clients can give us a less biased outlook on a family’s issues.

I was not particularly happy with Amy’s advice to the genetic counselor, which was to say to the couple “We’re not here to talk about me. We’re here to talk about you. Let’s focus on your case, OK?” I think it unhelpfully dismisses the couples’ concerns. It may be what the counselor is thinking but in my view that’s not how it should be verbalized or managed. I can think of a few alternative responses, depending upon the specifics of the situation:

  • “I appreciate your concerns and understand why you think a parental perspective might be helpful. But in my role with you, I am a counseling professional, not a parent. I have years of experience and professional training in working with couples in your position. My clients, whether or not they have children, often tell me how much they appreciate my expertise and insight. So I think that I can help you in meaningful ways. After meeting with me, you might want to talk to your friends and family members who have children to get their perspectives too.”
  • “You mentioned that you want your care providers to be parents – why do you think you feel this way? As we go through this session, let me know when you think a parental perspective would be important to the issue at hand and let’s see if we can figure out why my not being a parent might matter.”
  • “Some patients have raised this with me before. For many of them, it turned out that my perspective as a non-parent actually gave them a better understanding of their situation and helped them make what they felt to be a better decision. Let’s see if we can work together on this.”
  • “I don’t have children. But I listen very closely to my patients, and I have learned a lot from them about the issues and feelings that parents face. I think you can benefit from the many insights that my patients have shared with me.”

There are no doubt other ways to respond to these patient requests for self-disclosure and you may think my suggestions are inadequate. More than one research article has been written about how much counselors should share with patients about their professional lives and how they manage such questions. In the spirit of on-line peer supervision, I would like to hear from the Good Readers of The DNA Exchange about how they would have responded to the Ask Amy letter and how they handle questions from patients that probe counselors’ personal lives.

Patients are ongoing puzzles that we must continually work on solving, whether we are beginners or graying veterans. Some of the clues they give us have obvious answers, while others are more layered and complicated. The solution for one patient’s situation may not work for the next patient puzzle. All of us need to remain open to the help and perspectives of our peers and colleagues. We cannot grow if we engage in benign neglect.

 

 

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The List Returns: My Top 10 Stories in Genetics in 2019

2019!!  I’m going to declare it The Year of the Phoenix, with old promises rising from the dead (gene therapy) along with left-for-dead approaches (you came back with a vengeance, polygenic risk scores) and even older fears (remember when we were a post-racial civilization and genetic discrimination –  whew! – didn’t happen?).

Writing about 2019 got me thinking about the end of a decade, and so this year I am offering an end-of-the-decade special: two lists in one.  Here’s my take on the top ten stories in genetics for the 2000-teens (in no particular order):

Clinical use of exome sequencing

The rise of mega-databases

The ancestry-testing craze and the death of genetic privacy

Data sharing becomes the norm (kumbaya awards to gnomAD; ClinVar)

Nanopores! And other forms of heterogeneity in the F2 generation of DNA sequencing

Cell free DNA testing

Polygenic risk scores 2.0

NGS rewrites laws of economics by getting cheaper & better despite Illumina monopoly

Gene therapy rebounds

CRISPR

No surprise, many of these larger trends are reflected in the Top Ten for 2019:

 

  1. DTC: THE TRAIN HAS LEFT THE STATION BUT NOBODY KNOWS WHERE WE ARE HEADED

Can’t talk about genetics in 2019 without a word about DTC testing, as we persist in calling it for lack of a better word (consumer-initiated testing?  Not a better word, though possibly a better phrase…).  The thing is – wait for the irony – you can’t generalize about DTC anymore.  So what’s the biggest DTC story of the year?  I’m going with Ancestry branching out into the health and trait testing business.  This can hardly rate as a giant surprise, as they have hinted at it for years, but the big question was whether or not they would go with a 23andMe Fun Facts approach or something more medical.  Would they try and compete with Invitae or Color and offer a more comprehensive and more expensive CONSUMER-INITIATED, DOCTOR-APPROVED testing?  Seems like this choice would say something about where they see the field going…

And the answer was (drum roll): both.  Take your pick.  This actually does say something about the future, which is to say, we have no idea where the field is headed.  Their two-tiered approach debuts in 2020 and I expect it is more beta testing than market strategy.  I predict they are down to a single product by the time we (please God) inaugurate a new president in 2021.

 

  1. MILASEN

There are so many stories about the success of new treatments in 2019, that it was hard to pick just one.  Trikafta, the new CF combination therapy that will extend effective treatment to over 90% of the cystic fibrosis population?  Studiessuggesting the PCSK9 inhibitor inclisiran may offer a new option for individuals with a genetic predisposition to high cholesterol?

But with all these big stories to talk about, I’m going small: the development of a drug to treat a single individual, reported in October by the New York Times.  This n-of-1 drug was developed for Mila Makovec, a Colorado 8-year-old with an atypical form of Batten’s disease.  The drug, named Milasen, has improved but not cured the little girl, who has gone from 30 seizures a day to something less than 6 on average.  This example of highly personalized medicine was enabled by DNA testing, but also by the 3 million+ dollars Mila’s mother raised via a GoFundMe campaign.  Additionally, as the article points out, the nature of a custom drug is a challenge for regulators, who cannot use data to establish effectiveness or risks associated with treatment.  And without means to get FDA approval, these drugs will operate indefinitely in self-pay mode.

 

  1. FLORIDA MAN AND ACCIDENTAL PHILOSOPHER SELLS BUSINESS AND RETIRES FROM UNPAID ROLE AS ARBITER OF FORENSIC DNA USE BY AMERICAN LAW ENFORCEMENT

In 2010, retired businessman Curtis Rogers and his friend John Olsen founded GEDmatch, a website providing a set of tools to help adoptees find biological relatives.  “Premium members” paid $10 a month, most of which went to offset the cost of servers.  More of a hobby than a business, GEDmatch was staffed by volunteers.

Eight years later, Rogers described himself as shocked and surprised to discover via news reports that his site had been used by law enforcement to locate a suspected serial killer named Joseph DeAngelo, later convicted of a rape/homicide in 1977.  “It took a couple of weeks for me to really wrap my head around what was happening,” said Rogers.  GEDmatch, which was not a testing service like Ancestry or 23andMe, accepted DNA from a variety of sources, making it accessible to profiles derived from crime scene samples, and its DIY set of tools for finding relatives was tailor-made for the new field of forensic genealogy.

Did people who uploaded their DNA for genealogical purposes intend for it to be used by law enforcement?  And did their intentions matter?  Accidentally, this Florida man found himself the arbiters of forensic DNA use in the U.S.  How did he do?  Not bad, considering.  In the wake of the initial Golden State Killer hubbub, Rogers informed law enforcement that they could use GEDmatch only for crimes that included murder or sexual assault.

Then in December 2018, Rogers bent the rules to allow a search for an assault he described as “as close to a homicide as you can get” (an elderly woman playing the organ in church was choked and beaten).  This exception provoked a significant negative reaction from the GEDmatch user community, which in turn caused Rogers to rethink his approach, and in May he announced a new “opt-in” policy, restricting the police searches to those profiles whose users had provided consent.  Overnight, the new policy shrunk law enforcement’s access to GEDmatch to a meaningless fraction of the total database.  While responsive and thoughtful, this sudden about-face illustrated how much the forensic use of genealogical data rested entirely upon the decision-making of one many with no particular expertise and some conflict of interest (Rogers also mused allowed at one point that he might start charging law enforcement to use the site because, why not???).

This status quo held only briefly, with several latte-year events altering the forensic DNA landscape.  In September, the U.S. Department of Justice released interim guidelines for law enforcement that permits them to use DNA databases only for violent crimes like rape and murder, or to identify human remains, and only when traditional investigatory efforts have come up empty.  Two months later, a GEDmatch search occurred for the first time by court order, after a Florida court issued a subpoena.  And in December, Rogers sold the company and his de facto control of forensic DNA use in the U.S. to Virogen, a sequencing company specializing in forensic use of DNA.  Virogen claims it will maintain the opt-in standards set by Rogers even though those standards complicate its core business.  Anyone who takes that promise at face value should contact me; I have a bridge you might be interested in buying.

