Our recently published validation study was similar in design to prior studies evaluating the performance of noninvasive prenatal testing in that we analyzed a clinical cohort of maternal plasma samples collected from women undergoing either amniocentesis or chorionic villus sampling. Karyotyping or microarray analysis of those samples was used as primary reference standards to determine the performance of the noninvasive test.

As Palomaki and Haddow indicate, our study was not designed to determine fetal or birth outcome; rather, it was intended to evaluate test performance during pregnancy. As such, we indicate within the discussion that “we have used a method that prioritizes chorionic villus sampling over amniocentesis because of the placental origin of cfDNA (cell-free DNA)” and that “our method of evaluation has the potential to overestimate performance with regard to fetal outcome” and further that “prospective studies using the method described here with follow-up of birth outcome will further enhance understanding of clinical effectiveness.” Of note, it has long been known that chromosomal abnormalities hold clinical relevance, even if confined to the placenta, being often associated with prenatal or perinatal complications.

We also agree with Palomaki and Haddow that the copy number variants used in the study are limited in the number, size, and spectrum of genomic location, but with the exception of the self-imposed size limitation, the selection of samples was limited by availability: most of these copy number variants are individually very rare in the clinical population that made up our collection cohort. The 7 Mb size limit balances technical aspects driving sensitivity and specificity and is informed by accumulated historical experience of the clinical impact of copy number variants detectable by cytogenetic karyotyping (traditionally limited to ∼ 7 Mb by optical microscope resolution).

Based on our clinical experience, noninvasive prenatal assessment of genome-wide copy number variations is a novel methodology that today is primarily used by providers when invasive testing is not available or not desired by the patient. In the clinical samples tested in our laboratory to date, 25-30% of clinically relevant findings were unique to our test (eg, rare copy number variants ≥7 Mb and rare aneuploidies) and would not have been detected by conventional noninvasive prenatal testing.

We intend to publish our growing experience with these individually rare but categorically common findings. In sharing our experience with the community, we hope to increase the general understanding about the true prevalence, and clinical significance, of such findings.