The Top Ten Stories in Genetics, 2015: A Bacterial Editing System Goes Viral

Genetic modification was not invented in 2015. DNA was edited before CRISPR/Cas 9, just as books were printed before the Gutenberg Bible. Is it crazy to compare CRISPR to the printing press? Perhaps, time will tell. But the comparison does illustrate the enormous transformative power of technology made cheaper, faster and more efficient. It is hard to overstate the likely impact of CRISPR on medicine; it is already revolutionizing the development of new therapeutics from gene therapy to stem cell therapy to customized cell lines for drug development. Improvements to the technology and new applications for use have come so thick and fast that at times it seems like #crisprfacts, the hashtag invented to mock the CRISPR hype, can hardly keep up.

crispr facts 2

crisprfacts

crispr facts

Here’s mine…

Now is the winter of our discontent made glorious summer by CRISPR. #crisprfacts

Oh, yeah, and some other things happened too. Here’s the countdown:

  1. Roche Buys Billion Dollar Stake in Foundation Medicine

In January 2015, the Swiss pharmaceutical company Roche spent just over 1 billion dollars to obtain a majority stake in Foundation Medicine, a pioneer in cancer genomic testing. The deal not only symbolizes but may catalyze the mainstream role of genomics in cancer therapy, as tumor testing continues its rapid ascent from cameo performer to standard of care.

Foundation, which has yet to turn a profit, offers separate tests for solid tumors and blood-based malignancies. The tests offer sequencing of a large number of genes known to be implicated in cancer, but fall short of exome sequencing and examine only cancerous cells and not the germline comparison. Foundation reports are intended to help oncologists choose therapeutic options, including drugs and clinical trials. Roche’s involvement should increase marketing of the tests in the U.S. and abroad, and they likely hope that it will bolster research, such as identifying the markers of tumor DNA that could provide the basis for the highly anticipated ‘liquid biopsies’.

 

  1. Matchmaker Exchange Goes Live

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When you’re driving in traffic, other people are annoying. When you are in line at the supermarket, other people are annoying. But when you are trying to solve medical mysteries with a genetic test, other people are the answer.

Parenting a child with an undiagnosed genetic disease is a trip without guidebooks. Treatment is a series of guesses, prognosis is unknown. No one can warn you about what’s to come, or reassure you about what will pass. Genetic testing may reveal the apparent cause, but in cases where the variant has not been seen before it can only be confirmed by the second case. Patient networks built around genotype can improve treatment, clarify reproductive risk and provide emotional support.

Because clinically significant genetic changes are individually rare and collectively common, finding another person with the same gene variant or the same mutation in a tumor requires access to vast amounts of information and the means of searching it. Fortunately for us, we live in an age defined by the ability to access vast amounts of information and the means search it. But sharing genetic information on the internet has been complicated by rules designed to protect patient privacy and the hot mess that is our patient records system.

In September, a team led by Heidi Rehm announced the launch of the Matchmaker Exchange, a collaboration with multiple partners that provides secure sharing of patient information linking phenotype and genotype. Rehm described the new venture as “a reliable, scalable way to find matching cases and identify their genetic causes.” Congratulations to the field of genomics, and welcome to the Internet Age.

 

  1. Illumina Launches Helix, a Consumer Genomics Platform

Helix

In 2015, the consumer genomics industry is not so much an industry as it is a high tech field of dreams, a plowed-under cornfield in the cloud, waiting for the crowds to arrive. “They will come,” says the prophet in the James Earl Jones voiceover voice, “not even knowing for sure why they’re doing it. They’ll arrive at your door as innocent as children, longing for the future. They will pass over the money without even thinking about it; for it is money they have and peace they lack.”

But while back in Iowa poor Ray had to fight the bankers to keep his dream of a self-sustaining ghost baseball industry alive, capitalists are lining up to host the field of genomes. Both Google and Apple have cloud-based storage systems for DNA sequence data; Illumina’s proposal is unique in that you pay not for storage but for use. The company is betting that multiple third parties will develop consumer applications that require genomic information, smartphone apps that personalize your risk for side effects from pharmaceuticals or calculate the degree of relationship between you and your Tinder match. Helix holds onto your genomic digits the way Amazon holds onto your credit card information, making it easier for each new purchase to flow through them.

Illumina, the undisputed heavyweight champion of second generation sequencing, makes a forward-looking move here, tilling the soil in a hypothetical ecosystem. Two years ago, the ‘consumer genomics industry’ was a fancy synonym for 23andMe, one single tree that dominated the landscape. Ironically, the FDA pruning of 23andMe in 2013 that cut back their health and wellness business provided a little sunshine for smaller farmers, and in 2015 the first green leaves of a thousand consumer genomics products popped up out of the dirt, offering gene-based advice on the treatment of mental illness, on diets to suit your metabolic type, on the probability of cardiac events. These new shoots are individually weak – in many cases not rooted in the science, in others likely to be mown down by regulatory mechanisms not yet in place – but collectively they represent a widespread belief that there is money to be made in these fields.

 

  1. In Memento Moratorium

 “It is easier to stay out than to get out.”

                                                –Mark Twain

On April 18th, a group of Chinese scientists led by Junjio Huang published a paper in Protein and Cell describing their attempt to edit (but not implant) human embryos using the CRISPR/Cas 9 system. The goal was to alter the hemoglobin-B gene, which happened in 4 out of 54 embryos, although all 4 were mosaic – some cells were altered and others were not. This, the authors concluded, was not a success. Improving “fidelity and specificity,” they wrote, is a “prerequisite for any clinical applications of CRISPR/Cas 9-mediated editing.”

But failure or no, the publication ignited a firestorm of debate. On one thing the scientific community agreed: the experiment was evidence that the question of to edit or not to edit is in the offing. Improvements in the efficiency of gene editing are occurring so fast that the technology used in the study was itself a generation or so out of date before it made it into print. Can we do this? Not yet, say the authors of this paper. Should we do this? That is a much harder question, a question that launched a thousand editorials in 2015.

