Tag Archives: prenatal testing

by | January 8, 2022 · 5:25 PM

The Questions We Should Really Be Asking After Reading the NY Times Article About Prenatal cfDNA Screening For Microdeletions

As the genetic counseling world knows all too well, the New York Times recently published a story about prenatal cfDNA screening for chromosomal microdeletion syndromes. The gist of the article is that screening for microdeletions has a high number of false positives that produce significant patient anxiety and, in a very small number of cases, patients have elected to terminate a pregnancy before confirmatory diagnostic testing. The Times piece generated 1100+ comments on its site, including many from genetic counselors and physicians, not to mention vitriolic sturm und drang on various social media.

Clearly the article touched a collective genetic counselor nerve — a lot of the reaction has been more reflexive than reflective. Which is kind of surprising, considering that cfDNA for microdeletions is a so-so screen for a handful of rare conditions that genetic counselors have not widely agreed should be included on these tests.

Most of the criticism centered on the article not always making a clear and consistent technical distinction between a screaming test, er, uh, I mean, a screening test (which cfNDA is) and a diagnostic test (which cfDNA is not). This confusion has been an ongoing problem since the early to mid-1980s when AFP screening for neural tube defects — and maternal anxiety over testing — was first working its way into clinical practice (I remember one of my patients back then referring to AFP as “alpha-fucking protein”). Forty years later, and the anxiety and misunderstanding has not improved much.

Some of those criticisms are fair, particularly when the article describes cfDNA results as being “wrong” or “inaccurate.” To the specialist, the term false positive has a very specific definition,* and hence the source of the reaction to the article. But from a semantics standpoint, doesn’t the word false in false positive imply wrong? You can also think of calling a result “wrong” as an example of the tried and true counseling strategy of reframing, i.e. “Well, Jane, your test result actually says that there is more than an 80-90% chance your baby does not have a microdeletion.”

In my opinion the article otherwise does a decent job of highlighting the statistical complexities of cfDNA. The accompanying Figures are helpful in explaining what is essentially the positive predictive value of the tests. In fact, I think the graphics are better than the explanations and graphics on many of the testing laboratories’ websites. Many of these websites are even guiltier of muddling the differences between screening and diagnostic tests, and labs really should know better. It’s no wonder that patients might be confused and anxious when they read that a test is “highly accurate,” “an alternative to amniocentesis or CVS,” and can be assured of a “healthy baby” when results are normal. To be fair, some of the websites also address the distinctions between screening tests and diagnostic tests, but only if you click down into the rabbit warren of information.

I think most of the criticism by genetic counselors glosses over more important and fundamental questions that should be the focus of critiques of prenatal testing and our reaction to the Times piece (here I am defining prenatal testing as including screening and diagnosis). These critical questions include:

• Should we test for any condition prenatally? This is an ethically and for some a religiously complex question but it underlies all of the subsequent questions.

• If there is broad agreement that prenatal testing should be available, then what is its purpose? Realistically, with a few exceptions, is there any purpose beyond selective termination? While termination is an important option and benefit of the test for some, it’s not a course of action that all parents will choose. Some parents might decide to have prenatal testing for “preparation” but as I have argued elsewhere there is minimal data saying one way or another whether prenatal knowledge of a condition helps babies or their families, medically, emotionally, or developmentally (thought at least one study is beginning to address this shortcoming). If patients are going to be put through the emotional ringer of prenatal testing, we should be able to provide solid data on whether prenatal knowledge of a condition provides benefits in addition to the option of termination.

• What criteria should be used in determining which conditions should be subject to prenatal testing? Even if every genetic condition could be detected prenatally (and we might actually get close to that point one day), it wouldn’t make sense to test for many of them. Clinically rational and ethically acceptable criteria need to be developed to guide the selection of conditions to consider for prenatal testing.

• Who decides which conditions are screen-worthy? As Ilana Löwy and others have noted, commercial labs often spearhead this choice but decisions are reinforced and supported by the medical and genetics communities that order the testing. If no one ordered a test, labs wouldn’t offer it. As Liza Minelli, Joel Grey, and Scarface remind us, money makes the world go around. Are we screening for some conditions primarily because we can screen for them and labs offer it? What about input from patients, the public, multiple medical specialties, ethicists, social scientists, people with disabilities, and others?

• Is widespread screening for rare conditions the best use of laboratory and genetic counseling resources? Follow up of screen positive results consumes a significant amount of genetic counselor time and energy, to say nothing of patients’ anxiety and health care costs. Should these resources be focused on more pressing conditions?

