If more women were accurately counseled about what exactly cell free DNA is testing, they would immediately understand that their test results are never diagnostic.
Over at the blog for the Prenatal Information Research Consortium, I have a summary of a report from the largest study of cell free DNA (cfDNA) testing in a clinical setting. It reports some key findings:
- For all of Sequenom’s, Ariosa’s, Illumina’s, and Panorama’s marketing that their tests are “99% accurate,” the study found that in a high risk population, the positive predictive value (PPV), i.e. the actual chance that a “screen-positive” was a “true positive,” was only 77.4% for all conditions tested. (Some may recall a study of cfDNA in the general population only had a PPV of 45.5%).
- Nine patients terminated their pregnancies based on a “maybe,” i.e. without having diagnostic testing to confirm their cfDNA test results.
But, the study also makes clear what is being tested–and it’s NOT fetal DNA.
Labs say cell free fetal DNA
What do the labs say they are testing?
Ariosa, maker of Harmony, says on its website for healthcare professionals that it carefully measures fetal DNA, with a graphic showing how fetal DNA enters the mother’s blood stream:
Illumina states that its test verifi “directly analyzes cell-free fetal and maternal DNA”:
In a white paper from March 2014, Natera says that its test Panorama “analyzes maternal and fetal cell-free DNA” with a graphic showing fetal DNA entering the mother’s blood stream:
(All screenshots taken June 14, 2015).
Turns out, though, it’s not cell free fetal DNA.
Placental cytotrophoblastic cell line
In the report from the University of Washington Medical Center, the researchers reviewed over 600 patient files who had had NIPS testing. Their research showed that while cfDNA testing, also referred to as Non-Invasive Prenatal Screening (NIPS), can be a reliable screen when used as a second-tier test for women already determined to be high-risk, false positives and false negatives still occur.
One of the reasons for why false positives and false negatives occur is because of what is actually tested:
During pregnancy, placental cytotrophoblastic cells are shed into maternal circulation and contribute to the cfDNA in the maternal bloodstream.
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the source of non-maternal cfDNA during gestation is the placental cytotrophoblastic cell line. Aneuploidy in the cytotrophoblastic cell line with a diploid fetus may cause abnormal discordant NIPS result, whereas diploidy in the cytotrophoblastic cell line with a trisomic fetus may cause a normal discordant NIPS result.
- what is tested by NIPS is cell free DNA from placental cells shed into the mother’s bloodstream. It is this placental cfDNA that is tested by NIPS.
- There is a phenomena called “confined placental mosaicism,” where confined to the placenta, there will be cells with a chromosomal condition called “aneuploidy,” an extra or missing chromosome, like Trisomy 21 (Down syndrome) and Trisomy 18. Conversely, there are fetuses with those same aneuploidies while the placental cfDNA tested does not have aneuploidy cells.
- In the case of a false positive, the placental cells had aneuploidy, but the fetus did not and vice versa for a false negative, the placental cells did not have aneuploidy, but the fetus did.
Now, “placental cytotrphoblastic cell line” doesn’t roll off the tongue as easily as “cell free fetal DNA” and it doesn’t suggest the degree of certainty that “fetal” DNA does for a prenatal test. But even if “placental cytotrophoblastic cell line” is a mouthful, it’s what MaterniT21, Harmony, verifi, and Panorama are testing–not fetal DNA.
Standard of care recognizes cfDNA as testing of placental, not fetal, DNA
The American College of Medical Genetics and Genomics (ACMG) plainly stated that NIPS is testing placental DNA in its statement from 2013:
the sequences derived from NIPS are derived from the placenta
The graphic at the top of this post is from a talk given at the 2013 ACMG conference explaining how the cell free DNA tested is from the placental cell line.
The National Society of Genetic Counselors stated in its 2015 Fact Sheet on NIPS:
During pregnancy, cell free DNA from the placenta (predominantly trophoblast cells) also enters the maternal blood stream and mixes with maternal cell free DNA. The DNA of the trophoblast cells usually reflects the chromosomal make-up of the fetus.
And, now, in an article published on the largest review of cfDNA testing’s performance in a clinical setting it is again made clear that cfDNA tests placental cells, not fetal.
Yet, the testing laboratories still represent that it is fetal DNA.
Maybe if it was accurately labeled as placental DNA instead of fetal DNA, everyone–doctors, genetic counselors, geneticists, and patients–would understand that whatever the NIPS result, it remains a screening test with the chance of a false positive and a false negative.
A related post on this subject is at this link.