Early debates about what should or should not be allowed in DNA engineering did not focus on the human germline, but the consensus that evolved drew a line between somatic human uses for gene therapy, and changes that would affect eggs, sperm or embryos. Avoiding changes that would be passed down through generations confined any unintended effects to the individual, and sidestepped all the societal issues wrapped up in the concept of ‘designer babies.’ The moratorium that some scientists called for after word spread of the beta thal experiment is not new, and if heeded would reinstate a tacit agreement that had been in place since the 1970’s.

Oh, but it is easy to say you wouldn’t do something when you can’t. The Chinese paper resulted in an international summit on human gene editing in December, hosted by the National Academy of Sciences. The statement produced after 3 days of meetings endorsed somatic uses and germline research, but labeled any clinical use (i.e., use that could result in a baby with edited genes) irresponsible – for now. The note of caution may have obscured what is effectively a rejection of any hard and fast limitations. “As scientific knowledge advances and societal views evolve,” the organizers wrote, “the clinical use of germline editing should be revisited on a regular basis.”

 

  1. Sequenom Introduces a Non-Invasive Scan of the Genome

 Facts are stubborn, but statistics are more pliable.”

                                                            –Mark Twain

 In September 2015, Sequenom launched MaterniT Genome, an expanded version of its non-invasive prenatal screen designed to catch all microdeletions or duplications greater than or equal to 7 MB. This is simultaneously not that important at all and an illustration of everything we are dealing with now and a window into the future.

The new Sequenom test joins its stablemates VisiblitiT (tests for trisomies 21 and 18) and MaterniT Plus (tests for all the trisomies plus select, well-characterized microdeletion syndromes like Wolf-Hirschorn or Cri-du-chat).   All the tests report on fetal sex. Everybody reports on sex, and the most common form of informed consent for testing consists of an obstetrician asking the patient “do you want to do the test for gender?” (I can’t prove this but it’s true. Ask around.).

Of the three other U.S. purveyors of non-invasive testing, only Natera includes the option of a microdeletion panel. Although NIPT is the hottest selling thing in the universe, reaction to the microdeletion panels have been lukewarm, and here’s why: math. The Achilles heel of NIPT is positive predictive value, or the percent of the time that the test flags a pregnancy and is wrong. Even when a test is very accurate, the rarer the condition, the higher the percentage of false positives. Doctors and genetic counselors don’t like false positives because in real life a ‘false positive’ is a very frightened and very upset patient, and in real life some of these patients have ignored advice for follow up and terminated pregnancies that turned out to be unaffected (this sounds very extreme but remember that they are looking at a test labeled 99+% accurate, and under intense time pressure at just around the point when most people go public with a pregnancy).

Microdeletion syndromes are rarer than trisomies, so even as accuracy remains high, positive predictive value drops precipitously. Sequenom offers no estimates of PPV, and Natera’s own numbers suggest a PPV of just 5.3% for 22q11 deletion syndrome. In this context, the Sequenom genome-wide test seems like a curious step. Not only does it raise serious questions about PPV, but most of the deletions and duplications would be uncharacterized, meaning that counseling patients on the predicted effect of the change would be complex. None of this is exactly obvious in the Sequenom promotional material, which highlights 99.9% specificity and 92.9% sensitivity.

Why is a test likely to be used sparingly a top story for 2015? Because it has a ‘more information/less clarity’ aspect that is very 2015. Because it shows the quandaries into which we wander, when we take our limited 2015 knowledge into the realm of prenatal testing. And… because limited use may grow over time, as Sequenom no doubt knows, so that this may well be a first look at the prenatal testing of the future.

 

  1. Gene Expression? There’s a CRISPR for that.

crisperizer

When exactly did the reports on CRISPR start to sound like an infomercial? Maybe it was March of 2015, when scientists from Duke University led by Timothy Reddy and Charles Gersbach published an article describing their success using an adapted CRISPR/Cas 9 system to create a targeted increase in gene production.

CRISPR! It slices, it dices… No wait, there’s more…

In this case, the modified CRISPR program links a guide RNA that searches out the target DNA with a protein that catalyzes acetylation – so instead of gripping and snipping, your bonus CRISPR tool finds the appointed enhancer region and flips a switch, turning gene production on. And voila: “A programmable, CRISPR-Cas9-based acetyltransferase…leading to robust transcriptional activation of target genes from promoters and both proximal and distal enhancers.”

Clap on, clap off… the Clapper!ld0oalpb8u8le

Debates may yet rage about the nature of epigenetics and its intergenerational significance (hell, spellcheck still refuses to recognize it as a word) but no one argues about the importance of gene expression. Changes in gene expression are central to both development and stasis; altering gene expression provides a possible avenue of control of every process from learning to aging.

Amazing! And for far less than you might think! Does it come in red?

 

  1. A Prenatal Genetic Test Reveals Cancer in the Mom-to-Be

In the four years since non-invasive prenatal testing was introduced it has grown into a market worth over half a billion dollars annually in the US alone, with double digit growth projected for years to come. The number of invasive procedures has fallen off a cliff, with many women opting not to do amniocentesis or CVS after reassuring results on a non-invasive prenatal screen. But not everyone has been reassured. In March of this year, Virginia Hughes at Buzzfeed reported on the case of Eunice Lee, who learned she had cancer after the lab reported unusual results on her non-invasive screen.

This rare event – Sequenom suggested that one in 100,000 of their tests results pointed at a malignancy, with just over half of those subsequently confirmed – affects only the (thankfully) limited universe of pregnant women with cancer, but the story is more universally significant for at least two reasons.