• Many jobs in the genetics sector — labs and clinical providers — are dependent on the existence of genetic testing. Labs make their living off of testing but so do many genetic counselors working in clinics. While genetic counselors are not trying to push testing on patients, many genetic counseling jobs depend on the availability of genetic testing, either helping patients decide whether to have a test or explaining results to them once the testing has been completed. For better and worse, the genetic counseling profession has intimately identified itself with genetic testing. Clinics would employ far fewer prenatal, cancer, cardiogenetics, and other specialty genetic counseling jobs if there were not so many genetic tests. Think about how many clinical positions would evaporate if prenatal testing — or, really, almost any genetic testing — disappeared tomorrow. Some jobs would remain, for sure. But the demand for genetic counseling would likely drop off significantly if fewer tests were available. How much does this conflict of interest influence genetic counselors’ attitudes toward, and willingness to adopt, genetic tests, and how much does it subtly and subconsciously influence some of the strong reaction to the Times article?

• First and foremost, a patient’s decision to undergo — or not — prenatal testing should be preceded by a soul-searching exploration with partners and care providers about what parents want out of their children and addressing parental fears of disability, along with ethical and spiritual reflection. The decision requires more emotional expertise than numerical expertise. Should we be offering tests to all pregnant women that require them to master abstruse statistical knowledge in order to decide about whether to pursue testing? Even in a (unrealistic) world where all pregnant patients meet with a genetic counselor prior to testing and everything was explained in excruciating detail, many patients will misinterpret, forget, and misunderstand most of the technical information about false positives, false negatives, and distinctions between diagnostic tests and screening tests. What is the best way for patients to make medically and emotionally informed decisions? Laboratory website are less than ideal sources of information. Websites are essentially marketing tools, and marketing is antithetical to nondirectiveness. Chatbots alone don’t cut it for this purpose, although they could have an ancillary role.

• What message does it send to people with disabilities, their families, and their advocates if we continually add, seemingly willy-nilly, more and more genetic conditions to the prenatal testing list, especially, as I noted above, if they obtain no tangible benefit from testing? More testing readily begets further routinization of testing. And when you start testing lots of pregnancies for lots of conditions, you start creeping further into eugenic territory.

There are no easy solutions to any of these questions. Some may very well prove to be unanswerable and some parties will remain dissatisfied if we do manage to come up with some answers. It will involve vigorous and at times contentious debates among multiple viewpoints, and lots of people convinced that they are so damned right and why the hell can’t everybody else see that? But that doesn’t mean we shouldn’t be taking on the challenge. We may wind up with less than perfect answers, but they will be better than what we are doing now. The practice of genetic counseling demands it and patients deserve no less.

__________________________________________________________________

*- Another source of confusion here is the distinction between the false positive rate and a false positive result. The false positive rate is the number of pregnancies that do not have a condition but test positive. Thus, a lab can accurately claim that cfDNA for microdeletions has a false positive rate below 1%. You can see why a patient with a positive result might misinterpret that to mean there is over a 99% chance that her baby does indeed have a microdeletion. On the other hand, a false positive result is one specific patient’s test result which incorrectly indicates that a condition is present. Thus a patient who has a positive microdeletion result has an 80-90% chance that her baby does not have a microdeletion. Lord have mercy! You can see why pregnant patients might be confused. Then try to sort through all that while experiencing the joys of hyperemesis, or if you are a non-English speaking immigrant from a village in Central America working through an interpreter, or if you are also trying to figure out at about the same time the meaning of your rubella result, your HIV status, your nuchal thickness scan, and the results of your carrier testing.

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by | November 16, 2017 · 9:13 AM

The Routinization of Prenatal Testing and the Erosion of Patient Autonomy

As a long time admirer, reader and guest blogger, I am thrilled to have been invited to write as a regular contributor for the DNA Exchange.  Some recent statements about prenatal testing in the news brought to mind my very first guest post on the DNA Exchange, Information Detoxification, published 5 years ago.  So I am going to start this new chapter by going back where I began as a guest blogger, on the topic of the risks of routinizing prenatal genetic testing.

 

Last week, a genetic testing lab released a statement about their intention to use recent investments “with an eye toward making expanded carrier screening as routine as taking folic acid, noninvasive prenatal screening as routine as an ultrasound, and hereditary cancer screening as well-known as a pap smear.”  While this vision is quite positive for the lab’s investors, it is concerning for the future of reproductive autonomy. The underlying goal that all pregnant women should have prenatal testing is not unique to this lab.  In fact, there is increasing pressure towards expanding the use of these tests by many labs, likely representing the intense competition in the genetic testing business right now, driving the need to increase test uptake to the largest possible market.

