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In Tufts Study, 10 Cancer Cases Found Among 125K Illumina NIPT Customers


NEW YORK (GenomeWeb) – Researches from Tufts Medical Center and other institutions working with Illumina have published a new study in which they identified a total of 10 cases of maternal cancer in women who received a discordant or false-positive result after Illumina's non-invasive prenatal testing.

The data, which appeared yesterday in JAMA, represent a retrospective analysis of over 125,000 samples tested by Illumina between February 2012 and September 2014.

Though limited, the results provide the most comprehensive picture so far of the variation and patterns of abnormal NIPT findings in asymptomatic women later diagnosed with cancer, adding to previous findings including a high-profile case report earlier this year of a woman whose unknown cancer was detected after an abnormal result from Sequenom's NIPT service.

Diana Bianchi, the new study's lead investigator, told GenomeWeb that while it is only a first step, the hope is that her team's analysis can help begin the process of guiding the development of protocols for counseling or advising women who may receive an abnormal discordant NIPT result in the future.

For example, she and her coauthors estimated in their new study that among NIPT results that specifically show the presence of multiple aneuploidies, and that are discordant with follow-up fetal karyotyping, 20 to 44 percent may be explained by maternal cancers.

In other words, a woman with a NIPT result showing multiple aneuploidies, but whose fetus has a normal karyotype, may have a 20 to 44 percent risk of having an unknown cancer.

While three of the cases Bianchi and her team identified in their Illumina study learned that they had cancer, in part, because of their abnormal NIPT results, seven only learned that their abnormal NIPT result may have been associated with cancer after being diagnosed.

Danielle Bryant, one of these seven, spoke with GenomeWeb about her experience.

After two lost pregnancies, and with the knowledge of a close family member with Down syndrome, Bryant and her husband had developed a relationship with a genetic counsellor, Kathryn Murray — also one of the JAMA study's authors — who suggested with their third pregnancy that the couple opt for non-invasive prenatal testing.

"We were told that the test looked at [chromosomes] 13, 18, and 20. … It was described briefly what those meant, but we weren’t really paying attention because we were concerned mainly about Down syndrome," Bryant said. "So we had the test done at about 13 weeks, and four weeks later Kathryn Murray called and informed us that there was 80 percent chance the baby had trisomy 13 at that point."

The news was devastating. "We went from finally having a pregnancy that lasted to finding out that the baby might not make it past birth," Bryant said.

Abortion was off the table for the couple, and they also thought hard about whether to have a follow-up amniocentesis, which carries some risk. "We prayed and thought about it a lot," she said. "But decided we needed to know for sure to start preparing." Then, another several weeks later, Murray called the couple back and told them that the amnio results showed that the fetus was actually normal, with no trisomy 13.

"We were ecstatic, dancing around our house," Bryant said. But it wasn't clear what had caused the false-positive or discordant result. Murray suggested it could be that Bryant's placenta carried cells with trisomy 13, and Bryant consented to donate her placenta for further testing after delivery.

According to Bryant, there was no sense at that point that cancer was even a remote option for explaining the result.

Suffering some pregnancy complications, she ended up delivering early via c-section. Then, in a slew of further severe complications post birth, she ended up in septic shock, then a two-week coma, and a difficult recovery. Amid all of this, Bryant and her family stopped wondering what might be at the root of her false-positive NIPT result.

"We found out in late September that the placenta came back normal, so it was kind of just written off that this was a weird fluke."

Meanwhile, her OB was still in contact with Murray. Though she recovered from her post-birth health crisis, Bryant continued to have bleeding issues, and eventually received a colonoscopy which uncovered, 39 weeks after her initial NIPT result, a 10-centimeter stage III colorectal tumor.

"My OB then called Kathryn Murray and said, 'You're not going to believe this' … and they asked me to do another blood test before surgery." This test in a now un-pregnant woman, showed both trisomy 13 and monosomy 18, according to the Bianchi team's report in JAMA.

In September 2014, after Bryant's cancer treatment, the researchers asked for another, final blood test, which came back showing no evidence of any aneuploidies — encouraging, though not definitive evidence that her treatment had been effective.

Whether earlier detection would have made a difference in Bryant's case is unclear, though Bianchi and her coauthors reported in the study that the clinicians involved stated that earlier diagnosis would have had a positive effect on the care of Bryant and at least one other case in the study who presented with advanced symptoms.

At the very least, had the full results of Bianchi and her team's study already been available when Bryant received her initial test, Murray and her OB might have had more possibilities in hand to explain her discordant result.

Speaking with GenomeWeb last week, Bianchi said that though limited, the study results do provide a significant step toward the goal of being able to more proactively identify women with abnormal discordant NIPT results with undiagnosed cancer.