The first is how it reflects the challenges surrounding non-invasive testing, the first major testing modality to roll out as an industry unto itself. Since it’s inception, this technology has developed in a highly competitive and market-oriented environment (one Sequenom executive lied about early test results and would have gone to jail if she hadn’t died first) and many people have suggested that their pre-market studies were inadequate and self-serving. The FDA has pointed to non-invasive testing as an example of why laboratory-developed tests need more regulation. All of this criticism has continued despite the fact that the tests are extremely popular and largely successful, and have decreased the need for more expensive and more dangerous invasive testing. Because it is so new and because the early studies were limited, these funky results are an anomaly that put the testing company into an awkward spot. Although they look like cancer, they can’t be officially reported as cancer, because there are no studies to validate that claim. Ignoring them, on the other hand, seems like an ethical breach to me, given that there is some evidence that suspicions are correct. Sequenom chose to call the test non-informative, but alert the physician to their hunch. Other companies have chosen to say nothing in similar circumstances.

The second take home point of this story is how close we are to a new type of cancer diagnostic, one that will be used both as a screen and a test for recurrence or the effectiveness of chemotherapy. If prenatal testing is any model (and it is) it will appear soon, all the companies involved will sue one another frequently, and we will all work out the bumps as we go along. One of these days we will all be surprised to read about someone concerned about cancer who discovered she was pregnant.

Eunice Lee and Benjamin

Eunice and Benjamin  Lee

Ms. Lee, by the way, was successfully treated for colon cancer with surgery alone, and gave birth to Benjamin, a healthy baby boy.

 

 

 

 

 

 

  1. Baby With Cancer Responds to Treatment Using Genetically Modified Cells

The headline for this segment should have been, First Clinical Use of CRISPR Technology Saves Baby With Cancer, except no part of that sentence is true. The gene modification technology used wasn’t CRISPR but Talens, an older approach that is more expensive, less flexible and more technically demanding. It wasn’t the first use of gene modification as a therapy, just the first that presents a promising path to widespread use. And let’s not jinx the baby, five months into remission, with an overconfident use of the word cured.

And yet, 18-month-old Layla Richards is home with her dad and mom (probably mum; they say mum in Britain) 6 months after doctors counseled the family to consider palliative care for acute lymphoblastic anemia. If there was a miracle involved, it was simply the miracle of being in the right time and the right place – Great Ormond Street Hospital in London, which had on hand modified T cells intended for use in a clinical trial for the French biotech company Cellectis, slated to begin in 2016. The Cellectis process involves knocking out a gene in donor T cells so that they cannot attack host tissues – a step that eliminates the need to use the patient’s own cells, a personalized approach that makes it slower and more expensive. Several companies that have been developing autologous approaches saw their stock prices fall in the wake of this announcement. In the case of baby Layla, doctors say they were unable to find enough T cells to extract for treatment.

Who did what first is a subject best left to the historians (and the patent lawyers). This story represents where we stand in 2015, on the cusp of therapeutic innovation built not on serendipity, the great innovative engine of the past, but on knowledge and engineering. We are entering an age of miracles that are not miracles at all, because we can both explain and reproduce them. And we are entering it fast, with technology out of date before the gun goes off, like thoroughbreds groomed and trained who show up at the starting gate to find themselves racing unicorns.

 

  1. First Analysis of Large Data Sets Suggests: When It Comes to Variant Classification, It’s Clinician Beware, At Least For Now

 “The trouble with the world is not that people know too little; it’s that they know so many things that just aren’t so.”

                                                                                                -Mark Twain

Anyone arrogant enough to believe we were equipped to interpret the human genome must have found the last few years humbling, poor foolish person. But most of us, veterans of the diagnostic odyssey and the variant of uncertain significance, were prepared to admit that it was early days. The collective need for more information has in recent years overcome proprietary and competitive instincts, and convinced many researchers and commercial laboratories to share their data. The top story for 2014 was ExAC, a Broad Institute initiative that has aggregated exome data from over 60,000 healthy adults.

Preliminary analysis of that data is in, with a couple of headlines. One – no surprise – there’s a lot we don’t know. As expected, mutations that result in a loss of function are constrained in genes associated with severe disease – in healthy individuals, you should see limited loss of function in genes where disruption causes a severe phenotype. We saw this purifying effect in many genes, and 79% of them are not yet associated with human disease. That’s the knowledge gap that we need to fill.

Headline number two: lots of things we thought we knew are wrong. The extent of this may qualify as a surprise, although careful observers will not be shocked. Plenty of evidence existed that existing databases and analyses were larded with inaccuracies. The database ClinGen reported in June that among the 12,895 unique variants with clinical interpretation from more than one source, 17% were interpreted differently by the submitters. The ACMG guidelines for variant interpretations published in March stressed that variant “analysis is, at present, imperfect, and the variant category reported does not imply 100% certainty.” Analysis of ExAC, a preliminary report suggests, shows that most individuals carry a rare and presumably deleterious variant in a gene associated with dominant disease. Beyond inaccurate classification, this may be evidence of incomplete penetrance, subclinical presentations, or simply the resilience of the genome. Take home point, as stated by Dan MacArthur et al, “The abundance of rare functional variation in many disease genes in ExAC is a reminder that such variants should not be assumed to be causal or highly penetrant with careful segregation or case-control analysis.

 

  1. The Power of Gene Drive

“The only difference between reality and fiction, is that fiction needs to be credible.”                                                                                                 –Mark Twain

Do you know that moment in the movie when the hero has to decide whether or not to commit some morally ambiguous act in order to save thousands of lives? Remember that? Well, forget about it. That make-believe drama cannot compare with the real life dilemma facing scientists, regulators — all of us, actually – in light of this year’s signature story, a CRISPR-mediated system that can rewrite the laws of evolution to propagate traits devised in the laboratory.

