Prenatal cfDNA Sequencing and Incidental Detection of Maternal Cancer

Abstract

Background: Cell-free DNA (cfDNA) sequence analysis to screen for fetal aneuploidy can incidentally detect maternal cancer. Additional data are needed to identify DNA-sequencing patterns and other biomarkers that can identify pregnant persons who are most likely to have cancer and to determine the best approach for follow-up.

Methods: In this ongoing study we performed cancer screening in pregnant or postpartum persons who did not perceive signs or symptoms of cancer but received unusual clinical cfDNA-sequencing results or results that were nonreportable (i.e., the fetal aneuploidy status could not be assessed) from one of 12 different commercial laboratories in North America. We used a uniform cancer-screening protocol including rapid whole-body magnetic resonance imaging (MRI), laboratory tests, and standardized cfDNA sequencing for research purposes with the use of a genomewide platform. The primary outcome was the presence of cancer in participants after the initial cancer-screening evaluation. Secondary analyses included test performance.

Results: Cancer was present in 52 of the 107 participants in the initial cohort (48.6%). The sensitivity and specificity of whole-body MRI in detecting occult cancer were 98.0% and 88.5%, respectively. Physical examination and laboratory tests were of limited use in identifying participants with cancer. Research sequencing showed that 49 participants had a combination of copy-number gains and losses across multiple (≥3) chromosomes; cancer was present in 47 of the participants (95.9%) with this sequencing pattern. Sequencing patterns of cfDNA in which there were only chromosomal gains (multiple trisomies) or only chromosomal losses (one or more monosomies) were found in participants with nonmalignant conditions, such as fibroids.

Conclusions: In this study, 48.6% of participants who received unusual or nonreportable clinical cfDNA-sequencing results had an occult cancer. Further study of DNA-sequencing patterns that are suggestive of occult cancer during prenatal screening is warranted. (Funded by the NIH Intramural Research Programs; ClinicalTrials.gov number, NCT04049604.).

Figure 1.

Enrollment and Outcomes

Figure 2.. Distinct Cell-Free DNA Sequencing Patterns Associated with Malignant and Non-Malignant Findings

50kb sequencing traces from research whole genome massively parallel sequencing of cell-free DNA (cfDNA) from maternal plasma. The x-axis indicates genomic location. The y-axis represents the normalized segment representation for each chromosome, centered at 1.0. The green dotted lines show the upper and lower bounds expected from a euploid fetus. The orange line depicts the normalized segment representation as calculated from the sequencing data. A. Genome-wide cfDNA profile consistent with a euploid fetus in a participant without malignancy. B. Genome-wide sub-chromosomal and whole chromosome copy number gains and losses in a participant with colon cancer. C. Whole chromosome trisomies of chromosomes 8 and 14 in a case of confined placental mosaicism detected in placental biopsies. D. Sub-chromosomal losses at chromosomes 7 and 18 in a participant with multiple submucosal fibroids. E. A maternal chromosome translocation (4;15)(p16;q24) in a participant with clonal hematopoiesis of indeterminate potential. F. Borderline z-scores across multiple chromosomes that prevents assessment of fetal aneuploidy status in a participant with breast cancer.

Figure 3.. Whole-Body Magnetic Resonance Images

Case 1. A 30-year-old pregnant (28 weeks, 6 days) participant with stage 4 primary mediastinal large B-cell lymphoma. Image 1A: Composite coronal short tau inversion recovery (STIR) of the whole body demonstrates conglomerate mediastinal adenopathy or mass (red arrow) and lung nodules (yellow arrow). Image 1B: Axial STIR image of the chest demonstrates anterior mediastinal adenopathy/mass (red arrow) and multiple lung nodules bilaterally. Yellow arrow identifies one of several nodules in the right and left lungs. Image 1C: Axial STIR demonstrates a mass in or adjacent to the tail of the pancreas (red arrow). Image 1D: Axial STIR demonstrates a mass in the posterior right kidney (red arrow). Case 2. A 40-year-old pregnant (14 weeks, 6 days) participant with stage 3 breast cancer. Image 2A: Subtle lateral 1.5 cm right breast mass (red arrow) noted on axial STIR image of the chest. Image 2B: Lateral right breast mass more conspicuous on axial b-800 diffusion image (red arrow). Image 2C: Right infraclavicular adenopathy (yellow arrow) noted on axial STIR image of the chest. Image 2D: Right infraclavicular and axillary adenopathy (yellow arrow) noted on composite coronal STIR image of the neck, chest, and upper abdomen. Case 3. A 30-year-old pregnant (22 weeks) participant with stage 3 adrenocortical carcinoma. Image 3A: Composite coronal STIR of the whole body demonstrates a right adrenal mass (red arrow). Image 3B: Axial STIR image demonstrates a 6 x 6.3 x 5.8 cm right adrenal mass (red arrow). Axial b-800 (image 3C) and axial apparent diffusion coefficient (ADC) (image 3D) demonstrate diffusion restriction (red arrows). Image 3E: Axial b-800 image demonstrates retroperitoneal adenopathy (yellow arrows). Case 4. A 34-year-old pregnant (24 weeks) participant with a 17 x 15 x 13 cm intramural fibroid. Image 4A: Composite coronal STIR image of the lower chest, abdomen, pelvis, and thighs demonstrates a large left-sided intramural uterine fibroid (red arrow). Adjacent intrauterine fetus noted. Fetal head identified (yellow arrow).