 

I have mixed feelings about population screening for hereditary cancer, but the implications are completely different when considering prenatal carrier and cfDNA screening.  Although prenatal testing is important to many, it is crucial that women and their partners be given the opportunity to make autonomous and informed decisions about whether or not to take these tests.  The routinization of prenatal testing is problematic for several reasons: from a social and public policy standpoint, in regards to healthcare economics, and also for individual patient care.

 

Social and Public Policy

Advocating for reproductive autonomy and informed decisions around prenatal genetic tests was one of the first guiding principles of the genetic counseling profession.  This is in part due to the fact that the start of the master’s degree trained genetic counselor coincided with social movements in women’s reproductive rights and also the emergence of the field of bioethics.

The prioritization of patient autonomy in reproductive genetics also arose from the rejection of eugenic ideology and practices that were common in the early part of the 20th century which sought to encourage reproductive of the fittest and to discourage (sometimes forcibly) reproduction among those deemed as defective or unfit.

This history supports concerns that the routinization of prenatal testing may effectively stigmatize those who have an increased chance to have a child with a genetic condition, thereby limiting reproductive freedom.  This is especially troubling in the context of the current political and social climate with so many expressing racist, xenophobic, and ableist views, as well as increasing threats to health care security and social services.

 

Healthcare Costs

Issues regarding the cost of prenatal testing are complex and studies regarding the economic impact of expanding prenatal screening are needed.  Such data analysis is complicated by the variability and a lack of transparency in the costs of these tests.  While labs vary in their pricing, patients report receiving explanation of benefits representing that the amount billed to their insurance was many thousands of dollars –  amounts that likely exceed the entire cost of the prenatal care in some cases.  

Without peeling back all of the layers on this topic, there is one clear explanation for why routinization of prenatal testing does not make good financial sense.   Given that the purpose of prenatal genetic testing is to inform personal reproductive decisions, in order for these tests to be of value, they must first be desired by the fully informed patient.  No matter the price of a prenatal genetic test, it is a needless healthcare cost if the patient does not want it.  

 

Patient Care

Should all patients be routinely counseled about their options for prenatal genetic testing?  Absolutely.  Practice guidelines for prenatal genetic testing support offering these tests to all women in the context of counseling that supports informed and value-consistent decisions.  But this conflicts with the model that the testing labs seem to be promoting, which is to test everyone first and provide the information in follow-up, after testing has already been done.  This undermines patient autonomy and can cause harm.

 

When an individual would use results to facilitate reproductive decisions, testing can be empowering. What is often overlooked in our well-intentioned goals to provide patients with knowledge however, is the potential harm and disempowerment that may result when testing information is not desired.  Patients deserve the opportunity to make a choice about whether the information these tests provide is something they want to know or not.
It is imperative of genetic counselors to resist any suggestion that reproductive genetic testing should be routine.  I hope that all of us, whether working in the clinic or the lab, will continue to advocate for reproductive autonomy for our patients and hold firm in the goal that all patients should have the opportunity to make informed choices regarding prenatal genetic tests prior to testing.   How we move forward with this challenge in both practice and policy is a defining question for our profession.

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by | November 21, 2016 · 8:23 AM

Summing Up the Consequences of Election 2016: 3 Things That Could Change the Practice of Genetic Counseling

It’s been two weeks, and everyone is sick of hot takes on Life in Trump’s America and What Is the Worst Thing That Could Happen? (um, I’m going with nuclear war, but take your pick). I know, I’m sick of it too. But elections have consequences, and, like climate scientists and immigration lawyers, we need to put some thought into what this could mean for our field.

 

The potential repeal of the Affordable Care Act is a concern for everyone working in health care, as is the threatened dismantling of Medicare. Possibly, critics of the ACA will discover that it is easier to campaign than to govern, and that voting to take away health care from tens of millions of people isn’t as much fun as it was in the good old days when they had the safety net of a presidential veto. But hey I’ve always been a Pollyanna. Too cheerful, that’s me.

 

Point one: prepare to practice in a climate where there is more inequality of access.

 

Chances are, prenatal genetics will be affected by an empowered and emboldened anti-abortion movement.   A president has some limited ability to make access to abortion more difficult through executive orders – President Bush signed regulations that gave everyone in the hospital, including orderlies and cleaning staff, the right to decline to do their job in cases involving abortion – but the main issue is the Supreme Court, where as president Trump will get an opportunity to redefine the balance of right and left if and when any of the reliable supporters of reproductive rights leaves the bench. Ruth Bader Ginsburg turns 84 on March 15th and I know millions of people join me in wishing her a happy birthday and many, many happy returns. The Court’s other octagenarian, Anthony Kennedy, has been behind decisions that chipped away at abortion rights, but has also declined several opportunities to overturn Roe v Wade, and anyone replacing him would almost certainly be more explicitly anti-abortion.

