Tag Archives: cell-free fetal DNA

Guest Post: NIPS: Microdeletions, Macro Questions

by Katie Stoll

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. 

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At the recent National Society of Genetic Counselors Annual Education Conference in New Orleans, a presentation raised some important questions about noninvasive prenatal screening (NIPS). According to the speaker, a woman with a vanishing twin pregnancy underwent NIPS with an expanded microdeletion panel and the results showed findings “suggestive” of a chromosomal microdeletion syndrome.

The patient underwent amniocentesis with a SNP microarray and the results were normal. In a follow-up call with the NIPS lab, the genetic counselor learned that multiple copy number variants were observed (not originally reported) in the original sample. The lab suggested that these variants could be associated with a malignancy or fibroid tumor (and were of course unlikely to be associated with a microdeletion syndrome in the fetus).

As a result of this genetic counselor’s follow-up phone call and due diligence, the patient underwent an extensive work up for possible cancer, but no explanation was found. NIPS was repeated and this follow-up study was normal.

My first thought in hearing this case was – That poor woman! First a lost twin pregnancy, then concern for a severe condition in her baby, anxiety about the amnio, and worry that she may have Cancer. Although I am not a health economist, my second thought was – Holy Cow! How can our healthcare system afford all of the follow-up testing that may come downstream from these tests? NIPS is promoted as a test that will lessen the need for follow-up procedures such as amniocentesis, but will that remain true as the list of screened conditions increases?

In October 2013 Sequenom expanded their NIPS test to include screening for microdeletion syndromes and Natera followed suit in Spring 2014. Some new companies entering the NIPS market are also advertising screening for microdeletion syndromes.

The addition of microdeletions is a brilliant business strategy for expanding the testing market to include all pregnant women. Even though microdeletions are rare, their incidence—unlike that of Down syndrome –is not linked to maternal age. Women who are currently not offered NIPS because they are not included in the high-risk categories proposed by the American College of Obstetricians and Gynecologists (ACOG) guidelines could now be given a reason to undergo NIPS—even though the predictive ability of the NIPS for rare conditions is less than impressive.

Women who elect the test because of an interest in Down syndrome or because they are eager to learn fetal gender may unknowingly be screened for rare microdeletion syndromes which they know little to nothing about. To add to the complexity, a maternal microdeletion condition may be an incidental finding. In a poster presented at the NSGC meeting this year, Sequenom presented a series of 22q11 deletions detected with their MaterniT21 PLUS test. Included in this report were two mothers who were themselves incidentally diagnosed with 22q11 deletion syndrome. Based on the consent form on the Sequenom website it seems unlikely that these women had any idea such a result may occur.

Where is the evidence to support this expanded screening?

These tests are being performed despite there being no published clinical validation studies. There have been some case reports and proof of concept studies; however given that this testing has been commercially available for over a year now, there is shockingly little published about cell free DNA screening for microdeletions. An abstract from a poster presentation at the ACOG annual meeting in April 2014 evaluated 6 samples (or is it 7? – it is not clear from the abstract) from pregnancies known to be affected with microdeletions and 8 simulated samples. They conclude, “This is the most comprehensive, accurate validation of noninvasive microdeletion detection hitherto… This approach will enable accurate, noninvasive, prenatal population screening for these severe disorders.”

Proof of concept is one thing; proof of clinical validity is another. If we value evidence-based medicine, a sample of six (or seven) affected pregnancies is a long way from being a basis for population screening. Whether population-wide screening for extremely rare disorders is worth paying for is, of course, a question in itself.

