Three out of five NIPT laboratories returned normal or negative test results for samples taken from non-pregnant women in undercover test performance assessment
Clinical laboratory companies that offer genetic tests may want to be on the alert. Secret shoppers are submitting specimens for the purpose of assessing the quality, the accuracy, and the clinical relevance of the proprietary medical laboratory tests they perform.
One such report was published in GenomeWeb under the title “Undercover Assessment of Five Commercial NIPT Labs Points to Need for Better Quality Control.” The goal of the report was to emphasize the need for standards to ensure quality and accuracy of molecular assays and genetic tests.
This report discussed results from an undercover performance assessment of five commercial laboratories, each of which offers Non-Invasive Prenatal Tests (NIPTs). GenomeWeb reported that three test results reported normal or negative test results for a female fetus, despite the fact that the samples submitted had been taken from non-pregnant women.
This undercover performance assessment was conducted by Tamara Takoudes, M.D., and Benjamin Hamar, M.D., two Boston-based Maternal-Fetal Medicine specialists. Their findings were first reported in a Letter to the Editor of the journal Ultrasound in Obstetrics & Gynecology.
Takoudes is a Clinical Instructor at Harvard Medical School (HMS) and on staff at Beth Israel Deaconess Medical Center (BIDMC). Hamar is a Clinical Assistant Professor of Obstetrics & Gynecology at HMS and also on staff at BIDMC.
No Standard Test for Measuring and Analyzing Fetal DNA
The NIPT depends on cell-free fetal DNA in the mother’s blood to detect chromosomal abnormalities. But companies measure and analyze the DNA differently. Some clinical laboratories contend that fetal fraction, the relative amount of free fetal DNA compared to the mother’s DNA, influences accuracy of the test, while other lab companies argue that reliable results can be obtained without determining fetal fraction.
Takoudes and Hamar contend, however, that the amount of fetal DNA in a mother’s blood depends on a variety of factors, including the stage of pregnancy, maternal weight, sample collection methods, and shipping conditions. To determine how different NIPTs handle samples with little or no fetal DNA, the doctors sent blood samples from two non-pregnant women separately to the five NIPT providers, alleging the patients were in their 12th week of pregnancy.
Three of the medical laboratory companies returned normal or negative test results for a female fetus. They were Sequenom Laboratories, Illumina, Inc. (NASDAQ: ILMN), and Laboratory Corporation of America’s (LabCorp) (NYSE: LH) Integrated Genetics. The other two laboratories, Ariosa Diagnostics (Pre-IPO: AROS) and Natera, cited insufficient fetal DNA and provided no test results, noted Takoudes.
Like Ariosa and Natera, Sequenom’s NIPT measures fetal fraction. But the researchers say that the lab company incorrectly found fetal fraction to be about 4% in both samples. Illumina and LabCorp’s Integrated Genetics NIPTs base their results on Illumina’s Verifi test, which does no measure of fetal fraction.
These results “raise concerns about the need for quality standards in NIPT,” stressed the study authors. Similar to other prenatal assays—such as karyotyping and fluorescence in situ hybridization, which require a minimum number of fetal cells—“it seems reasonable that for NIPT, an analogous control measure should be applied,” noted the study authors in the letter they sent to the Ultrasound in Obstetrics & Gynecology.
Authors Call for Professional Societies to Set and Enforce Test Standards
While this test has shown promising accuracy, “we urge professional medical and laboratory societies to set and enforce appropriate quality-control guidelines for NIPT that are consistent with standard laboratory practice as in other commercially available tests,” wrote the authors of the study.
Takoudes told GenomeWeb that NIPT providers are increasingly marketing their tests to the general OB/GYN community, despite lack of standard methodologies for the assays or how results are reported.
Natera, which uses an assay that distinguishes between fetal and maternal DNA, agreed that better quality controls are needed for NIPTs. The company’s Vice President of Marketing and Business Development, Solomon Moshkevich, stated that “from now on doctors and actual pregnant patients must think twice when receiving a negative result with female sex from one of those three labs because they won’t know if it reflects the fetal or maternal DNA.”
Illumina Defends Its Verifi Test Results
In an e-mail to GenomeWeb, Tristan Orpin, Illumina Senior Vice President and General Manager, Reproductive and Genetic Health, called the assessment of the quality of Illumina’s NIPT assay “invalid,” because the test was not designed to analyze samples from non-pregnant women.” He noted that Illumina’s Verifi test is designed to detect fetal aneuploidy from maternal serum.
Orpin also pointed out that Illumina’s reported result of “no aneuploidy detected” was correct, since there was no aneuploidy to detect and that the presence of two X chromosomes was also a correct result, which did not imply there was a female fetus.
“Peer-reviewed publications have shown Verifi to have industry-best performance and the lowest false-negative rates without the requirement to measure fetal fraction or exclude low fetal fraction samples,” he continued.
Critics called the study flawed because it only used two samples from women who were not pregnant. Anthony Gregg, M.D., Professor and Chief, Division of Maternal-Fetal Medicine at the University of Florida Obstetrics and Gynecology, agreed that results reporting no aneuploidy and two X chromosomes were correct. “The [study] authors fail to recognize the differences in platforms, methods for determining fetal fraction, and the important point that the test is useful only in established pregnancies,” he told GenomeWeb.
Why NIPT Should Not be Used as a Diagnostic Test
The GenomeWeb report noted, however, that it is impossible to know how many pregnant women with little or no fetal DNA in their blood may have received false-positive results from clinical lab companies that do not measure fetal fraction or do not measure it correctly.
Takoudes said that, because the prevalence of Down syndrome in women receiving NIPT screening is very low, there is a very high chance of receiving a correct negative result. “I think it’s a very good test, but it should not be used as a diagnostic test, and the patient needs to receive a lot of counseling,” she added.
While providers offering this specialized test are limited, the lesson here for pathologists and medical laboratory managers is that medical professionals are raising the bar on quality and accuracy of clinical laboratory tests. This is particularly for proprietary diagnostic assays where the results would influence a patient’s diagnosis and treatment of a serious illness.
— by Patricia Kirk