 

When asked last week on Sixty Minutes what would happen if Roe v Wade were overturned, Trump said that control of abortion law would then revert to the states, and that women who wanted an abortion might have to “go to another state.” This is correct (shocking but true) and you can make your own determination about the relative impact that would have on affluent and educated women  versus poor women, and teenagers, and other vulnerable parties.

 

The more complicated truth is that Roe v Wade is not going to disappear overnight, although there is a real and important long term threat. Should further changes create a Supreme Court majority ideologically opposed to abortion, they will have to wait until an appropriate case arises to make any changes. State lawmakers would no doubt be happy to present them with a test case, but making laws takes time, and then there are challenges and lower court decisions and demonstrations and pundits talking on the news before SCOTUS makes an actual decision. Even then, there is the hope that one or another of the anti-abortion faction hesitates to overturn 40+ years of precedent (See? You thought I was joking when I said I was an optimist).

 

A recent Supreme Court decision disallowing TRAP laws (targeted restriction of abortion providers) will stand, and so does the coalition that voided them, at least for now. For the moment, this should limit the chronic deterioration of access to abortion in Southern and Midwestern states that we have seen over the past decade. I believe it remains important to monitor changes that adversely affect our patients’ ability to obtain an abortion related to genetic findings, including decreased coverage, increased cost, logistical obstacles and changes that necessitate travel.

 

Point two: be vigilant about the threat to reproductive rights, but don’t expect dramatic changes in the near term.

 

Here’s something we don’t talk about enough: there is evidence to suggest that prenatal testing itself is likely to be a target of the anti-abortion movement. In fact, it already is. The National Conference of Catholic Bishops issued a directive in 2009 that forbids prenatal diagnosis “if undertaken with the intention of aborting an unborn child with a serious defect.” This decree limits the use of prenatal testing in some Catholic hospitals, a growing segment that includes one in six hospital beds in the country today. Many Catholic institutions including schools and hospitals refuse to pay for insurance plans that cover prenatal testing, restricting availability for all their employees, regardless of their own beliefs.  Other employers with an anti-abortion agenda could do the same thing.

 

More evidence that prenatal testing is on the radar screen of the anti-abortion movement: state laws have been advocated, and in two instances passed, that specifically forbid women from seeking a termination for reasons of genetic defect. These laws don’t get a lot of ink because they are a) unconstitutional (under Roe) and b) virtually impossible to enforce, since they require a prosecutor to prove motivation. This doesn’t mean they are not important. They were written by people whose agenda it is to limit abortion by any means, but they were chosen as a vehicle because they tap into a larger uneasiness about prenatal diagnosis.

 

The laws may not be enforceable, but they are chilling. Abortion is already medicine’s stepchild. Why would doctors or hospital administrators be eager to offer a procedure where they have to think twice about whether or not they could get in legal trouble? And the laws show an intent that could be more fully realized through other means. You may not be able to prove a woman’s intent in seeking an abortion, but you can certainly document a counselor’s intent if he or she offers the option of termination after a prenatal diagnosis. Will we see attempts to limit what can say to our patients? If this seems impossible to you, consider that 35 states currently have script laws detailing what a woman must be told before she can have an abortion, and a number of those require providers to give inaccurate and misleading information. In 6 states, women must be ‘informed’ that personhood begins at conception. In 5 states, women must be ‘informed’ that there is a link between abortion and breast cancer. If they can require us to lie to patients, don’t rule out the possibility that they can forbid us to speak.

 

Advances in prenatal testing are revolutionary.   NIPS is the fastest growing medical test in the history of medical tests. We will continue to see changes that widen the scope of what we can diagnose prenatally and improve our ability to predict outcomes more accurately, and at an earlier phase in pregnancy.  This is going to reduce the incidence of a whole range of genetic conditions — for those who use the  test. But improvements in prenatal diagnosis don’t improve access; in fact, improvements in prenatal diagnosis are fueling the debate over what types of prenatal testing are acceptable. If the courts and the politicians and the public don’t accept the idea that pregnant women have a right to prenatal testing as a part of normal prenatal care, then laws and limits to insurance reimbursement may put it out of reach of many Americans.

 

If prenatal testing is only available people who have enough money, or the right education, or live in certain parts of the country, it is not just unfair to individuals but fundamentally changes the societal impact of offering the tests. The necessary consequence of offering prenatal diagnosis and the option to choose only to some people, is that the birth of a child with a genetic defect or disease will gradually change from being something that can happen to anyone to something that only happens to ‘some people’. Don’t we already see this happening to some extent with Down syndrome? People are right to think hard about the potential consequences of prenatal diagnosis, but restricting prenatal testing so that access is unequal doesn’t limit the harm, it multiplies the harm.