 

  1. ASCENSION HEALTH PATIENTS, MEET OUR NEW ASSOCIATE, DR. GOOGLE

Maybe they should have called it Project Canary in the Coal Mine.

Ascension Health’s Project Nightingale struck a nerve this November, when the Wall Street Journal reported that they had hired (or, in HIPPA-compliant terms, entered into partnership with..) Google to collect and analyze identifiable health data from the electronic medical records of their patients.  HIPAA forbids the sharing of a patient’s medical information without express consent, but allows for access within a medical system if it is used to improve patient services.  While Google denied any intention to use the data for other purposes or to link it with Google subsidiaries such as Calico (a partner with Ancestry, the largest of the consumer genealogy databases), many skeptical observers pointed out that health data is a valuable commodity in which Google has a previously expressed interest.

Sans accusation, it is fair to say that Project Nightingale raises legitimate concerns about the adequacy of existing privacy regulations in an age when the quantity and richness of data accessible through large health system EMR’s and genomic databases is unprecedented, and there are players like Google potentially capable of connecting the dots between genomic and health outcome data to draw conclusions about individuals and families.  It is unlikely that the architects of HIPAA envisioned the size and scope of Ascension Health (78 hospitals and over 2600 ‘points of care’ according to… Google) and there is no way that HIPAA rules governing internal partnerships were designed with Google in mind.  What could happen?  I don’t know, and neither do you, and that is actually the point.

 

  1. INVITAE INVESTS IN CHATBOTS

If you attended a genetic counseling conference this year, you likely heard a great deal about chatbots, even before reports in November of Invitae’s plans to purchase chatbot pioneer Clear Genomics for $50 million dollars (drinks on you, Shivani Nazareth!!!).  The move represents a clear (no pun intended) double down on Invitae’s other significant 2019 initiative: expanding into the world of consumer-initiated testing.  Chatbots, in this story, play the role of support staff, allowing us to triage questions and concerns that require genetic counseling from those that do not, a crucial step in expanding the use of genetic testing or screening without sacrificing our commitment to informed decision-making and responsible return of results.  In fact, relieved of menial question-answering, the GC staff are able to take more time with those who need it, and practice the sort of personalized and therapeutic relationship-building that characterizes genetic counseling at its best.

Do you sense a *but* coming?  I sense a *but* coming.

But… I have to say that while I buy the potential of chatbots for this purpose, my own view of the future is a bit of a choose-your-adventure story with alternate endings.  In the darker version, institutions and insurers decide, once the automated information-givers are in place, that this system is not intended to enable genetic counseling but to replace it.  So, yes, let’s embrace GC-Siri, but at the same time, let’s double down on producing data to support the value of the (human to human) genetic counseling experience.

 

  1. DATA SHARING HITS A MILESTONE

The clinical value of genomics is based not just on our power to sequence, but on our ability to interpret the variant calls, and for improving interpretation, there is no resource more powerful than past experience – an early-days problem for the nascent field of genomics.  ClinVar, the government-funded repository of variant calls, was developed to provide a way to maximize the value of our collective experience of the relationship between genotype and phenotype.  A real-life exercise in game theory, ClinVar represented an act of trust: hand over your work for the common good and, if enough people participate, everyone will benefit.

The result?  In December 2019, ClinVar announced that the number of shared records has passed one million.  Routinely consulted by clinicians and researchers, ClinVar has become an invaluable resource to the world.  Congrats and thanks to the thousands of volunteers who have organized data, searched records, curated variant calls and worked to promote the gospel of data sharing.

And by the way an example of government doing what private industry cannot, in the service of the public good.

 

  1. CRISPR PRIME PROMISES TO A CURE FOR YOUR GENETIC DISEASE DELIVERED IN TWO DAYS OR LESS

A novel CRISPR technique, reported in an October article in Nature, uses reverse transcriptase to introduce a desired transcript into a DNA strand, without the messiness and unpredictability of CRISPR’s double-stranded breaks.  The technique was widely hailed as a way of improving reliability of the ‘replace’ aspect of CRISPR as a ‘search and replace’ function for DNA.  And called CRISPR prime, so I guess they will give me my money back if it isn’t delivered to the right chromosome in two business days (this joke has fallen flat multiple times but I believe in it and I have the courage of my convictions).

Will CRISPR prime be transformational?  Despite the excitement it is too soon to tell, but here’s what the story represents to me: the incredible pace of technological advancement in the CRISPR era continues unabated.  Prior to 2012 – LESS THAN 8 YEARS AGO – most people excited about CRISPR probably thought of it as an intriguing way to improve yogurt.  In less time than it typically takes to bring a single drug to market, CRISPR has launched a multi-billion dollar industry, with the first CRISPR-mediated therapies approved for human trials (and, less positively, the first CRISPR gene-edited babies already past their first birthday in China).  If CRISPR prime doesn’t deliver, something else will; I’d put an Amazon-sized bet on that.

 

  1. THE UK BIOBANK FUELS A NEW ERA OF POLYGENIC RISK SCORES FOR… EVERYTHING.

Move over, Iceland.  Your collection of genomic and health history information was good but how can a small island nation with a genetically homogenous population compare with the vast genomic richness of… England?

Okay, so 94% of the half million participants in the UK Biobank are white.  But, as papers appear almost daily, it is hard to deny the fundamental impact of the UKB as a research resource.  Funded in 2002, the dataset combines the results of genomic testing with phenotypic measures of more than 2400 traits, and survey data covering everything from sexual history to political preferences.  And with only a handful of restrictions and a $2500 fee for use, UKB data is available to almost everyone, and it has been used to link common genetic variants with everything from depression to obesity to income.

In turn, this mass outpouring of genetic association studies has spawned a sub-genre of “genetics is not deterministic” PSA’s, like this one from Kevin Mitchell, and I’d like to collectively thank you all for your efforts.

Because volume is the message, it is hard to single out a single UKB-themed story, but in the spirit of reductive end-of-year list-making, let me focus on an article on the genetic basis of same sex sexual behavior published in Science in August.  The authors of this study, which reported on a GWAS of data drawn from the UKB and the 23andMe consumer customer database, identified results indicating genetic associations that accounted for 8-25% of the variation between individuals who had participated in same-sex sexual behavior and those who had not.  The authors were extremely careful to explain that a single same-sex experience was not the same thing as homosexual orientation, and in fact further analyses indicated that there were genetic differences between the two.  Additionally, the article made clear that while patterns emerged in a population, individual results were insufficient to indicate likelihood of homosexual behavior on an individual level.  The authors even constructed a website putting this into more user-friendly language, in case anyone found the Science article inaccessible.

So it could come as a surprise to no one that, 6 weeks later, an app called “How Gay Are You?” went up for sale through the DTC gene-testing marketplace Gene Plaza.  Under intense public pressure from the authors of the study among others, this app was removed in November.  Was it only a bit of harmless fun, like the app that claims to identify your inner superhero?  Maybe not says science journalist Emily Mullin, who pointed out on twitter that the person responsible for the app is based in Uganda, where homosexual behavior can get you the death penalty.  Ha ha adorable.

Sure, this example fails to illustrate the medical value and legitimacy of many UKB-based gene tests reported in 2019.  But it says something profound about how quickly the marketplace moves to commercialize genomic associations, and the difficulty of controlling how the information is used – but also (a bit more optimistically) that a response and clear communication from scientists can mitigate misuse.

 

  1. POPULATION SCREENING

The steep fall of the cost of DNA sequencing has transformed genetic research and made exome sequencing a staple of medical management.  It has also opened up the possibility of population-level screening programs, including research programs like the UK Biobank and the U.S. All of Us project and clinical programs like Geisinger Health System’s MyCode.  Is genetic screening of healthy individuals a good idea?  That depends on the circumstances. How about by government decree, without consent, for purposes of tracking a vulnerable and restive minority population?  Hmmm… pretty sure even George Church and David Ledbetter are a hard no on that one.