Gene drive is a term for a biological process that increases the probability that a given gene will be passed along to the next generation. In 2014, Kevin Esvelt and George Church at Harvard (et al) wrote a paper describing how CRISPR could be used to insert a tricked-out version of an edited gene that included the machinery to hack out the corresponding gene from the other parent and replace it with a copy of itself, complete with the gene drive complex. Introduce this zombie gene into any fast-replicating population and the allele frequency doubles with each new generation until there aren’t so many wildtype alleles left to convert.

Welcome to 2015, when a hypothetical is always just one grad student project away from reality. In November, Sharon Begley at STAT reported that success with fruit flies in the UC San Diego lab of Ethan Bier had led to a collaboration with UC Irvine’s Anthony James, who has developed an edited mosquito gene that destroys the parasite that causes malaria. Success could mean the most effective means of malarial control ever devised, and one that effectively spreads itself.

Herein lies the dilemma: this intervention is not so much introduced as unleashed. Although Church and Esvelt recently published a paper detailing strategies for containment and reversal of gene drives, concerns remain over the specter of unintended consequences. The Pentagon and the United Nations are reported to be concerned about the potential for weaponized insects. Scientists and ethicists have expressed alarm about the unknowns associated with any disruption of an evolved ecosystem. But the WHO reports that in 2015 there were 214 million cases of malaria and almost half a million deaths. So here’s the movie pitch: the mosquito is a terrorist killing 1500 children every day. You, the scientist, can reprogram the mosquito, with unknown impact on the entire planet. The developing and developed world can’t overcome their mutual distrust to make a plan. Do you release the zombie mosquito?

Buy it as a movie? No one would. It’s just too out there.

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Party Pooper?

The Annual Education Conference (AEC) of the National Society of Genetic Counselors offers a balanced mix of the academic, the clinical, the professional, and, perhaps most importantly, the social. Some of my most cherished professional relationships were formed at the AEC after I struck up a conversation with a genetic counselor who I had not previously known but who wound up sitting next to me in the audience, joined me on a panel presentation, came up and asked me a question after a talk I gave, or perhaps most commonly, unwinding at a bar after a marathon of lectures and workshops. Professional demeanors discarded, guard down, shoes off at day’s end, sipping an interesting beer or a fine single malt Scotch, you can easily become BGCCF (Best Genetic Counseling Comrades Forever). Sometimes I can’t remember a blessed thing I heard all day at the AEC but that post-plenary bar conversation often opened my mind to new and exciting ideas and warm companionship.

Capitalizing on the social networking aspect of the AEC, some corporate sponsors have taken to hosting evening parties and dinners. Maybe it is just my imagination, but the number of these soirees seem to have increased over the last few years. Free food, a generous open bar, genetic counselors eager to socialize and compare notes – what a great way to live it up on our meager travel budgets, freed from the worry of trying to justify several glasses of wine when you submit your receipts for reimbursement. So who can complain?

Well, me, for one.

Okay, so I admit to being an ethical stick in the mud who can suck all the fun out of the dance hall. But now that we have acknowledged yet another of my social failings, let me pose this question for discussion – Is it appropriate for genetic counselors to accept free fare provided by corporate sponsors at the AEC, particularly at non-educational activities?

Stick In The Mud Bobby

Stick In The Mud Bobby

To be clear – I am not taking the corporate sponsors to task. They are businesses, and doing business is what businesses do. With so many labs competing for our samples, they should and will do whatever ethical actions it takes to keep their genetic counselor customers happy. If we told them they would be more likely to get and keep our accounts if they donated that money to Action Against Hunger instead of catering to slightly hungry genetic counselors who want to party a little, I am sure they would do that (not to split hairs too finely, but, all else being equal, selecting a lab in part because it participates in what you consider to be ethical practices such as donating to charitable organizations based on the company’s ethos is different than using a lab because it donates money to feeding clinicians at a conference). The ethical burden is on us, not the sponsors, who are responding to a demand that we have – silently? – created and fostered.

I can already hear the complaints of “Oh Jeez, Bob, can’t you just let us have a good time? I mean it’s just a few drinks and some good food. I give that lab a lot of business. Why can’t I get an occasional treat out of it? So I am nibbling on shrimp atop a round of fried polenta topped with basil pesto while sipping a glass of Nebbiolo. Enough with your puritanical ethics already. Really, what harm is gonna’ result?”

Puritan Bobby

Puritan Bobby (not my real wife)

Perhaps none. But is a practice ethical until harm results? What would patients think if they knew that the very labs that were analyzing their specimens were also providing us with food and spirits? Maybe many of our patients would not care, and might even be slightly envious. But other patients might be surprised if they learned that the lab where you sent their specimens to be analyzed was also wining and dining you. Or what if one day a lab became embroiled in some financial funny business or God forbid a scandal from sub-standard laboratory practices and word leaked out that the lab was in the practice of courting counselors with culinary baksheesh? We would feel awfully awkward and might appear to be guilty by association.

One could legitimately ask whether an occasional gift of food and wine really affects our decisions about which labs we use. Probably many practitioners would deny it or suggest that it does not affect their decisions but may sometimes affect their colleagues’ choices (“I’m very ethical and would never let a glass of wine stand between me and my patients’ best interests. But maybe that is not so true for a few other genetic counselors.”). On the other hand, it is hard to believe that labs would spend valuable cash on activities that resulted in a loss of business. This stuff must be successful on some level or else they wouldn’t do it. TANSTAAFL. We may not be consciously aware of how these influences work. Vide Blind Spots. Which leads me to pose more uncomfortable questions – Should we include attending a corporate-sponsored after-hours bash in our conflict of interest statements when we publish articles or make professional presentations? Many hospitals and other employers of genetic counselors ban vendor sponsored lunches in our offices, so how is this any different? If the free food and drink is not directly connected to an educational activity, would this be a violation of the Stark Law on the part of the vendor, since  just about all labs receive Medicare and Medicaid reimbursement?

By the way, yes, you can call me Mr. Guilty. I have attended my share of these events, but, after a long discussion with my conscience (who I also met at the bar), over the last few years I have decided to avoid them.