 

Point three: we need to make the case that genetic testing is a part of good prenatal care and that every pregnant woman has a right to it, if she chooses.

 

There are other issues to consider but these three jump out at me as points of concern for genetic counseling practice as we move forward with a new administration. What can we do?  Hope for the best. Make our own spaces – schools, clinics, workplaces – into welcoming and inclusive environments for those who don’t feel safe in the current climate. Be vigilant, and bring changes that affect patient care to public attention. Talk to other counselors. Talk to me; I would love to hear your take and your stories.

 

 

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by | September 1, 2015 · 2:34 PM

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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by | July 11, 2013 · 10:27 PM

Guest Post: NIPS Is Not Diagnostic – Convincing Our Patients And Convincing Ourselves

By Katie Stoll, MS

Katie Stoll is a genetic counselor in Washington State. She graduated from the Brandeis University training program in 2003 and since that time has held positions in the areas of prenatal, pediatric and cancer genetics.

A couple of years ago we were just beginning to learn about a new prenatal testing technology termed Noninvasive Prenatal Diagnosis. It was soon relabeled as Noninvasive Prenatal Testing, and now the American College of Medical Genetics and Genomics recommends this be taken one step further by terming it Noninvasive Prenatal Screening (NIPS) to highlight the limitations of this new technology.

As currently reported by labs, NIPS presents new challenges for genetic counselors. Of particular importance is figuring out how to convey to patients and healthcare providers why relying on sensitivity and specificity alone may lead to misinterpreted results. In the absence of positive and negative predictive values there may be a tendency to assume that the high sensitivity and specificity reported with NIPS means that these tests are more powerful – more diagnostic – than they actually are.  

It is imperative that we understand both what the terms mean and how they relate to a person’s likelihood of having a condition.   Sensitivity measures the true positive rate – the proportion of actual positives which are correctly identified as such (e.g., the percentage of fetuses with Down syndrome (DS) who have a positive test result). Specificity measures the true negative rate – the proportion of actual negatives which are correctly identified as such (e.g., the percentage of fetuses who do not have Down syndrome who have a negative NIPS result for DS).

A test can have both a high sensitivity and specificity without being a good predictor of whether the condition is actually present. The likelihood that a positive test is a true positive result also depends on the incidence of the condition.

Sensitivity Graph

Genetic counselors are used to thinking about aneuploidy screening in terms of PPV, as this is generally the format for reporting maternal analyte screening such as Integrated , Quad screens, etc. Analyte screening takes into account the prior probability based on maternal age and provides a PPV as the end result. For instance, an analyte screen result may be reported as Positive with a 1 in 50 chance of Down syndrome. The PPV with analyte screening lets us know how many patients with a “positive” test will actually have a pregnancy affected with the condition and reporting results this way makes it clear that this is a screening test.

Can we apply the same interpretation to NIPS results?  Some labs provide a “risk score” which appears similar to what we see with analyte screening, but I am told by the labs that the vast majority will be reported as either >99% chance or <.01% chance.  Some labs do not report a risk score, instead giving essentially a positive or negative result. But does this mean that greater than 99% of women who receive a >99% or a positive result are actually carrying a fetus with Down syndrome or other chromosome condition?

Given that women 35 year and older are a population targeted for NIPS let me work out the expected NIPS results given the approximate sensitivities and specificities reported for a hypothetical population of 100,000 thirty-five-year old women (while I cannot tell you the specific number of women age 35 who give birth per year, CDC data suggests that for the past several years about 400,000 – 500,000 women in the age 35-39 have given birth each year in the United States – so 100,00 births annually by 35-year-old mothers is probably in the ball park of the national trend.

The performance data vary significantly from lab to lab – for the purpose of this illustration, I am using sensitivity and specificity in the range of what has been reported.  The data below are based on the chance of Trisomy 21, 18 and 13 at the time of amniocentesis for a woman 35 at time of EDD1.

Down Syndrome

Trisomy 18

Trisomy 13
Incidence

1/250

1 / 2000

1 / 5000
Affected Fetuses

400

50

20
Sensitivity

99.5%

98.0%

90.0%
Specificity

99.9%

99.6%

99.8%
Total test positives

498

449

218
True test positives

398

49

18
False positives

100

400

200
Positive Predictive Value

80%

11%

8%

If we add all of the positive results together in a population of 100,000 thirty-five-year old women we see that 1165 (1.2%) have positive test results for Trisomy 21, Trisomy 18 or Trisomy 13.  Note, though, that only 465 of these results will be true positives. This indicates that the majority of the time (greater than 60% using these statistics), a positive result on NIPS for a 35-year-old woman will be a false positive – and this doesn’t even include calculations for sex chromosome aneuploidy which some NIPS labs also screen for.