But in the unregulated environment of laboratory-developed tests, we adopt first and report out results later. Accompanying this process is a lack of transparency – labs performing NIPS with microdeletions have not made performance statistics publicly available and thus patients and providers have no way of determining the accuracy of microdeletion NIPS. In a webinar hosted by Sequenom , the presenters were asked about the positive predictive value (PPV) of Sequenom’s screen for microdeletions. One speaker replied, “We have calculated them. However, what we would like is essentially to wait a little bit to give you more clinically relevant results. Because so much depends on the fetal fraction of the sample and so on and so forth, so we feel that the more appropriate number to release is after we have done 50,000 samples, how many have we found, how many have we reported back, how many were confirmed, how many were in line with the clinical picture.”

Shouldn’t the accuracy of the test be publicly known before it is run clinically on 50,000 women?

Labs have given us only a glimpse of their performance statistics. I was previously provided information from Natera regarding estimated PPVs for the microdeletions on their panel, but I cannot locate this information anywhere in the public forum. The table I was provided stated a 1/19 PPV (5.3%) for 22q11 with a Fetal Fraction >6% and dropping much lower (to 1/45) with decreased fetal fraction (interesting thread here of multiple women with a 1/19 chance of 22q11 on their NIPS result).

In a letter to the editor, former CMO of Sequenom Allan Bombard and colleagues reported that they had evaluated 264 samples from pregnancies with known microdeletion and microduplications or “enriched genomic mixtures” and report a 100% sensitivity and 99.3% specificity. Applying these statistics to 22q11.2 deletion syndrome (the most common microdeletion syndrome on the panel with an incidence of 1 in 4,000) indicates a PPV of about 0.036 or 3.6% . The overall PPV would be expected to be lower given the very low incidence of the other microdeletions on the panel. At the NSGC meeting this year, Sequenom presented some preliminary data from a series of 120,726 samples screened from October 2013 – July 2014 with test performance that exceeds those estimates. Although they did not have complete follow-up data for positive and negative results, a press release from the company following the NSGC meeting reports “high positive predictive values (estimated combined PPV ranged from 62% to 94%)”.

The limited information available suggests PPVs for microdeletion syndromes fall within a broad range of <3% – >90%. Published peer-reviewed studies are needed to help clarify the PPV associated with this testing so that healthcare providers and patients can make informed decisions about utilizing and interpreting this testing.

About a year and a half ago I published a piece on the DNA Exchange that discussed the importance of PPV in interpreting NIPS results. This was written for an audience of genetic counselors, but the posting is being increasingly used as a venue for patients to share their stories and seek information about their test results. Many patients report considerable anxiety – “the waiting is killing us…we have been devastated for the better part of 3 weeks now” – and some express regret for undergoing this testing at all, “I too wish I would of just done the typical old fashion test so nothing was in the back of my mind and hours of my life would be given back…” Recently, a woman remarked that she did not consent to additional testing for microdeletions and indicates her frustration with not being able to find information about the PPV for this test, “Not only are they essentially experimenting on us…they are not transparent about the potential problems with validity or low PPV.”

As genetic counselors, we are implicated in these companies’ approach. We should be demanding better evidence before leading our patients towards testing that could create this kind of distress. We need to be asking good questions, and we should demand good answers. If we cannot figure out how reliable a screening test is from a thorough review of the literature, I think we really need to ask ourselves if we should be offering it in a clinical setting.

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NIPS SPIN

Advertising is the art of making whole lies out of half truths. ~Edgar A. Shoaff

Every few years a new screening technology comes zooming down the prenatal pike, sometimes arriving more quickly than we might like. First there was maternal age, with the magical age of 35 as the cut-off. Low maternal serum AFP arrived in the 1980s and the OB community embraced it virtually overnight when ACOG’s Committee on Professional Liability issued a statement that practitioners could be held legally liable if they had not offered this screen to a patient who had given birth to a child with Down syndrome. This was followed in short order by the Triple Screen, The Quad Screen, nuchal thickening, Integrated Screening, etc., each one a statistical notch above its predecessor. The latest iteration – cell-free fetal DNA or Non-Invasive Prenatal Screening (NIPS)  – stands head and shoulders above the rest. Two of our colleagues have already discussed the limitations and strengths of NIPS here on The DNA Exchange.*