But enough of my thoughts. This is about all of us, not just me. What do the Good Readers of The DNA Exchange think about this? Are there better ways to foster collegial and professional relationships with labs that are transparent and ethical, and that allow labs to maintain and grow their volumes? Complete the admittedly unscientific poll below and also share your thoughts in the Comments.

Voodoo Bobby Doll

Voodoo Bobby Doll

And please, be gentle with your Bob Resta voodoo dolls.

 

Thanks to Emily Singh for realizing the graphics and to Maureen Flynn for a thoughtful discussion that sparked and helped shape this posting.

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Masking The Truth?

A recent hereditary cancer multigene panel result got me to thinking again about the thorny problem of incidental findings in genetic testing. My goal here is not to criticize the lab, whose staff was very helpful and open in our discussions, but rather to encourage open debate about the scope of results that clinicians want from genetic testing and how this jibes with patients’ expectations. Our expectations might be quite different from what patients want, and this plays an important part at the end of this story.

My patient was recently diagnosed with breast cancer, and had a family history of breast cancer. One relative with breast cancer had already undergone BRCA testing, with normal results. The family history was non-specific but contained a hodge-podge of cancers that gets you to scratching your head – breast cancer, a primary brain cancer, a non-smoking relative who died before 50 of lung cancer, an aunt who died of some type of gynecologic cancer, and a few other malignant odds and ends. Given her relative’s normal BRCA results, we agreed that she would be best served by multigene panel testing, after a discussion of its potential downsides.

Like 87% of my patients, no cancer-linked pathogenic mutations were identified. However a pathogenic EPCAM point mutation caught me by surprise.

For those not familiar with the genetic architecture of Lynch syndrome, five genes are linked to Lynch syndrome – MLHL1, MSH2, PMS2, MSH6, and EPCAM. The underlying mutational basis is different for EPCAM than for the other 4 Lynch genes. EPCAM is MSH2’s upstream neighbor. Mutations in EPCAM itself do not directly cause Lynch syndrome. Instead, large gene deletions in the distal part of EPCAM result in loss of its poly A tail that should signal the end of the coding region. RNA transcription does not stop, leading to an EPCAM/MSH2 chimera of a transcript. By a mechanism not fully understood, this results in hypermethylation of the MSH2 promoter and absent/reduced expression of the  MSH2 gene product. EPCAM deletions constitute a small but significant minority of Lynch syndrome gene mutations and so labs routinely analyze EPCAM for large deletions.

EPCAM

So why was the lab reporting a point mutation in EPCAM? My first (insecure) reaction was “Well, I guess point mutations in EPCAM cause Lynch syndrome. Just another in the steady stream of new genetic findings that flew under my radar but that everybody else seems to know.” I breathed a small sigh of relief and a temporary break from my professional insecurity when further reading of the report confirmed my understanding that point mutations indeed do not produce Lynch syndrome.

Autosomal recessive EPCAM point mutations are linked to congenital tufting enteropathy (CTE), an uncommon disorder characterized by diarrhea so profound that patients often require ongoing total parenteral nutrition. Clearly my patient did not have CTE nor did any of her children, who were all well past the age when CTE would have manifested. The issue here, as any genetic counselor will tell you, is for the health of her grandchildren. Each of her children has a 50% chance of having inherited the EPCAM mutation. If a child has inherited the EPCAM point mutation and if the child’s spouse is also an EPCAM point mutation carrier, then my patient’s grandchildren from this mating would have a 25% chance of having CTE. Essentially my patient’s multigene panel test was transformed into a carrier screening test for a metabolic disorder for the next generation (The punster demon in me who I cannot control just remarked “Her grandchildren’s risk? Now that’s real NextGen sequencing! Or maybe NextNextGen.”).

Godfrey Hardy

Wilhelm Wienberg

Wilhelm Wienberg

But, statistically speaking at least, the patient should not worry too much about her grandchildren. The frequency of CTE is between 1/50,000 and 1/100,000, which hardyweinbergs out to a carrier rate of about 1/135. Thus, the likelihood that my patient would have a grandchild affected with CTE is 1/2 (the chance that her child would be a carrier) x 1/135 (the chance that her child’s spouse would be a carrier) x 1/4 (the chance that the grandchild would inherit two mutated EPCAM alleles) = 1/1080. Using the time-honored genetic counselor’s trick of reframing, there is a 99.9% chance that my patient’s grandchild will NOT be affected with CTE. Did my patient really need to know this in the midst of her cancer treatment?

I recognize that some patients undergoing multigene panels are still in their reproductive years and this information could be important to them. And one could argue that this situation is no different from other genes included on multigene panels that are also associated with different disorders when they occur recessively – NBN, BRCA2, ATM, fumarate hydratase. But I would counter that those other recessive disorders are qualitatively different situations. The same type of mutations that predispose towards cancer when they occur in the heterozygous state also predispose towards ataxia telangiectasia and the other recessive conditions and so one cannot avoid knowing that the patients carries the mutation. However, EPCAM point mutations are not linked to cancer and thus are not relevant to the reason why the test was performed to begin with. The lab included the EPCAM point mutation because of the nature of their testing platform, which can’t help but detect EPCAM point mutations.

But should the lab have masked the results? Labs mask all kinds of genetic test results, hence the list of incidental findings that the American College of Medical Genetics recommends be reported to patients undergoing whole exome/genome sequencing even if they were not seeking that specific information (CTE is not on that list, though of course this patient did not have whole exome/genome sequencing). From a counseling standpoint, it might be an undue burden on patients to layer on a whole other level of psychosocial concern when they come to us primarily concerned about their cancer risks or treatment options and are not even thinking about their descendants’ risks of having rare genetic diseases. Another downside to reporting EPCAM point mutations is that it increases the frequency of finding variants of uncertain significance (VUS), the problem child of multigene testing. As fate would have it, a few days later another patient’s test revealed an EPCAM VUS.