Notably, the negative predictive value for NIPS is very high indicating that a negative test result is a true negative >99% of the time. But how do we reconcile that for many women, the chance of a false positive with NIPS may be higher than the chance of a true positive result when that seems to be contradicted by way the labs are reporting the results? 

In trying to explain the chance of a false positive result to patients with a “positive” test report in hand, I have found that I am met with disbelief. I can understand why – if a test says there is a>99% chance of Down syndrome and the lab says the test has >99% sensitivity and >99% specificity, how could this test be wrong?

While genetic counselors understand the limitations, the reporting practices of the labs place us in a position in which we have to work hard to convince our patients that NIPS is only a screening test.

Currently four labs offer NIPS in the U.S. and all have different strengths and weaknesses in their reporting practices. All could be improved by making the limitations of this technology more obvious.  In some cases the language used in the reports gives the appearance that NIPS is diagnostic. For example, one company’s report suggests that the healthcare provider should advise for “additional diagnostic testing”.  The labs vary in whether the need for genetic counseling following a positive result is recommended.  Additionally there is variability in the transparency of how the performance data are derived.

Given that the performance statistics vary significantly, we need to be sure to take these details into account when considering PPV. I  encourage genetic counselors and other healthcare providers to critically look at how the performance data are derived.  The sample sizes on which these numbers are based are often quite small and the confidence intervals can be broad.  I was surprised to see in the fine print of one report that the performance data “excludes cases with evidence of fetal and/or placental mosaicism.” Given that mosaicism is a known cause of false positive results and because mosaicism cannot be definitively determined through NIPS, it doesn’t seem accurate that these cases should be excluded from calculations of test performance.

The pitfalls of interpreting NIPS results is a challenge we need to address because NIPS is increasingly taking place without the involvement of genetic counselors in pretest or post-test counseling. There is real concern that patients are making pregnancy decisions based on screening tests with the misunderstanding that NIPS is diagnostic. 

I write this as call to the NIPS labs to change their reporting practices to better emphasize the screening nature of this technology. Providing some positive predictive value estimates would be tremendously helpful as we try to make sense of NIPS results for our patients. While it may be difficult to provide individualized risk assessment, a general table of how prior probability impacts individual test performance would be beneficial for interpretation. Furthermore, eliminating language from the reports that suggests these tests are diagnostic and giving more transparency to ways in which performance data are calculated would also be welcome changes.

As genetic counselors, we strive to ensure informed decision-making for the clients we see. Key to informed decision-making is an understanding of the limitations of this evolving technology. As fellow patient advocates, I hope the genetic counseling community will join me in requesting increased accountability and responsible reporting on the part of the labs regarding NIPS.

I would like to acknowledge Evan Stoll, retired GAO data analyst for his contributions to this piece.

Please Note: Authors who contribute to The DNA Exchange cannot offer medical advice. Many commenters have raised interesting and thoughtful questions about NIPS. If you have undergone NIPS and have questions, you should meet with a certified genetic counselor. To locate a genetic counselor, go to the  Find A Genetic Counselor section of  the website of  The National Society of Genetic Counselors.

  1. Hook EB. Prevalence, risks and recurrence. In: Brock DJH, Rodeck CH, Ferguson-Smith MA, editors. Prenatal Diagnosis and Screening. Edinburgh: Churchill Livingston, 1992.

 

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by | March 13, 2013 · 10:54 PM

VARIATIONS IN A MINOR KEY: SOME THOUGHTS ON PRENATAL TESTING IN AN ERA OF WHOLE GENOME SEQUENCING

James Watson is many things – geneticist, Nobel laureate, agent provocateur – but in the realm of psychiatry he is first and foremost the parent of a son with schizophrenia.  So when he spoke in 2007 at the World Congress of Psychiatric Genetics, it was as a family member, albeit a family member with an unusually good grasp of the science.  And it was as a family member that he exhorted the scientists in the audience to keep up the good work, so that “someday we could identify those individuals destined to suffer from mental illness in utero, and weed them out.”

How often do you hear an audible gasp in the midst of a plenary talk?  The dismay and the indignation were palpable.  Researchers throughout the day interrupted their talks on GWAS to express in the strongest possible language that the goal of their work was to understand the pathophysiology of the disease and perhaps to aid in diagnosis – not to provide pre-symptomatic risk  assessment and not – no, never – not to be used prenatally.

“But if this is what families want,” I asked one speaker later that day.  “How do you propose to restrict testing, once the means to test is available?”