But a report by the NY Times in February documented that involuntary “free health checks” of a Muslin minority population by Chinese authorities included facial scanning, fingerprinting and a DNA test.  This perversion of health care is even more nefarious in the context of Chinese repression of the Uighars, over a million of whom are rumored to be in ‘re-education camps’ serving indefinite sentences for the crime of belonging to the wrong ethnic group.  Thermo Fisher, the Massachusetts-based company that provided the equipment used for population sequencing, announced that it has ceased sales to China as information on the genetic testing program began to surface in the news.

How do they plan to use DNA sequence data?  Will individuals be tracked using DNA profiles or groups of individuals sorted by genotype?  I doubt even the Chinese know.  But genetics has always had a dark side, and even the most ambitious of early eugenicists could hardly have imagined the power of population-level sequencing programs, and the toxic potential of new-fangled technology and ancient prejudice.

 

  1. ZOLGENSMA AND THE COMPLICATED MORAL MATH OF MIRACLES

There is no bigger story in genetics in 2019 than the success stories in gene therapy, which have brought help to a handful, and hope to many.  Two years removed from the first FDA approvals in 2017 (two immunotherapy drugs and Luxturna, for a rare inherited retinal disease), the 2019 update includes a handful of new market entries and a robust pipeline, with some tantalizing year-end hints about promising results in gene therapy trials for sickle cell disease and beta thalassemia.  Nowhere is the optimism felt more keenly than the SMA community, where parents now have competing options to treat what was until recently a death sentence for their affected children.

But as this story by the Washington Post indicates, access to those options poses a world of new challenges.  Zolgensma, a gene therapy for SMA, made headlines as the world’s most expensive drug at 2.1 million dollars per patient, and that fact means that insurance companies are going to take a long hard look at who qualifies for the treatment.  This article concerns a toddler turned down for the drug because as a type-III SMA patient she is not severely affected enough to qualify – although she has difficulty walking and can anticipate lifelong disabilities.  Since the use of the medication is only approved for children under two, there’s no room for a wait-and-see attitude.

The economics of gene therapy are built on a model of one-and-done treatment that replaces lifelong care, a promise that in these early days is aspirational at best.  But even if it goes according to plan, the model doesn’t account for children like the adorable, moon-faced Daryn Sullivan, whose lifetime medical costs might not be so outrageous as to make 2.1 million up front sound like a bargain.  With other diseases, off label use might include genotypes that are not the best case scenario for use, where we anticipate improvement not cure.  If it’s the best medicine can do, can we pay 2.1 million for anything short of a miracle?

For all these substantial challenges, the biggest translational obstacle may be something more subtle, captured not in the article but in the comments.  Daryn’s parents, it turned out, knew during pregnancy that the child would be born with SMA and chose not to end the pregnancy.  Will our increasing ability to identify and prevent genetic disease make us less willing to fight the hard fight for access to treatment?  “I had the deepest sympathy for the Sullivans,” one reader wrote, “until I read the part where they KNEW their baby was doomed to a terrible wasting disease, but continued the pregnancy anyway.”  A quick review showed about 10% of the 320 comments said something similar: “people create children with disorders and then demand that everybody else pay for their treatment no matter what the cost.  Shameful.”

In the past 10 years, we have addressed many of the technical challenges to gene therapy.  In the next decade, we will have to confront the potentially even more challenging issues of access and empathy.

 

THAT’S IT FOR ME IN 2019!  HAPPY NEW YEAR, EVERYBODY!!!!  GOOD LUCK TO US ALL IN 2020 (WE’LL NEED IT).

 

 

 

 

 

 

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Genetic Counselor Reinvented

I have a confession to make. Now that I am half way through my 60s – not exactly elderly, but too old to die young – I have become increasingly insecure about my relevance to the field of genetic counseling. My ethos, counseling style, and knowledge base are still anchored in the previous century. My anxieties are heightened by practicing in a field dominated by young, very bright, highly trained people. I fret that I am viewed by my colleagues with bemused, grandfatherly respect and not as a key player who is relevant to the practice of genetic counseling or to the many exciting pathways that the profession is pursuing. Call it fear of being thought of as a vetus crepitu (Old Fart sounds so much better in Latin).

Then too there are the demands of employers to see ever more patients, the promise/threat of artificial intelligence to replace/supplement genetic counselors, and increasing demands to access genetic counseling through means other than a brick-and-mortar face-to-face interaction. It’s enough to make me want to call it quits and enter a peaceful retirement where my stressful decisions will be “Should I sleep another hour?” or ” Which show should I binge-watch – all 5 seasons of ‘The Wire’ or ‘Breaking Bad’?” Omar, Stringer Bell, Mr. White, Leonel and Marco Salamanco (“The Cousins”), Gustavo – I hardly knew ye and heartily miss ye.

I was mulling over these thoughts and insecurities the other day when I had an Aha! Eureka! Fall-Off-My-Ass moment that will revitalize my moribund career and make me the envy of genetic counselors of all ages. I have 36+ years of experience with more than 20,ooo patients and a shopping bag full of clever counseling phrases (“Families can be complicated sometimes.” Pause, look directly at the client, and give a slight , knowing, supportive nod of the head. or “There’s no need to rush into making a decision about genetic testing in your situation. Testing  is important  – pause an extra beat to focus attention on the next words – but not urgent.”). I have parlayed this experience into an e-asset by reinventing myself as a biotechnochimaera of a genetic counselor and a chatbot. Ecce – ChatBob!

Deciding to become ChatBob wasn’t exactly brain surgery. Well, actually, it was brain surgery. My cousin, a brain surgeon, and my niece, a computer whiz, worked together to implant a variety of neuronanochips, teeny-tiny receivers, micro-routers, and other itty-bitty doodads into my cerebral cortex and other important sections of my brain. Anyone with an internet connection can now access my brain for the purposes of genetic counseling. The microrouters and neuronanochips allow multiple people to simultaneously  access my CNS. I don’t know how that stuff works; my niece explained it to me but I didn’t really understand a word she said. But I don’t have to understand how it works because it does it’s job automatically.

Okay, the external portion of the hardware is a bit, uh, geeky but, hey, it’s the beta-version. Undoubtedly some product designer from Apple will eventually turn it into a fashion statement that will make even the hippest hipsters suffer a serious case of cool-envy.

Because I have been a genetic counselor for so many years I have heard every possible question and because I can do it in my sleep, patients in any time zone have access to ChatBob 24/7. The neuro-computer connections hook up to a deeply embedded part of my unconscious mind so I am usually unaware that a counseling session is even taking place (admittedly, that sometimes used to happen when I saw patients in person too). I can binge watch whatever television series I am in the mood for while the Counseling and Education Center of my brain – the striatum bovis stercis – subliminally and simultaneously counsels dozens of patients. Labs download test results directly into my brain which then sends a message to patients’ computers so they can immediately access their reports and my clinical interpretation.

I am in great demand by laboratories and hospitals wanting to free themselves of the burden of the salaries of multiple genetic counselors. I can be easily integrated into Epic or any other electronic health records platform. Researchers looking to allow people from all demographics to have easy access to genetic counseling in research projects are pounding on my e-door. ChatBob is a researcher’s dream because all the counseling is done by one counselor so they don’t have to control for counselor variability in skill, experience, or style. ChatBob is scalable to a population level;  hey All of Us , why not take All of Me? Telegenetic counseling startups are pleading with me to replace their entire staff.  I’ve had inquiries from Google wondering if they can implant advertisements in my brain for products related to patients’ genetic test results.

There have been some mishaps and a few crossed wires. These have mostly been the result of my cousin being a disbarred neurosurgeon (one of the disconcerting things about being awake during neurosurgery is that you can hear the surgeon say “Oops” in the middle of the procedure) and because my niece, being a teenager, has more important things to pay attention to than the details of her uncle’s neurocircuitry. So occasionally when a patient asks a dumb question the reptilian part of my brain overrides my Counseling Center and responds with something like “What a dope. Weren’t you paying attention to what I just neurotransmitted? I’ve already said twice that daughters can inherit a BRCA1 mutation from their fathers and that genes absolutely cannot skip generations.” A few patients have managed to integrate themselves into some of my dreams. It made for some awkward moments when a couple of patients managed to tap into the primal portions of my brain that house my implicit biases, fantasies, fears, and unfiltered thoughts. But hey, that’s to be expected in the pioneering stages of any world-changing technology. Kind of like Alexa “inadvertently” listening to your private conversations. Employers are not troubled by these occasional mishaps because all they care about is that I am counseling high volumes of patients and saving them oodles of money.