NIPS is big, as in global big. One lab makes its brochure available in more 20 languages, from Afrikaans to Xhosa (the pregnancy gods must be crazy, dropping pamphlets out of The Cloud). Tens of millions of women around the world are likely to undergo NIPS in the near future. And pregnant women are a “renewable resource” –  a whole new batch pops up every day and many women will have two, three, or more children. Competition for market share among labs is stiff and there is little incentive to dissuade women from undergoing prenatal screening. It’s not that labs coerce women to undergo screening, advocate eugenic agendas, or run roughshod over personal autonomy. All labs would support a woman’s right to decline prenatal screening and Lord knows they stay away from the abortion discussion. But if enough women decline, then there is no incentive to offer the screen. The companies have something to sell and will spin their product to attract customers.

Which brings me to the subtly misleading implications of the name Non-Invasive Prenatal Screening. Sure, NIPS is non-invasive. But so is ultrasound, AFP, HCG, etc. All of these screening tests are non-invasive and therefore do not carry a direct risk of fetal loss. NIPS  is no different from the rest in that sense. It is superior to other screens in terms of having a very low first positive rates, high positive predictive value, and high sensitivity. But NIPS is still an alternative to other screening tests, not to amniocentesis or CVS.

Yet the websites of companies that offer NIPS communicate a different message that subtly suggests that NIPS is in fact an alternative to amniocentesis/CVS instead of an alternative to, say, the Integrated Screen:

First we thought the PC was a calculator. Then we found out how to turn numbers into letters with ASCII – and we thought it was a typewriter. Then we discovered graphics, and we thought it was a television. With the World Wide Web, we’ve realized it’s a brochure. ~Douglas Adams

The suggestion that NIPS is a diagnostic test is further reinforced by reassuring text in large, appealing fonts – Comprehensive, Accurate, Trustworthy, and, my personal favorite, No Confusion. Such wording conflates screening tests with diagnostic tests. Who could resist a test that boasts to be >99% accurate, especially when combined with images of smiling, beautiful parents and babies so cute that you wish your touch screen would allow you to hug them? It is easy to see why parents might be confused and some genetic counselors feel that 75% of their patients may think that NIPS is diagnostic. Yes, the labs also offer comparison to other screens, information about the conditions being screened for, links to disability focused websites, and acknowledge the role of diagnostic testing. But information does not sell products; images and impressions do.

http://en.wikipedia.org/wiki/The_Treachery_of_Images

The Treachery of Images by René Magritte

NIPS is a pretty good screening tool that can help patients decide if they want to proceed to diagnostic testing such as amniocentesis or CVS. However, the first step in the process of considering any testing should be a soul-searching and difficult discussion between parents and with their care providers about views on disability, parenthood, expectations for their children, and beliefs about pregnancy termination (I can’t prove it, but I am pretty sure that discussion is not taking place anywhere near as frequently as it should). For parents who feel it is important to know the chromosomal status of their baby, the next step is to outline the pros and cons of screening tests, emphasizing that a screen only provides a probability that a child may have a particular chromosomal disorder. The risk estimate provided by the screening test may help parents decide if they wish to undergo diagnostic testing.

One might counter that labs are commercial entities engaging in good old American advertising, which everybody knows is not exactly a strictly honest business. But prenatal screening is not like trying to sell Coke vs. Pepsi or Ford vs. Toyota or Chia Pet vs., well, whatever it is that Chia Pets are in competition with. We are talking about babies, our deepest hopes and dreams, and the core values that define our humanity. This demands a higher standard and this is where genetic counselors need to work with their laboratory employers to elevate the discussion.

 


* Missing from much of the professional  discussion about NIPS has been the viewpoint of people with disabilities, their families, and their advocates. As Rachel Adams points out, the Down syndrome community in particular might feel particularly targeted by a test named Maternit21 – but that thorny topic is for another day.

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