“They can’t,” he replied.  “They must not.”

Ah.  Of course.  They must not – I will pass that along.

Five years later, it is not GWAS but whole exome sequencing and whole genome sequencing providing all the buzz at conferences.  Solving the diagnostic odyssey!  Revolutionizing cancer treatment!  Ushering in an era of personalized medicine!  It’s very exciting.  Prenatal testing is rarely mentioned, and then only in passing – while prognosticators sing happy songs of a not-so-far-off day when every baby will be sequenced at birth.

Sequenced at birth?  Will it even be necessary?  Maybe Mom and Dad have baby’s DNA already, on a hard drive or a memory stick or downloaded onto their cell phones along with the ultrasound pics.

This is not the genome sequencing story you are seeing in the papers or the blogs.  It’s not what researchers are excited about.  The ones we hear are all about science journalists getting their DNA decoded and setting off on odysseys of self-discovery that involve hours of consultation with clinical and academic superstars who donate their time. We hear about kids with strange constellations of symptoms finding answers after years of disappointment.  Those are heartwarming tales: anecdotal and difficult to imagine at scale, but hopeful and exciting nonetheless.  But there is another theme playing, in a minor key, and I hear it faintly, hidden beneath the violins and the trumpets.

I hear it, an unspoken question, when we debate the utility of genomic information.  What does to mean to say that information is actionable? (Prevention? Treatment? Cure?  Prenatally, there is only Yes or No.)  Can patients handle uncertainty?  (And what will we lose, when pregnancies are terminated just to be on the safe side?)  Doesn’t everyone have the right to know what is in their own DNA? (The information is available – why not use it?  What could possibly go wrong?)

Whatever tests are available postnatally will find their way into prenatal use.  The gateway technologies – PGD, cell-free fetal DNA testing – are in place. And there is no use saying, “they can’t, they won’t, they shouldn’t” because they can and they will – and sometimes they should.  There will be good uses too: success stories and disasters averted.  A blanket “no” is not an option, and granting anyone authority to pick and choose which uses are worthwhile vests altogether too much power in the hands of any one person, or profession, or bureaucratic entity.

The same tests can be done before or after birth, but the experience is entirely different.  Uncertainty after birth is an opportunity.  The least useful information is that which will absolutely come true, no matter what you do.  Uncertainty before birth is a crisis.  Anyone who has ever discussed a variant of uncertain significance with a pregnant mother can tell you that.  But what are the chances there will be developmental delay?  Are you certain that the heart will be affected? How sure are you that this means anything?  Not nearly sure enough.  Please understand that.

In general, notions of genetic determinism increase the likelihood that genomic testing will have negative consequences.  Fatalistic attitudes about the power of genes could lead people to overestimate the meaning of elevated risks and underestimate the meaning of reduced risks.  Anxiety, stress, missed mammograms – you have heard this before.  Shrug.  People are grown ups.  They will figure this out.  Information is power.

But we are in a whole new universe trying to reconcile underpowered and often misunderstood predictive testing in the context of prenatal use.  So please, in telling tales of all the wonderful things that genome sequencing will do, save space for a mention of what it cannot do.  Make sure they understand that there are great wide cracks in our crystal ball.  Do not oversell the value of genotype in the absence of phenotype.  Remember that in the end neither researchers nor physicians nor genetic counselors will dictate how this new technology will be used.  Others will make that call, and we will be in the choir, singing songs of praise laced with sorrow.

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by | November 11, 2012 · 4:43 PM

Resistance Is Futile: A New Paradigm for Genetic Counseling?

For with this detection there arises new lines of approach in the field of preventive medicine, and the sociological consequences may be far-reaching.

– James V. Neel, from his 1948 plenary lecture, “The Detection of The Genetic Carriers of Hereditary Disease”, delivered at the first annual conference of the Human Genetics Society of America (which eventually changed its name to the American Society of Human Genetics)

The technical advances in genetic testing over the last 5 years have been stunning. Much of what I thought of as Not Going To Happen For A Long Time  has now happened yesterday. Along with these breakthroughs is the unstated but increasingly common suggestion that everyone should taste the fruit of testing in Gregor’s Genetic Garden of Eden.

In the old days (like a year or two ago) only a small portion of the patient population were thought to be candidates for genetic testing, those for whom it made medical sense and who were emotionally ready for the ramifications of the knowledge. Genetic counselors used their skills to help patients select the appropriate test and to guide them through the clinically, emotionally, and financially complicated decision-making process. Some chose to undergo testing while others delayed or declined it. We did not really care what patients chose to do; our role was to go through the wringer with them.