I don’t recommend other genetic counselors biotechnoconverting to ChatBob because I want all the business and I want to have the best presentations at national meetings. Plus, it is kind of a permanent thing, so you can’t just back out after using it for 90 days or whatever. And you have to do lots of explaining to skeptical TSA workers at airport security checkpoints. But these are small sacrifices to make in order to stay in front of the genetic counseling peloton. I will be seeing you in my rearview mirror for the next 10 years.


Thanks to Emily Singh for realizing the ChatBob graphic

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Sometimes I Wish I Wasn’t Right, Especially When I Am Being Ridiculous

So it goes

So it goes

So it goes

So it goes

But where it’s goin’ no one knows.

And So It Goes by Nick Lowe (1976)

Nearly ten years ago I wrote a DNA Exchange piece, “GeeKnowType – The Unique Gene Boutique,” an absurdist skewering of some of the DNA test offerings of direct-to-consumer labs. My online emporium offered imaginary testing for characteristics such as the clearly hereditary but mirror-obvious like eye color as well as traits that would be best described as “genetic,” such as sexual preference. I used dark humor to illustrate important points about the misuse and misunderstanding of genetic information. By the way, I know that nowadays we are supposed to call it “consumer-initiated testing” but it’s hard decide who really initiates testing when consumers are bombarded with over-hyped targeted advertising based on their viewing history or after watching disarmingly charming television commercials filled with story-telling about the power of genetic testing. “Personal, powerful, and perfectly priced,” as one website describes it. And if you believe that advertising does not influence your spending choices, well then that’s just proof of how well it works. Any con man will tell you that the easiest people to con are those who believe they are too clever to be duped.

Alas, I must report that fact has now robbed my fiction of its falsehood. All the absurd tests, or reasonable facsimiles of them, that I conjured up at the beginning of the decade are now commercially available at the end of the decade. Below I’ve reproduced part of my original posting along with links to vendors that now offer a real version of my imaginary tests.

M-eye Color©: Everyone thinks your eyes are brown, but you swear they are hazel. Who’s right? Only your eye color genes know for sure.

Update: Eye color is now often included as part of a package, so you really don’t have much choice about whether you actually want the information. And this “harmless” test has entered the creepy realm – preimplantation genetic testing  can be used to choose an embryo that has the most desirable eye color. God help us.

SwitchHitter©: Am I right-handed or left-handed? Do I have situs inversus or just a poor sense of direction? With the powerful awareness of your genetic handedness, your cilia will always beat in the right direction.

Update: Not offered directly by vendors that I am aware of, but SNPs for handedness are available and could potentially be accessed by downloading raw DNA results to a third party interpreter.

MyGeneColor©: What is your favorite color? Cerulean? Or is it really a cool shade of pinky-purple? Busy people don’t have time to recall these details. No worry – MyGeneColor will find out for you. You will never again be at a loss, whether you are painting your walls or painting your nails.

Update: This site makes the claim, among others, that DNA ancestry testing indicated that “African heritage generated rich, warm color palettes.” An extraordinarily genetically and culturally complex continent reduced to a few stereotypical hues. Oy.

GeneSequins©: How chic is your fashion sense? The Human Genome Project has proven that your Hip Quotient is genetically determined. We recommend that GeneSequins be run along with our RightWeigh and MyGeneColor products to give you a complete picture of your personal style.

Update: See the same site mentioned in above discussion about color preferences. British ancestry or an aptitude for math (!) suggested a preference for a plaid print crossed with geometric lines. Or read about it in the International Journal of Clothing Science and Technology.

 

RightWeigh©: Your scale says you are overweight, but you know you cannot weigh that much. In fact, research has shown that scales tell us more about our parentage than our eating habits. With your true genetic weight, you will no longer be a slave to unreliable scales that invariably add pounds to your real weight. Say good riddance to diet and exercise!

Update: You can choose between a more “authoritative” test from a reputable lab or from your basic shop-for-it-all site. Or even discover your “true” waist size. There’s clearly something unscientific about how clothing manufacturers are measuring so-called slim waists.

WhichWay©: Not sure if your sexual preference runs to men, women, or both? Ask your genes and they will tell.

Update: As thoughtfully critiqued on The DNA Exchange by genetic counselor Austin McKittrick, there’s an app for that, called 122 Shades of Gray.

 

WellRead©: How do you know which authors you like? More importantly, which ones do you actually understand? Should you be reading The New Yorker or People, James Bond or James Joyce?  Let us read your genes so you can read genetically appropriate literature – and save money on unnecessary magazine subscriptions.

Update: Okay, not exactly the same thing but this site claims it is possible to predict your genetic “word reading ability.”

Now don’t misread me, unless of course you have “inferior” word reading ability. It’s not that I am a stuck-in-the-2oth-century old school genetic counselor who thinks that DTC testing is the Eleventh Plague to scourge mankind (well, to be honest, most of the time I’m not that curmudgeonly). DTC offers the potential for a wide range of people who could benefit from genetic testing that has real clinical value. But when all tests, regardless of validity, carry the imprimatur of DNA, how are consumers supposed to distinguish the sensible from the nonsense?

In a parting note, less than 2 years ago I posted another satirical piece called “Sour Grapes: A Tragicomic Dystopia in The Consumer Genomics Counseling Space,” about an imaginary near future in which virtual home assistants arrange genomic testing and then offer to sell consumer and medical products based on DNA analysis. Well, sad to say, in a Moore’s Law type of “progress,” the gap between my predictions and their actualization has shortened to less than 2 years. 23Mofang, a Chinese DTC company, now offers specific skin care products based on a genetic predilection to saggy skin. I am starting to understand why seers and prophets are often portrayed as tragically shunned characters. I think I am going to get out of the predictive satire business.

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Guest Post: If Gay Means Happy, Then Why am I so Sad?

By Austin McKittrick

Austin is a genetic counselor for Genetic Support Foundation, a non-profit genetic counseling group, where he provides telehealth genetic counseling from his home base in Vancouver, WA. He a first time blogger, long time reader of the DNA Exchange.

 

A study recently published in Science sought to answer the age-old question: Where’s the ‘gay gene’? As a member of both the genetics and LGBTQ+ community, this headline naturally piqued my interest. I’ve always thought that this question is inherently a double-edged sword: by ‘proving’ that non-same sex attraction is in some way genetic, the whole ‘it’s a choice’ argument can finally be put to rest. But finding a scientifically detectable ‘cause’ for non-heteronormative behavior naturally brings up an equal (if not greater) level of concern.

The intentions of researchers are often not what is embodied by the products of that research. I honestly don’t think that the creators of genetic testing for ancestry thought that this testing would one day be used by the Canadian government to try to sort out where migrants to their country are ethnically from. But maybe they should have.

Even when we think we understand the genetics of a trait, the outcomes often aren’t as straightforward as we once believed. Particularly for a trait such as ‘nonheterosexual behavior’, where social, religious, family, and political influences also strongly affect one’s beliefs and how they may choose to reconcile those beliefs with their lifestyle. Genetics is leaping forward faster than the majority of us had probably anticipated, and we’re getting a real lesson about putting the cart before the horse.

There are some issues with how the study was conducted, as sexual identity is very complex and some of the questions have been viewed as being too binary and focused on behavior rather than sexual orientation. The researchers categorized people into two buckets: those who have EVER had ONE or more same-sex sexual experience are categorized as ‘nonheterosexual’ while those who have never had a same-sex sexual experience are categorized as ‘heterosexual’. They do make an attempt later in the study to outline that sexuality is a spectrum, but that assertion is buried amongst other extrapolations.