So after stewing on this and discussing it with colleagues, I was considering asking the lab to mask EPCAM point mutations in the future. But then I met with the patient to review the results. Not only was she not upset, she was excited and grateful about learning the information. She said that she underwent the testing to learn what risks her family faced, and as far as she was concerned, the CTE risk fit into her expectations even though I had never discussed it with her beforehand. Nor is she apparently an outlier. At this year’s ASHG conference, researchers from the Kaiser Permanente Northwest Center for Health Research discussed the results of an ongoing study in which 320 non-pregnant women have been randomized into two groups that underwent carrier testing. 200 women received usual care and 120 women underwent genome sequencing for 750 carrier conditions and ~100 secondary findings. Women in the genome sequencing arm were required to receive results about life-span limiting conditions but could elect to receive results of all or some of five broad categories of findings (serious outcomes, mild outcomes, unpredictable outcomes, adult onset diseases, and medically actionable secondary findings). To date, 90% of those in the intervention arm have elected to receive results in all categories. Patients can’t seem to get enough genetic testing.

Maybe this enthusiasm stems from the excitement and sexiness of undergoing genetic testing, which for most people is a new thing and so there is still lots of gene spirit. Or maybe patients just don’t know enough to not want extensive genetic testing and eventually reality will set in when enough people undergo genetic testing and patients may become more reluctant to learn tons of questionably useful information (although the experience of 23andMe suggests otherwise). Maybe that day will come. But for now, whether genetic counselors like it or not, many – though by no means all – patients want to know a lot about their genetic make-up and want a choice in what they can know, even if it is not of immediate clinical value. The clinical utility of a test does not necessarily equal its emotional utility.

Cost is no longer a factor; until recently, genetic testing would include the minimal number of genes because of the expenses involved. Nowadays, however, it essentially is no more expensive to run 5 genetic tests on a sample than 500 genetic tests. Patients and their families are the primary stakeholders so patient demand and expectations should be an important factor in determining the shape of genetic testing, though genetic counselors should offer guidance through our wisdom and experience.

We also need to include all concerned parties in this discussion, such as the disability community and other patient groups affected by genetic diseases. And we need to serve as a counter-balance to some of the “Rah-Rah Ain’t genetic testing grand” advertising of some genetic testing labs. This will require open minds, finely honed counseling skills, and the development of new educational resources that will help patients better understand the bewildering array of genetic diseases and the strengths and limitations of genetic testing. At the end of the day, genetic counseling is still primarily a psychological encounter between two human beings. Here is where the future of genetic counseling lies.

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1193 to 4

Prenatal diagnosis of Down syndrome has long presented an ethical dilemma for the genetic counseling profession. As genetic counselors are fond of saying , we strongly support women’s reproductive decisions, including both continuing and terminating pregnancies wherein a fetus has been diagnosed with Down syndrome or other condition. But also in the oath that genetic counselors swear to,* we claim to be strong supporters of the rights and dignity of people with disabilities. The disconnect between these ethical imperatives leaves genetic counselors open to justifiable criticism from people with disabilities, their families, and their advocates. How can we simultaneously support people with disabilities while at the same time participate in a screening program whose primary purpose is to sort out fetuses who have certain disabilities?

The typical response to this criticism is that patients have choices about whether or not to undergo prenatal screening for Down syndrome, and genetic counselors try to be value neutral in supporting patient choices (for the moment leaving aside the economic and social realities that limit women’s choices and that genetic counselors have no control over). One of the purported benefits of prenatal screening for Down syndrome is that it allows couples to prepare for the birth of a child who may have special needs. And as many of my patients’ obstetricians used to say to them, we can be better prepared medically for the baby’s birth. Seem like reasonable points, no?

Well, they do seem like reasonable counterpoints. But this got me thinking – just how much research has been done on the extent to which prenatal diagnosis enhances familial adaptation to a diagnosis of Down syndrome, and how much does it improve the medical and developmental picture for the newborn with Down syndrome? In short, I wanted to know how much benefit people with Down syndrome and their families gain from prenatal diagnosis.

To help answer this question, I performed a PubMed search using these broad terms: Down syndrome, prenatal diagnosis, prenatal screening. I set the parameters to English language articles with abstracts for the ten years prior to September 18, 2015. This produced 1373 articles, 176 of which I eliminated because they were not primarily about prenatal screening for Down syndrome, leaving 1197 articles. I then read the abstract of each article for evidence that the research addressed the benefit of prenatal screening to postnatal adaptation of families or improved medical outcomes for liveborn children with Down syndrome.

1193 articles addressed sensitivity, specificity, assessing test performance, comparison of screening techniques, patient anxiety, ethical critiques both pro and con, program implementation, patient education, economic/cost benefit analysis, circulating placental DNA, maternal serum biochemical analytes, ultrasound markers, psychological responses, termination rates, decision making, etc..

The number of articles that addressed my primary question? Four.

And even this number is a bit of a stretch. Two of the four articles were speculative pieces about how prenatal diagnosis may one day allow options for treatment. These two articles shared a primary author and one article was basically a slight update of the earlier article.

The other two articles reported on the experiences of women who received a prenatal versus a postnatal diagnosis of Down syndrome. One article reported that women had a difficult time with how the diagnosis was delivered whether it was prenatal or postnatal. The other article reported that a majority of women who received a prenatal diagnosis of Down syndrome and continued the pregnancy felt that they would undergo prenatal screening in future pregnancies for emotional preparation.

I recognize the shortcomings of my quick analysis. No doubt I missed a few articles. PubMed search results vary significantly with the search terms and parameters, and I swear sometimes with the phase of the moon (speaking of which, the upcoming eclipse of the Blood Moon/Harvest Moon September 27-28 should be spectacular, though it may affect PubMed searches that are conducted during the event). Abstracts may not accurately convey the research findings. And of course the search does not include articles published in languages other than English or that were published before September, 2005. So if you know of articles that I missed, please point them out in the Comments section below. Heck, do a PubMed search yourself and see what you come up with. Prove me wrong, please.