Now, though, this model of genetic testing only for the select few may be replaced in the near future by the idea that everyone – healthy, sick, high risk, low risk – should have genetic testing. Population scale genetic testing, with its promises of personally tailored medical care and better health outcomes, assumes that everyone – except for a handful of Luddites, people who do not own mobile phones or have Twitter accounts, Flower Children, and conspiracy theorists – will incorporate DNA into their routine medical care. Genetic testing becomes a foregone conclusion, not an ethically and emotionally weighty matter to be carefully explored and considered. If everyone has a genetic test and everyone carries gene mutations, doesn’t that make everyone a patient?

Think I am overstating my case? Perhaps. Then again, recall the many professional and popular articles you have read that are variations on this theme: The time is near when you will walk into your doctor’s office with an inexpensive DNA Chip that contains your entire genome and that will guide your doctor in choosing the best medications for you and select the most effective screening tests. You will live to be 100, enjoy a lusty sex life, and have healthy children. While the $1000 genome may not be a shining example of truth in advertising, affordable genetic testing is upon us.

A second case in point is the introduction of cheap carrier testing for a huge number of mostly obscure genetic conditions, what has come to be called Universal Carrier Screening. I will risk stating the obvious and point out that the word “universal” implies that the test is for everyone. At $99, it is hard to say no.

A third case in point is newborn screening, which is as close as it gets to universal genetic testing. The conditions screened for with those heel sticks continues to increase but the primary justification is not “treatment before symptoms develop.” Rather, testing is predicated on reducing the number of families caught in The Diagnostic Odyssey, that emotionally and financially draining parental journey to find out what medical disorder their child may have. Based on this premise, there is no logical stopping point for including disorders in a newborn panel. Every genetic disease is a potential source of a diagnostic odyssey. In fact, the rarer the syndrome, the better it is for inclusion in newborn screening since uncommon conditions are less likely to be diagnosed by most practitioners.

Another area of pervasive genetic testing is the recommendation for universal fetal aneuploidy screening during pregnancy, made even more tempting by high detection/low false positive non-invasive tests.

Genetic screening is offered to everyone prior to conception, during pregnancy, and at birth. Testing all adults allows the rest of the camel into the tent.

Genetic counselors are not the driving force behind universal genetic testing, although undoubtedly we have some complicated role. As I have discussed elsewhere, we probably have less influence on patients’ decisions than we  think. Larger social, economic, and ethical forces are at play, in much the same way that the introduction of amniocentesis, newborn and carrier screening, and the birth of the genetic counseling profession were all products of their times.

The role of genetic counseling when it comes to genetic testing, then, may no longer be primarily to help patients make decisions. Instead, genetic counselors may become Phenotype Counselors who interpret and integrate results of genetic tests that were run – and possibly chosen through online services – before patients walked into our offices.

Ilana Löwy’s book “Preventive Strikes: Women, Precancer, and Prophylactic Surgery”

If I am right, genetic counselors are likely to encounter controversies and dilemmas. Ethical values like nondirectiveness and autonomy become less forceful if individually tailored health strategies can help prevent or attenuate serious illness. Think of how many  oncologists consider their high risk cancer patients crazy for not having BRCA testing or believe that known BRCA mutation carriers are making poor choices for not undergoing risk-reducing surgeries.

Eugenic concerns, the voice and dignity of the disability community, the psychological sequelae of coping with test results, and worries about the other downsides of genetic testing may be pushed to the wayside by the power of the still unproven assumption that medical spending will become more cost-effective, clinical decisions will be wiser, and everyone will be healthier if their genomes are analyzed. In fact, people with disabilities themselves will likely see some treatment and diagnostic benefits from genomic testing. And because laboratories and lab-based counselors will likely play critical roles, defining and protecting against conflict of interest becomes even more critical and complex.

Both good and bad will come out of universal DNA testing, though it is difficult to predict what measure of each. But so much genetic information available on so many people must give one pause. The history of genetics demonstrates that every advance in genetics is fraught with social complexity and dangers. We may have a more sophisticated knowledge of genetics than our predecessors, but we are neither wiser nor more ethical.

I  close by reminding you that knowing our past helps us better understand why we are here and what may happen if we go there. To that end, let me bring to your attention two recently published books about the history of genetic counseling and the history of medical genetics: Telling Genes: The Story of Genetic Counseling in America by Alex Stern (The Johns Hopkins Univ. Press, 2012) and The Science of Human Perfection: How Genes Became the Heart of American Medicine by Nathaniel Comfort (Yale Univ. Press, 2012). The authors, my good friends and colleagues, provide an informed and critical historical understanding of  genetic counseling and genetic medicine. Everyone should read these books. It will do your souls – and your counseling philosophy – good.

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