The data sets for this study were collected from the UK Biobank, as well as direct-to-consumer testing company 23andMe. Companies such as these encourage their customers to consent to having their DNA used for research, promising that their selfless contribution will further the field of genetics and healthcare. In all actuality, it appears that this data is being sold to entities that are using it for less medically noble endeavors. Aside from individuals not fully understanding that their data could be used for such ‘research’, they may actually unknowingly be participating in research that could potentially lead to discrimination and other harms against them in the future.

The authors of the ‘gay gene’ study determined that ‘like other behavioral traits, nonheterosexual behavior is polygenic’. There you have it folks: it’s not ONE gene. It’s LOTS of genes! Is that better? Worse? Depends on what you do with that information…

Enter GenePlaza, a company that boasts that it can take the DNA information that you’ve received from companies like 23andMe and Ancestry.com and use its internal apps to tell you things like how smart you are or how good you are at math (in case your grades in school didn’t tell you already). With data taken from this new study, GenePlaza proposed that for $5.50 they could tell you exactly how gay you are.

Backlash to the announcement of the app was swift, and a petition was quickly announced in an effort to get the app shut down. Although at the time of this publication it not yet reached its goal of 2,500 signatures, it appears to have been effective as there is no sign of the app now on GenePlaza’s app site.

It’s tempting to want to give GenePlaza the benefit of the doubt. ‘Oh they just thought it would be a harmless app’ or ‘They probably just thought it’d be a good party trick’. However, the revelations that the app’s developer, Joel Bellenson, is based full-time in Uganda paired with the news that this year Uganda is announcing plans that would make the death penalty punishment for homosexuality makes it seem that something more nefarious may be at play.

As the authors of the study said, we should resist ‘simplistic conclusions because the behavioral phenotypes are complex, because our genetic insights are rudimentary, and because there is a long history of misusing genetic results for social purposes.’

Some have raised concerns about the motivation of such research studies. But once something like this is out of the bag, it’s very difficult to put back in. No matter the motivation, this is another shining example that when it comes to genetic technology, we regularly need to be asking ourselves not only ‘Can we?’, but ‘Should we?’.

 

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MUTYH: Who should be screened? How should we screen? Who decides?

As recently discussed on the DNA Exchange, general population screening for any health condition has both risks and benefits, and sound health policy should weigh all of these factors to ensure that we are doing more good than harm. But the debate about what, who, and how we should be screening for hereditary cancer risk seems to be mainly an academic exercise practiced by some in the clinical genetics and public health communities. While we continue to debate the merits of population screening, the commercial laboratories keep pushing forward, making these tests readily available to the general population through direct to consumer (DTC) testing products.

Often the cancer genetic test isn’t the main product that the customer is seeking, but rather may be a bonus of sorts provided along with ancestry and other DTC tests. Such is the case for the new health reports for MUTYH variants that 23andMe began releasing this past summer. Individuals who inherit one MUTYH pathogenic variant may have a slightly increased risk for colon cancer. Individuals who inherit biallelic pathogenic variants have a very high risk for colon polyps, colon cancer and other cancers and are said to have MUTYH-Associated Polyposis syndrome, or MAP.

Earlier this year, 23andMe received clearance from the FDA to release information about two variants in the MUTYH gene that are common in individuals of European ancestry – G396D and Y179C. The basis for this 510(k) approval is that it is substantively equivalent to the 23andMe BRCA test (which evaluates for three founder mutations most common in individuals of Ashkenazi Jewish ancestry). The company recently reported that they have over 10 million customers, with approximately half of those accessing the health portion of the testing (in contrast to ancestry alone). And considering that about 80% of those customers are of European ancestry, I estimate that of the approximately 4 million people received the new new MUTYH Genetic Health Risk report. Through this report. I estimate that about 250 people may have learned that they have MAP and about 60,000 customers learned that they are carriers for one of these two MUTYH variants. 

So who should be screened for MUTYH variants? If you ask 23andMe the answer would be everyone. How should we screen? According to 23andMe, screening should be done by a two variant genotype panel. And who decides who is screened? From what I gather, this new health report was not driven by customer demand, nor were healthcare providers calling for more access to MUTYH testing. Generally our guidelines recommend MUTYH testing only in very specific circumstances, such as when a patient has multiple adenomatous polyps, or if they have a sibling who has been diagnosed with MAP. But it is not the healthcare providers or guidelines directing who is screened. Presently it would seem that 23andMe decides who gets screened for MUTYH variants, and with the blessing of the FDA. I am curious to know how my genetic counselor colleagues are handling or are likely to handle such cases. What would you most likely offer to a patient that comes for genetic counseling with a heterozygous positive DTC MUTYH variant report, and no family history concerning for MUTYH polyposis or other hereditary cancer syndrome?

 

My hunch is that most genetic counselors would offer follow-up clinical testing, and that this will usually be at a minimum a full analysis of MUTYH. I certainly can see the benefit of identifying patients who have biallelic MUTYH variants to allow for earlier and more frequent colonoscopy screening and prevention of some cases of early onset colon cancer for those who may not otherwise have known that they were at increased risk. Since the announcement of the new health reports by 23andMe I have been curious about how many individuals with MAP could be identified through this stepwise screening, first with 23andMe and then follow-up clinical testing of the entire MUTYH gene for all of those who first have one or two variants detected through 23andMe.

Staying with the estimated 4 million 23andMe customers of European descent who opted for the health reports, I estimate that there are about 390 total people out of the 4 million who have MAP, and of these about 250 would be identified through testing the two common variants alone (homozygous or compound heterozygous for Y179C/G396D.  (My calculations and assumptions are all available here.) Through this stepwise screening of sequence analysis only for those who are first found to have at least one common variant, we would identify approximately 374 of the total 390 people with MAP, while missing about 16 people who carry two less common MUTYH variants. The cost per MAP case identified depends on the cost of follow-up genetic testing. Publicly available pricing suggests that single gene analysis of the MUTYH gene through a clinical lab is typically between $500-$1,500 per test for complete single gene analysis, although clinical testing may be priced as low as $250 to more than $2,000 per test. Thus, through this stepwise process (full gene analysis for those with one or more common variants first identified) the cost for clinical genetic testing would be somewhere on the order of $42,000 – $378,00 per MAP case identified. Given that general population guidelines recommend colon cancer screening should begin at age 50 and because approximately 75% of colon cancer in individuals with MAP occurs in patients under the age of 50, this genetic screening approach, and initiation of colonoscopy screening at an earlier age than typically recommended, could prevent as many as 94 cases of early onset colon cancer in this 23ndMe screened group, with cost per case prevented in the range of $168,000 to 1.5 million. It is important to note that this only considers genetic testing. A more complete economic analysis may include genetic counseling costs, additional cancer screening costs, as well as the estimated cost for genetic testing in other family members.

23andMe isn’t the only company that has an interest in MUTYH screening. Several labs offer DTC, or the close relative of DTC testing, the so called “patient-initiated, physician-mediated” testing in which an individual may request testing themselves, and a physician contracted by the lab signs off on the test order to bypass the need for FDA scrutiny (a discussion for another post). MyHeritage, who previously offered only ancestry testing recently began offering a “health” component which includes four variants in the MUTYH gene (including the two common European variants). Color Genomics and  Invitae  both consumer-initiated, physician-mediated tests as well as clinician ordered tests that provide a more complete analysis of MUTYH and other cancer susceptibility genes. 

Is more comprehensive testing such as full gene sequencing better when it comes to MUTYH testing in the general population? It depends on how better is defined. I can certainly appreciate that detecting those additional 16 individuals with MAP (and being able to prevent about 4 cases of early onset colon cancers) that would have been missed in our 23andMe population of 4 million people would be one benefit to more comprehensive testing. But what’s the trade off? 

At the recent American Society of Human Genetics meeting in Houston, Invitae presented data reviewing MUTYH variants found in analysis of a cohort of 270,806 patient samples that were submitted for multigene hereditary cancer risk panels. They reported that through a more complete analysis of MUTYH they discovered 5,929 patients with pathogenic or likely pathogenic variants in MUTYH, of which 1,377 (23%) of these patients carried one or more variants other than G396D and Y179C. That’s no surprise – in fact it fits well with our current understanding of the population frequencies for these genetic variants as well as our appreciation that about 80% of variants detected through MUTYH testing in a population of mostly individuals of European Caucasian ancestry are the G396D and Y179C variants.