Beyond their calculation of up to a 44 percent incidence of cancer with a discordant multiple-aneuploidy result, she and her colleagues also found that NIPT results demonstrating a single autosomal monosomy may warrant additional attention.

However, the group's analysis doesn't necessarily paint the full picture. For instance, the overall incidence of cancer in the cohort was much lower than would be expected.

"We didn't have complete follow up on all the women, so it's possible there are cases of cancer that had normal NIPT results — or additional cases with abnormal results that were not reported back to the [Illumina] clinical laboratory," Bianchi said. "It's not complete ascertainment."

Meanwhile, it's also not yet clear what clinicians should do with a suspected cancer-associated NIPT result, even with the Bianchi team's new data and risk estimates. In a recent study published in JAMA Oncology, investigators in Belgium reported on full-body MRI results for three mothers with aberrant NIPT results, which all showed the presence of a tumor.

But for MRI or other specific follow-up measures to be mandated for all women with discordant NIPT results, Bianchi and her colleagues' results will have to be replicated and solidified further, she stressed.

"The key issue is what is the pattern either in the whole genome or in 13, 18, and 21 — what is the clue that this woman needs a workup for cancer," she said. "I think this retrospective data has value. What jumps out especially are the multiple aneuploidies and also the monosomies. These are not findings you see in a viable pregnancy … and then the fetus has a normal karyotype, so that tells you something is wrong." However, she said, it will take more work to precisely define what follow-up steps such results should lead to.

Overall, Bianchi and her co-investigators retrospectively examined 125,426 cases submitted for Illumina's NIPT service between early 2012 and late 2013. Among this cohort, only three percent, 3,757 cases, were positive for one or more aneuploidies.

A total of 10 cases who were diagnosed post-NIPT with a cancer of some kind were reported back to Illumina, and in eight of these the researchers were able to collect and review additional detailed clinical and sequencing data.

Then, by examining the 10 cancer cases in the context of the entire 125,000-case dataset, the investigators calculated an estimate for the risk of cancer in women with certain types of discordant NIPT results, specifically those showing multiple aneuploidies.

The group identified 39 patients from the total cohort with this multiple aneuploidy pattern, 16 of whom had a discordant or normal fetal karyotype. Another four had a concordant follow-up fetal result, and for the remaining 19 no information was available.

Among the 16 cases with discordance between the NIPT result and fetal karyotype, seven, or 44 percent, were from women later diagnosed with cancer. Assuming all the remaining 19 discordant cases did not have cancer would imply that only 20 percent of such aneuploidy results were associated with cancers — hence, the group estimated a 20 to 44 percent chance that any discordant multiple aneuploidy result is due to maternal malignancies.

The Bianchi study also uncovered several cases, like Bryant's, of maternal cancer associated with a single, rather than a multiple aneuploidy result. Additional data will be key in uncovering more about these results and how they could be useful in assessing a woman's risk of having cancer.

In a commentary accompanying the study in JAMA today, Robert Romero and Maurice Mahoney, wrote that the Bianchi team's data is the most comprehensive so far and an important advance over previous single case reports or small series.

Ideally, the two doctors wrote, the researchers' estimate of cancer prevalence in discordant multiple aneuploidy cases should be tested to see if it holds up in a larger, more appropriate dataset, ideally a cohort study.

Meanwhile, labs, or companies with similar data in hand, namely the other commercial NIPT providers, could provide a valuable service by sharing their experience to improve the accuracy of the analyses derived by Bianchi's team.

Another step forward would be the establishment of a registry, something Bianchi also advocates, to collect additional discordant NIPT results not only showing multiple aneuploidies, but also single aneuploidies.

While the new data is a significant step forward, much complexity remains, highlighting the importance for women who receive this testing to be properly educated and consented as to the power of NIPT technologies to uncover such findings.

Just last month Bianchi published a commentary in Nature calling for standardization of consent and patient counseling procedures to make sure women understand that they could learn something not only about their fetus but also about their own health when they receive NIPT.

Questions have been raised about how companies should be dealing with cases of false-positive or discordant NIPT results, especially as more case reports of maternal cancers have emerged, and amidst unclear standards for informed consent. According to Bianchi, Illumina has used the data collected so far to put together its own protocols in terms of the steps it now takes to obtain patient consent and communicate with ordering physicians in the case of discordant findings, and to help guide appropriate follow-up for the most worrisome findings — those showing multiple aneuploidies or monosomy.

"I think it's important to emphasize how rare this situation is, though," Bianchi said. "Only a small fraction of women has a positive aneuploidy screen, and the recommendation is then that they get an invasive procedure — and only in the case where the fetus has normal chromosomes, only then do they go through this process."