The Combining Effects of Cell-Free Circulating Tumor DNA of Breast Tumor to the Noninvasive Prenatal Testing Results: A Simulating Investigation

Abstract

Massively parallel sequencing of circulating fetal DNA in the plasma of pregnant women is a common method for noninvasive prenatal testing (NIPT) of fetal trisomy 13, 18, and 21. However, circulating DNA is not restricted to pregnant women, with increased levels of plasma DNA also frequently detected in the plasma of cancer patients. Among pregnant women whose NIPT results were inconsistent with the fetal karyotype, a small number of patients have subsequently been diagnosed with a previously undetected malignancy. However, the extent to which circulating tumor DNA (ctDNA) affects the results of NIPT is still unclear. We examined serum from 50 nonpregnant women with breast tumors by NIPT. These samples were then added to serum containing trisomy 13, 18, and 21 fetal DNA to figure out the extent to which maternal tumors can interrupt NIPT results in pregnant women with breast tumors. Concentrations of cell-free DNA (cfDNA) were higher in both pregnant women and breast tumor patients, relative to nonpregnant healthy controls. Among the 50 samples evaluated, 3 produced false positive NIPT results for trisomy 13, 18, or 21, indicating that genomic copy number variations (CNVs) had occurred. Simulation testing also showed that ctDNA can increase the standard deviation of the associated z-scores, which lower absolute z-scores by decreasing the proportion of circulating fetal DNA relative to total DNA. Of the 50 samples tested, 9 fell within the equivocal range and 8 produced false negative results for trisomy 13, 18, or 21. Data presented here show for the first time that ctDNA is able to affect NIPT results in two ways. First, ctDNA can lead to false positive results due to the detection of genomic CNVs in tumor DNA. Alternatively, ctDNA can increase the likelihood of a false negative by decreasing the proportion of circulating fetal DNA in serum.

Low-Coverage Sequencing of Urine Sediment DNA for Detection of Copy Number Aberrations in Bladder Cancer

“…[11][12][13][14]18 Following recent developments in sequencing technology, next-generation sequencing has become widely used in noninvasive prenatal testing chromosome copy number detection due to its high throughput, high sensitivity, and low cost. [19][20][21][22][23][24][25] Therefore, we presumed that low-coverage sequencing In this study, the low-coverage whole-genome sequencing method was used to compare the chromosomal copy number variation in urine sediment DNA from patients with bladder cancer, patients with benign bladder tumor, and normal controls. The chromosomal copy number variation in urine sediment was significantly higher in patients with bladder cancer than in patients with benign bladder tumors or normal controls.…”

“…Droplet digital PCR may be used to quantify a single mutant alleles and deep targeted sequencing may be used for assessment of multiple allele panels. [25][26][27][37][38][39] Moreover, comparative genomic hybridization technology can be used to detect chromosomal aneuploidy in urinary exfoliated cells from patients with bladder cancer. Because of background interference from other DNA in urinary exfoliated cells, this method has limited sensitivity and specificity and has not been widely used.…”

A Case Report of a Feto-Placental Mosaicism Involving a Segmental Aneuploidy: A Challenge for Genome Wide Screening by Non-Invasive Prenatal Testing of Cell-Free DNA in Maternal Plasma

“…However, NIPT cannot produce a diagnostic result, due to technical and computational limits and also to biological issues. Common biological causes of false-positive NIPT results include placental mosaicism [ 13 ], fetal chromosome rearrangements, a vanishing twin [ 14 ], and maternal chromosome abnormalities or malignancy [ 15 ]. An inherent limitation of NIPT, irrespective of the approach taken, is the discordance between NIPT and invasive prenatal diagnosis, mainly due to confined placental mosaicism (CPM).…”