The presented statistic that is getting the most attention in the news since the meeting is Invitae’s assertion that 40% of individuals in the cohort with biallelic mutations would have been missed by the targeted variant testing. But the necessary context that is missing here is that about 90% of those that would be “missed” in that 40% would have one of the two common variants paired with a second other, undetected variant. Through a stepwise approach in which only individuals with one or more of the common variants on first screening through 23andMe had follow-up clinical sequence analysis, approximately 96% of the total MAP cases would be identified. That means there would be only about 4% of individuals who would have biallelic variants that both would have gone undetected by a stepwise approach that begins with a two-variant screen.

If we were to ask Invitae who should be screened, I believe they would likely agree with 23andMe that everyone should be tested. Where they differ is in how the screening should be done, with Invitae advocating for more complete next generation sequence analysis for all people rather than targeted SNP panels. I can appreciate the logic in this argument that this strategy would detect more cases of MAP, especially in people who are not of European ancestry. But how would the cost of testing compare for the number of cases detected? The devil is in the details of how this testing is done and who pays for it. Invitae currently offers a patient-initiated, physician-mediated cancer gene panel for $250. If people elected this test and paid for it on their own instead of having 23andMe, given that it is considered a clinical test and no follow-up studies would be needed, then we would not see the additional cost in follow-up clinical testing (although we may see more downstream costs with follow-up for variants, including variants of unknown significance in other genes on the panel). My sense though is that people seek out tests like 23ndMe for reasons other than to know there MUTYH or other cancer gene status. So if we are considering the total cost of clinical testing for all people rather than just for those who present with at least one of the common mutations on a screening DTC test we would see quite a dramatic increase in the cost to identify a case of MAP as well as the cost to potentially prevent a case of colon cancer before the age of 50 (61-fold increase over the stepwise approach).

What is difficult to tease out in these analyses is that most tests that include MUTYH are not ordered with a high suspicion or concern for MAP. In most cases, it is included as part of a bigger panel, and MUTYH is not the primary reason for testing. In the case of 23andMe it comes along as part of a bigger ancestry, traits and health screen. In the case of Invitae it usually comes along as part of a multigene cancer panel for which the primary indication is usually for evaluation of genes other than MUTYH. So should we consider that extra information provided by the MUTYH analysis in patients a bonus or a burden? As DTC and consumer-initiated testing becomes more common, and as clinical testing panels more often include MUTYH, are we spending more time counseling patients about MUTYH results that are unlikely to significantly affect health outcomes or screening recommendations for the patient or their family members? I worry that patients may put too much value on these results as a possible explanation for their cancer, when it may unlikely be the case. And I feel conflicted about how much we should be advocating for family member testing when there is such a small chance that their care and outcomes will change as a result. 

The focus right now seems to be on the question of how we should be screening for MUTYH. I think we are engaging in the wrong discussion here – I think we should go back to the heart of this and really take a close look at why we are doing this testing?  What is driving adoption of expanding genetic testing to include analysis of genes such as MUTYH? And how should we integrate these technologies into practice in a way that will help the most people and cause the least harm. We need to critically consider the statistics that are presented and carefully weigh the costs versus the benefits of expanding testing. 

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Given that we are just a week away from the annual NSGC conference, I’d like to make a plug for the 3rd annual ‘GC’s Got Talent’ hosted by Genetic Support Foundation on November 6th from 7-10 pm. The event will be Emceed by the ever engaging and talented DNA Exchange blogger, Bob Resta. In addition to storytelling, dancing, singing and comedic acts, a silent auction will showcase the artistic and creative talents of GCs. It’s not too late to sign up to share your talent and we are seeking storytellers for the themes: “Confessions of a Genetic Counselor” or “Most Awkward Moment in my Career”…Contact  info@geneticsupport.org for additional info.

2016 talent show

 

 

 

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All For BRCA, BRCA For All?

Should all women undergo BRCA testing? This question has been an item for discussion once it was given the authoritative weight of Mary-Claire King, the widely respected genetics researcher who has made invaluable contributions to the discovery and elucidation of the BRCA genes. The appeal is clear. Under current protocols, many women at increased risk of carrying a pathogenic variant are not undergoing BRCA testing. It breaks my heart each time I meet with a 40 year old mother of young children who was just diagnosed with a preventible serous epithelial ovarian cancer or a triple negative breast cancer. Furthermore, a significant number of pathogenic variant carriers are missed by just about every set of testing guidelines. Not only that, guidelines are so complex, evolving, and variable that no one can keep track of them any more, except maybe the unsung  heroes among the support staff at commercial laboratories who are tasked with verifying insurance coverage for genetic testing all day every day. I half-jokingly tell my oncology colleagues at tumor boards that my new criteria for genetic testing are are simple: 1) Does the patient have cancer? 2) Does the patient have genes?

I understand the appeal of population BRCA screening. Risk mitigation strategies and enhanced screening have the potential to reduce morbidity and mortality, or, more simply put, it could reduce suffering and saves lives. This benefit looms particularly large in the face of that sly and nasty devil, fallopian tube/ovarian cancer. But the benefits – and I don’t mean to diminish them – can lead us to subconsciously overstate upsides and downplay downsides. As Guido Calabresi and Philip Bobbitt pointed out more than 40 years ago, allocating medical care is full of tragic choices, i.e., no matter what course of action we choose, some people will suffer and some people will benefit. The hard part is deciding who should benefit and who should suffer. Let me be clear, though, that if BRCA population screening were to be implemented, I hope that my concerns prove to be unfounded or are addressed up front.

So what are my worries? First off, I am not convinced that population BRCA screening is high on the list of public health priorities in the US. It doesn’t make the CDC’s list of pressing public health initiatives. About 100 million Americans are affected with one or more neurological diseases. According to the USDA, in 2018 about 37 million Americans lived in food-insecure households, including 6 million children. Eight hundred thousand Americans will have a stroke this year. Half a million Americans struggle with homelessness. About 380,000 children are born prematurelyForty thousand people die from a gun shot each year.

In comparison, my back of the napkin calculations suggest that of the approximately 42,000 breast cancer deaths and 14,000 ovarian cancer deaths in the US each year, roughly  5% of breast cancer patients and 15-20% of ovarian cancer patients carry a BRCA mutation (I am not including other high risk breast cancer related genes such as PALB2 and TP53, but their inclusion would not substantively change the calculations). This would amount to theoretically saving about 5000 lives annually. This rough estimate is based on the very unlikely assumptions of full population participation in both genetic testing and follow up cancer screening and risk reducing strategies, and that these strategies save lives. While the evidence is pretty good that risk-reducing saplingo-oophorectomy reduces ovarian cancer mortality in unaffected BRCA mutation carriers, the mortality/morbidity reduction benefit of combined mammography and breast MRI is less well established. Risk-reducing mastectomy significantly reduces breast cancer risk and disease and treatment morbidity but the mortality reduction is not as great as one would hope, especially as a woman gets older. And many healthy BRCA pathogenic variant carriers delay or decline mastectomy. At most, about half of unaffected BRCA pathogenic variant carriers undergo risk-reducing mastectomy.

Would the resources devoted to  saving lives through population BRCA screening justify a reduction in allocation of resources to other far more common health problems or disparities within cancer care itself, such as racial and economic differences in access to care, morbidity, and mortality? Of course, numbers are not the only deciding factor for resource allocation, which is ultimately an ethical decision that society arrives at in a somewhat unpredictable and disorganized fashion. On the other hand, those numbers cannot be ignored. Population BRCA screening may prove to be cost-effective but that does not necessarily mean it would be the best use of limited health care dollars and resources. It is not exactly a zero sum game, but no matter how you slice and dice it, all health care problems cannot be covered with even the most generous allocation of resources. Eliminating the hundreds of billions of wasted health care dollars in the US might start to address resource limitations, but, realistically, drastic reductions in unnecessary spending are not likely to happen any time in the near future nor is it guaranteed that the saved dollars would be reapportioned to other areas of health care. Which lives “deserve” to be saved and which diseases “deserve” to be prevented? Tragic choices, indeed.