If we are going to honestly present prenatal screening as a choice, the choices have to be more than Abort or Carry To Term, unless of course we want to make the uncomfortable acknowledgement that the primary purpose of prenatal screening is to avoid the birth of children with Down syndrome. Pregnancy termination is important for many couples and we should support patients in their reproductive decisions whatever their motivations, but we also need to show a wider range of benefits from prenatal screening.

Ten years and not even a handful of published research about the benefits of prenatal screening for people who have the very condition that is being screened for. Come on, we can do better than this. Our patients deserve better. Shame on us.

 

* – Okay, I admit that I made up the oath part, but it is so ingrained into our core ethos when we are trained that it may as well be the genetic counseling equivalent of the Hippocratic oath.

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Ohio seeks to criminalize abortion based on a prenatal diagnosis of Down Syndrome. Can they do that? The answer may be more complicated than you think.

This fall, the Ohio State Legislature will vote on a bill that would make it illegal for a woman to get an abortion if she is terminating the pregnancy because her fetus has Down syndrome. If passed – and it is expected to pass – the bill must be signed by Governor John Kasich, who happens to be running for the Republican nomination for president. That should tell you everything you need to know about the chance of a veto.

Ohio is poised to join North Dakota as the second state to restrict abortion from being used to prevent the birth of a child based on a prenatal diagnosis. North Dakota’s law does not specify Down Syndrome, but makes it a crime to perform an abortion that is sought because of a “genetic anomaly.” You might think this restriction is unconstitutional under Roe v Wade — and you might be right about that – but as of today the North Dakota law remains on the books. Abortion rights advocates considered a challenge, but decided that the law was impossible to enforce, and therefore not worth the time and expense.

Beyond the Orwellian specter of a law that parses women’s motivation — and the perversity of allowing abortion only when a fetus is healthy – these laws demonstrate a deeper truth: anti-abortion activists have taken aim at prenatal diagnosis. Rick Santorum’s attack on amniocentesis in 2012 may have been badly articulated, but ideologically like-minded employers have embraced his call to cut off funds for prenatal testing. Genetic counselors may not feel that prenatal testing and abortion are two sides of the same coin, but it is important to understand that the rest of the world sees a clear and causative relationship between testing and termination.

Geneticists are not fortune tellers – a point we are forced to make frequently – and it is hard to predict what will happen in the courts BUT you have to assume these laws would not survive a legal challenge. If it stands it is hard to imagine a prosecution. How do you prove motivation?

Does that mean it doesn’t matter? A recent Bioethics Forum post noted that It seems odd to allow prenatal testing for Down syndrome – which the American College of Obstetricians and Gynecologists has recommended should be offered to all pregnant women – and then deny women the opportunity to decide what to do with the information.” This was meant as a criticism of the law, but there’s amore chilling implication. If you want to prevent abortions based on prenatal diagnosis, you can restrict the right to abortion OR you can restrict the right to prenatal diagnosis. One of these things is unconstitutional. What about the other?

There are objections you could raise. Free speech! Yes, but telling your patient about prenatal diagnosis isn’t going to help if her health plan refuses to pay for it. The sacred doctor-patient relationship! Yes, but remember that many states already have laws requiring doctors to read from a script to any woman seeking termination. In some states women seeking abortion are told, by law, that abortions are associated with breast cancer. Are you surprised to hear about this alarming association? That’s because it isn’t true.

If you believe that a fetus is exactly the same thing as a baby – and despite widespread uneasiness with abortion most people do not – then prenatal diagnosis is offensive. One typical and less confrontational approach to this attack is to talk about the value of prenatal diagnosis apart from termination. This feels like safer ground, but I would argue that it is short-sighted. Even if prenatal therapies improve, and there are some promising things in the works, testing will remain a vehicle for giving couples the option of termination, and when we deny that fact we look cagey and defensive. We open ourselves to the same charges of hypocrisy that we throw at anti-abortion advocates who cloak themselves in the language of the women’s rights movements. “We are just empowering women,” they say of mandated anti-abortion scripts. No, you are not. “We are fighting for women’s health,” they say, of regulations that put abortion providers out of business. No, you are not.

We need to be prepared to make the argument for what we do. Carefully and sensitively, but transparently, and without shame. We help families have healthy children and that’s a good thing and not a bad thing. We help people make the choices that are right for them. People in this field know that restrictions on prenatal diagnosis are not empowering. We know who they will end up hurting – the poor the young, the vulnerable – all the usual suspects. Prenatal diagnosis is not going away anytime soon. But keeping it available to everyone is going to take work and vigilance.

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@laurahercher

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Guest Post: Sometimes It’s Okay To Fail

by Lisa Demers and Stephanie Snow

Stephanie Snow, MS, CGC has 11 years of prenatal genetic counseling experience. She worked as a clinical site coordinator and genetic counselor for the FASTER study and as a clinical research coordinator for the NEXT study. Lisa Demers, MS, LGC has 12 years of prenatal genetic counseling experience and currently works with Ariosa Diagnostics as a Medical Science Liaison.

The landscape of prenatal screening is changing. The use of non-invasive prenatal testing (NIPT) in clinical practice is already common and is being adopted quickly by generalist obstetricians and maternal fetal medicine specialists. While the cell-free DNA technology is innovative and the impact on patient care is significant, there is a rising chatter about NIPT failures – the 1-8% (depending on the company) of reports that return without a test result. This is a dual issue – there’s the underlying “annoyance” that NIPT occasionally fails to produce a result, and then there are publications suggesting an association between fetal aneuploidy and test failure. The latter is a conversation for another day.