Then too there is the problem of health insurance, or, more precisely, the lack of it. BRCA testing on a population scale would presumably lower the cost of genetic analysis to affordable levels and labs would likely absorb the costs of those who can’t pay (or at least would figure it into their pricing). However, it is in the follow up of mutation carriers where the annual costs start to pile up. Annual mammography and breast MRI, mastectomy, reconstructive surgery, and salpingo-oophorectomy would not likely be available to the ~14% of the US population who lack health insurance, with even higher rates of non-insurance among young women, the very population who theoretically would benefit the most from BRCA testing. Yes, the cost of treating those women for cancer is much greater than the cost of screening and risk-reducing surgery, but if the women do not have the financial wherewithal to pay for surgery and screening then those interventions just aren’t going to happen. Before we even think too hard about implementing population BRCA screening, the national health insurance crisis must first be addressed. BRCA screening could unintentionally result in further health disparities for low income women.

Even among women identified at high risk of developing breast cancer and who have health insurance, uptake of MRI screening is low even in facilities where MRI screening is available, with some demographic variability in uptake. Thus, innovative efforts are needed to improve outreach, education, and motivation to participate in semi-annual screening that would likely last for decades. In addition, if population BRCA screening becomes a reality, more MRI machines will need to be purchased, more radiologists will need training if they don’t routinely read breast MRI images, and more surgeons will be needed to perform mastectomy and reconstruction. A commitment to BRCA screening requires a lot more resources than just increasing the availability of genetic testing.

I admit that I am a professional worrier, and maybe all of my concerns are just another expression of my character flaws. No doubt many of the Good Readers of The DNA Exchange will have strong differences of opinion with me. I want to save lives and avoid cancer treatments just as much as the next person, and maybe even more so than many others after having spent two plus decades watching women and their families go through the nasty physical and existentially threatening experience of chemotherapy, disfiguring surgery, radiation therapy, and dying all too young. On the other hand, there are many more people suffering from other serious and potentially preventible health problems. Are they less worthy? Tragic choices are so…..tragic.

 

” And tell me how does God choose,

Whose prayers does he refuse?”

– Tom Waits, “The Day After Tomorrow”

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Vocab Rehab

Our word choices in speech and writing are often reflexive rather than reflective. Some words become so engrained into our vocabulary that we use them out of habit rather than after careful consideration. We think we are communicating clearly because everybody “knows” what a particular word means so we don’t pause to consider what the word might really mean or suggest. This can be particularly true of professional vocabulary, wherein we are inculcated with a set of specialized terms and word choices early in our training that are later reinforced throughout our careers by journal articles, books, and at educational meetings.

Even the rhythm and meter of spoken language can silently work their way into professional oral presentations. The next time you attend a multi-day conference pay attention to how the speakers at the end of the conference may unconsciously repeat the speech patterns of the speakers from the previous days. I first noticed this phenomenon about 10 years ago at an annual genetic counseling education conference during which a few speakers at the beginning of the conference frequently used a high-rising terminal (i.e., a rise in pitch at the end of a sentence). By the last day of the meeting it seemed like every speaker was raising their pitch at the end of too many sentences and it was starting to drive me crazy (I’ve since adapted). The “right” way to speak or write is the one that we encounter most often and most recently by respected members of our professional and social circles.

Reflexive vocabulary usage can sometimes mislead or confuse. Let me offer two examples of  vocabulary used by – but not unique to – the medical genetics community that in my view need some reconsidering and revision: whole exome/genome sequencing and gender neutral pronouns (for related discussions, see my prior postings about the words “psychosocial.” and “mutation“).

Whole Genome/Whole Exome Sequencing – These are inaccurate and misleading terms. The descriptor “whole” suggests that the entire genome or the entire exome is being sequenced. In fact, the analysis usually includes a lot of the genome or a lot of the exome – but not the entirety of either.  They don’t quite go the whole nine yards. The limits of some “whole” techniques and platforms become even more salient when you understand that they may not reliably detect some of the most common DNA-based disorders such as Down syndrome, fragile X syndrome, and alpha-thalassemia. I suggest that we drop the word “whole” and simply call it genome sequencing or exome sequencing, a practice I’ve already seen in some journal articles. But it should include a descriptor that indicates which technology was used to sequence the genome – short read, long read, optical mapping, etc. Each has its strengths and limitations and knowing which technique was used informs us as to which conditions are reliably or unreliably detected.

Incidentally, genome was coined (as genom) in 1920 by the German botanist Hans Winkler. Until the discovery that most DNA was non-coding, the word genome implied the sum of an organism’s genes. Now that we know that only a smidgen of an organism’s DNA are genes as we understand them today, the 20th century sense of genome does not align with the current sense of genome that refers to the entirety of an organism’s coding and non-coding DNA. Exome, on the other hand,  arose out of 21st century technology. The earliest article I could find in PubMed that used exome in it’s title or abstract was a 2008 publication about J. Craig Venter’s exome (Venter was the senior author).

Gender Neutral Pronouns and Verb Agreement – I wholeheartedly support the use of gender neutral or third gender pronouns in English, even if I think a few of them like zie, zir, and ver will not likely catch on. The vagaries of language evolution could ultimately prove me wrong but no matter how conscientious and respectful you try to be, these neologisms entail learning new words that have no clear etymology to guide the user or listener as to their meaning. However, pronouns such as “they” or “them” as a singular subjective or objective pronoun or “their” as a singular possessive pronoun have gained more linguistic traction. These pronouns have historical usage as a a singular form. Take the sentence I wonder who left their mobile phone on their seat in the auditorium? Whoever it is, they are not going to be happy when they realize it. “They” is a pronoun substitute for the singular “that person.” This sentence would have been perfectly clear and acceptable in just about all English dialects well before gender neutral pronouns became a subject of debate and discussion. Further, “they” and “them” do not have a linguistic history of denoting a specific gender.

My question, though, is not about which pronouns will survive the test of time but rather which verb form to use with that pronoun. Does it call for the plural or the singular verb form, as in “They are” or “They is?” I vote for “They is.”

I confess to being a bit of a fanatic about the arcana of grammar and syntax, but I am not a language tyrant. Language evolves so quickly that the “rules” desperately try to keep up with usage. Good writers instinctively know the rules and then go about flaunting and manipulating them. I am not trying to be snobbishly picky when I raise the question of pronoun/verb agreement. There are two important issues raised by verb choice in this situation, one of meaning and one of value judgment. “They is” clearly communicates the meaning of one, and only one, person rather than a group of people. The value judgment implied by using the singular verb  is implicit acceptance and acknowledgment of the person’s choice to not identify as being of male, female, or any gender. The slightly jarring effect of hearing a singular verb follow a typically plural pronoun makes “they” stand out in the sentence. It’s not just any old use of “they.” It’s a special case that reflects and honors the desires of that person.

Yeah, I know. “They is” just sounds plain wrong. But it only sounds wrong because we are used to having heard it another way for our entire lives. If the singular verb is used more frequently and consistently, the dissonance will fade. I remember the endless discussions about whether one should use a singular or plural verb with the word “data.” Now, it’s like Who Cares? “Date are” and “Data is” both now sound equally fine and either form is considered acceptable by most authoritative usage guides. Rule-obsessed grammarians can argue all they want; the rest of us just get on with our linguistic lives.

No doubt some of you will disagree with my suggestions. So I open up the discussion to the Good Readers. What do you think? And is there other vocabulary that needs reconsidering and discussion?

 

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Mind Games

As is the case with many topics in genetics, I learn the most in my time away from the office, researching questions for friends and family. And the genetics questions du jour are almost all related to pharmacogenomics (PGx) testing. More specifically, PGx testing for psychiatric medications. Maybe you are getting these questions too? For me, they usually go something like this:

Are these genetic tests that promise to tell you what

antidepressant medication will work best for you a real thing?

And if they are, why isn’t everybody taking them?

I have witnessed friends and family members struggle with medication management for depression, anxiety and mood disorders. People in these situations are often desperate for help and quite vulnerable. I can fully appreciate the hope that a simple genetic test could provide the answers to ease the journey. But as we find with many things in genetics, the reality is much more complicated than the hopeful answer we wish we could give. Ultimately, I know my position on this will disappoint many who are looking for that silver bullet. While there are a handful of applications for pharmacogenomics in specific situations related to psychiatric medications that have evidence to support their use, there is little evidence that multigene panels in this area lead to better outcomes. There is concern that harm may come because of the use of this unproven information to guide important decisions with prescribing and dosing of psychiatric meds. 

My conclusions regarding these tests are in part based on critiques from reputable sources on the current state of commercially available PGx psychiatric panels, including the American Psychiatry Association Workgroup for Novel Biomarkers and Treatments. This workgroup performed a detailed review of several commercially available tests and concluded that there is a lack of sufficient evidence to support the widespread clinical use of the proprietary combinatorial pharmacogenomic models used by these labs. There are many publications that highlight issues with existing studies about these tests including concerns related to conflict of interest and problematic study design. The financial sector is also following this topic closely given much has been invested based on the promise of these testing products being adopted broadly. Recognizing the strong commercial drivers at play here also causes me to view laboratory claims with a dose of skepticism. 

But when it comes to the general public, I think the commercial push to see these tests more broadly adopted is drowning out the voices of the experts who are urging caution. It seems that since many in the field of psychiatry aren’t convinced that these tests are ready for prime time, the labs have decided to bypass the most relevant specialty, and go straight for patients and primary care providers. Additionally healthcare payers are banking on the promise that these PGx tests will more than pay for themselves by allowing for better precision in prescribing of expensive medications. Payer support is helping to move psychiatric PGx testing to the mainstream.

New pharmacy-laboratory partnerships are emerging to promote these tests. Last year, PGx lab Genomind®  announced a partnership with Albertsons Sav-On, Jewel-Osco and Acme Sav-On pharmacies: pharmacists can discuss PGx testing with patients and, if the patient consents, the pharmacists will directly contact the prescribing provider to “suggest the Genecept® Assay. ” The  sample can be collected right in the pharmacy. Last month, Myriad Genetics, Inc. announced a similar program with Kroger Prescription Plans to promote GeneSight®  genetic tests in Kroger pharmacies. From the GeneSite® press release: “pharmacists at more than 2,300 Kroger stores will provide counselling about GeneSight® to eligible employer group members and facilitate testing with their prescribing healthcare professionals.”

Pharmacists are now direct marketing genetic testing to patients. And while members of the pathology and clinical laboratory space are taking some issue with this, there hasn’t been much public concern raised by the broader medical genetics community about this proposal to have pharmacists providing “genetic counseling” and facilitation of genetic testing.   

It will be interesting to see how these programs evolve with greater attention from regulators. With several years of push and pull between labs marketing these tests and clinicians raising concerns about their clinical utility and safety, the FDA has recently started to flex their regulatory muscles in this space. In Oct 2018, the agency published a Safety Communication, warning patients not to change management based on PGx results without first discussing with their healthcare provider and to be aware that claims made by genetic testing laboratories about PGx tests are not supported by sufficient clinical evidence. The FDA cautions healthcare providers in the use of these tests and directs providers to FDA-approved drug and genetic test labels. Lastly, the communication advised test manufacturers not to include specific drug information that is inconsistent with FDA-approved drug labeling. In April, the FDA sent a letter to Inova Health System with concern that the clinical validity of their PGx tests had not been established for the reported intended uses. Shortly after this letter was issued, Inova elected to cease offering their MediMap® tests. The FDA has been in communication with several other laboratories and stated that “most firms addressed the FDA’s concerns by removing specific medication names from their labeling, including promotional material and patient test reports.”

Some of the critiques I have heard about the FDA’s engagement in regulating these tests is centered around whether or not the FDA should be the authority on the evidence required to support the relationship between certain variants and drug metabolism. A frequently referenced pain point is the difference between the PGx genes/variants that make the cut per FDA drug labeling and the evidence grade rating per the Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network (CPIC). In looking at most of the commercially available PGx tests on the market today though, it is clear that many of the variant-drug connections included on lab reports are not consistent either with the FDA-approved list or with CPIC guidelines

For example, the sample GeneSight® report available online as of the day of this posting, under the category of “Mood Stabilizers” shows three drugs in the red bucket, “Significant Gene-Drug Interaction” and no drugs in the green, “Use As Directed” bucket. Top of the red list is lamotrigine (Lamictal®), which has a footnote that reads “Use of this drug may increase the risk of side effects.” The justification given in the Gene-Drug Interactions table is a variant in the UGT1A4 gene. Search of the CPIC database gives the UGT1A4 – lamotrigine pair a “D” level rating. According to the website, the CPIC D Level is defined as follows: “There are few published studies, clinical actions are unclear, little mechanistic basis, mostly weak evidence, or substantial conflicting data. No prescribing actions are recommended.” How might this report affect a person with bipolar who is struggling to find the right medication? One can imagine that it may be difficult for both the patient and the prescribing provider to feel comfortable with a treatment plan when not supported by this genetic test report.

For the same GeneSite® sample report, under the “Antidepressants” heading, there are a total of 22 antidepressents for which analysis is available, with only three in the “Use as Directed” green bucket. Top of that long list of 22 drugs in the red, “Significant Gene-Drug Interaction” bucket is bupropion (Wellbutrin®). Bupropion is a medication commonly used to treat depression and has been approved by the FDA for use since 1985 with a generic version of this drug readily available. There is no data in the CPIC database to support the assertion made my GeneSight® of a “Significant Gene-Drug Interaction” with bupropion. And interestingly, the only three antidepressant medications that made it to the green “Use as Directed” category are expensive drugs for which no generic version is available: levomilnacipran (Fetzima®), desvenlafaxine (Pristiq®), and vilazodone (Viibryd®). If I received this report and didn’t know better, I might assume that these drugs would be worth the high price tag if they are genetically the most likely to treat depression without the potential for side effects. There is no gene-drug information in CPIC about any of these three preferred medications, and I didn’t have to look very far beyond the GeneSight® report to see the long list of side effects and contraindications associated with each of these medications. But imagine the difficulty a prescribing provider might have in convincing a patient to consider forgoing the expensive new drugs in the green bucket to consider a more affordable medication with a longer history of success in treatment from the red bucket. Lab reports are not often looked at as one piece of the puzzle, but rather as the *truth* by patients. And as I have previously written on a different topic, it is incredibly difficult to convince a patient that an expert assessment may be more trustworthy than what is printed on a test report. 

Regulation of genetic testing is a big and thorny issue, and I don’t claim to have easy solutions for improving these challenges. But what I do hope to do is to begin a conversation with my fellow genetic counselors on what role we should have in the dissemination of information regarding PGx testing. I feel it is our professional obligation to understand, to the best of our abilities, the evidence or lack thereof when counseling our patients, consulting with other healthcare providers and discussing these tests with friends and family. When people first started asking me about these tests, my initial feeling was one of hope and optimism. Of course it would be wonderful if a simple genetic test could provide a clear path towards the best medication for those who are suffering. Now, after having spent hours down the rabbit hole to try to better understand the current state of this field, I remain hopeful that these tools may someday provide real benefit for the masses. Unfortunately, it seems to me that at the present time, this wild west of the competitive genetic testing marketplace has resulted in bigger but not necessarily better panels, including information that is often not evidenced-based. I worry that these reports could lead people down a wrong, and potentially dangerous path.

So for now when my loved ones ask me, “are these genetic tests that promise to tell you what antidepressant medication will work best for you a real thing?” I will give the more cautious and complicated answer. While this technology holds promise for the future, the evidence we have at this point does not support that these tests will help guide better care and lead to better outcomes for most people. And I will continue to do my best to support them on the journey forward, wherever the bumpy and winding road may lead.

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