Although these “no call” results frustrate patients and their doctors, the negativity surrounding these failures is surprising. The concept of a test failing is not new in medicine, and certainly not within prenatal medicine. Increasing rates of maternal obesity are just one reason for limited prenatal surveillance, with one study demonstrating that 41% or less of fetal survey ultrasounds on patients with a BMI of 30 or higher were able to be completed on the first try. When it comes to first trimester measurement of nuchal translucency (NT), the FASTER trial noted an overall 7.5% failure rate, either because of an inability to measure or due to inaccurate measurement. In a review of patients within one clinic, where nearly 50% of patients had a BMI over 25 and 25% had a BMI of 30 or more, 4% of patients had an NT failure on the first attempt and of those who opted for a second attempt, 18% failed. Overall in this population, 2.7% of patients did not achieve a NT measurement.

This is not to say that test failures are necessarily bad. When an NIPT test fails, it is often because quality metrics are in place to ensure proper test performance – just as there are standards for NT measurement which are established by the Fetal Medicine Foundation (FMF) and the Nuchal Translucency Quality Review (NTQR) program. An NT may “fail” because a patient presents for screening outside of the appropriate gestational age requirements or because of suboptimal fetal positioning. The nuchal translucency measurement is critical in obtaining aneuploidy risk assessment when combined with serum biochemistry, and even the slightest over or under estimation dramatically impacts clinical care. Such is the case with NIPT quality metrics. These metrics are in place to ensure appropriate risk assessment for the pregnancy, with the most important of these being fetal fraction. Fetal fraction is greatly affected by maternal weight, with obese women less likely having the required minimum concentration of fetal DNA in circulation. Here again, maternal obesity reduces our ability to accurately assess the well-being of a fetus.

In reality, any test failure rate can be a nuisance to a busy clinic. Having patients return for an additional visit is inconvenient to patient and provider alike. However, there are biological and technical reasons for at least some NIPT tests to fail. The thoughtful provider will consider the various metrics involved with the NIPT options and select one that balances high quality metrics (including fetal fraction) and low rate of technical failures.

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I Am Curious (About Yellow)

Race is  a particularly salient issue in the current US national discourse. The horror of the shootings at the African Methodist Episcopal Church in Charleston, South Carolina and the controversy around the validity of the claims of an apparently white-skinned woman who identifies as black are but two contemporary examples of the controversial and often ugly history of racial classifications, the racial lexicon, and race relations. Perhaps this is why I was particularly struck by a sentence that I recently chanced upon in an article about the heritability of esophageal cancer: This meta-analysis showed there was a significantly [sic] association between PLCE1 rs2274223 polymorphism and esophageal cancer in yellow race populations [bold not in original]. 

Graphic by Emily Singh

Yellow Race. It has been a long time since I have seen that term in any medical or professional literature other than when I am rooting around in the history of eugenics. In our supposedly enlightened times such terminology is the same kind of bad as Brown Race and Red Race. I am not implying that this marks a resurgence in racism against Asians or a renaissance of racial hierarchies. Indeed, encountering yellow race in these articles was remarkable precisely because of its rarity nowadays.

The authors of the article have East Asian names, and the journal is published in Asia, so I assume that yellow race was not intended to be a racist slur or an ironic appropriation of a pejorative term by the very people it was meant to belittle. The racial vocabulary in this instance most likely stems from the nuanced and sometimes awkward complexities of language translation, cultural differences, and the regretful disappearance of copy editors from journal publishing houses (note the grammatical error in the quoted sentence from the abstract, using an adverb where an adjective is called for). A quick PubMed search yielded several other articles that used the term yellow race; the authors were invariably from countries where English is not the primary language. Not all articles were authored by East Asians; one had Brazilian authors. Several articles were from journals published in non-Asian countries, such as The Saudi Medical Journal,  Human Reproduction (Oxford) and Obesity Surgery, published by Springer, the mothership of the Journal of Genetic Counseling.

Putting aside the contentious debate about the biological reality of race and the appropriateness of using racial classifications in medical, biological and governmental analyses, I am intrigued by the question of why some race-based terms are socially acceptable and why others are condemned. You can use black or white when referring to race without too much eyebrow raising, but not yellow, red, or brown. Some skin color-based vocabulary has been replaced by apparently less offensive ethnic or geography-based but no less vague names like Hispanic or Asian. True, African-American and Western European are also common, but black and white appear at least as frequently in medical, biological, and popular publications. Even the federal government’s  Census Bureau and the annual National Vital Statistics Reports on annual births in the US use black and white to racially categorize mothers. Imagine the uproar if these official reports classified Asians as yellow, Native Americans as red, and Hispanics as brown.

US Census Bureau 2010 Racial Classifications

 

I have been stewing on this for a few weeks, trying to come up with an explanation. Does it stem from some complicated sociohistorical narrative about the forced immigration of slaves from Africa to the US, compared to the relatively more voluntary immigration to the US from other continents? Is it somehow related to the continuing social effects of slavery, which was not experienced by other immigrants (not to imply that other groups did not experience other forms of abuse and prejudice)? Greater social inequities among blacks in a society where whites are the power group and other groups are “in between” whites and blacks on the social hierarchy? An unstated and perhaps unconscious belief that the two groups are biologically different? The result of conflating race and ethnicity and lack of a clear distinction between race and ethnicity? The shortcomings and biases inherent in any scheme that tries to parse the continuous spectrum of humanity into discrete biological categories? The inconsistent ways that people self-identify their ancestry (see my posting about ancestry in the context of genetic counseling)?

Mostly, though, these sound like half-baked explanations. Perhaps it is just a stochastic linguistic persistence with no underlying rational explanation. Aluminum foil is still often called tin foil even though it hasn’t been made from tin since World War II (of course, aluminum – or aluminium, outside of the US and Canada – foil is less emotionally charged and socially complex than racial terminology).

Really, though, I don’t have a good answer. But I am interested to hear what the Good Readers of this blog have to say about it.

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