Cell-Free Liquid Biopsy Test for Ovarian Cancer Proves 91% Accurate

A recent analysis investigating the use of an experimental cell-free DNA (cfDNA) liquid biopsy found that the test was 91% accurate at identifying early-stage epithelial ovarian cancer (EOC), a higher rate than that of other tests currently available.

The study, published in Clinical Cancer Research, showed that the new testing method could help to overcome challenges with diagnosing high-grade serous ovarian cancer (HGSOC), which is typically diagnosed at late stages and is the most lethal EOC subtype. HGSOC has a 5-year survival rate of 40% or less when diagnosed at late stage.

Currently, the most reliable way to diagnose EOC in women with a known pelvic mass is through surgery followed by pathological assessment, and there are no effective screening tools for asymptomatic women. Liquid biopsies utilizing cfDNA could act as a noninvasive, dynamic assessment of disease status in patients with cancer with cfDNA methylation and serve as a promising strategy for early detection.

Researchers performed reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs) between patients with HGSOC and participants with normal ovarian and fallopian tube tissue. After, hybridization probe capturing was performed for 1677 DMRs and constructed the cfDNA liquid biopsy test, known as OvaPrint, on an independent set of cfDNA samples to distinguish between HGSOC and benign masses. A total of 372 samples (tissue, n = 59; plasma, n = 313) were analyzed.

For the development of OvaPrint, RRBS was performed on flash frozen tissue from 35 HGSOC (stage 1, n = 25; stage 3, n = 8; stage 4, n = 2) samples as well as 15 normal fallopian tube tissue and 9 normal ovarian samples. Of the 1677 statistically significant DMRs identified, the median with was 242 bp (IQR, 152-411) and the median number cytosine-phosphate-guanine (CpG) groupings per region of DNA was 11 (IQR, 7-18). The DMRs strongly separated HGSOC from normal fallopian and ovary samples on a uniform manifold approximation and projection plot and with hierarchical clustering.

Interestingly, hierarchical clustering also revealed 2 distinct HGSOC clusters, one of which more closely resembled methylation patterns of normal tissue compared with the other cluster.

Generalizability of the test was accessed using an external EPIC array data set of 99 HGSOC and 12 normal fallopian tissues. Methylation β values between HGSOC and normal tissue were compared for 772 (hypermethylated, n = 383; hypomethylated, n = 389) of the 1677 DMRs that overlapped with at least 1 EPIC array CpG probe.

The researchers developed a targeted assay and used it to profile plasma-derived cfDNA methylation in 182 benign ovarian tumor samples and 82 HGSOC samples of various cancer stages. Fourteen of the HGSOC samples had matching tissue previously sequenced by RRBS, and the remaining samples comprised an independent sample set.

After sequencing, mean β values were input into a machine learning model to assess whether OvaPrint could discriminate between individuals with HGSOC and individuals with benign ovarian masses. The risk assessment concluded that OvaPrint has excellent power to discriminate between HGSOC and benign samples, with an estimated area under the receiver operating characteristic curve of 0.936, indicating high sensitivity and specificity.

Only a small subset of HGSOC samples (n = 12) were consistently misclassified with low OvaPrint scores (<35) across multiple cross-validation repeats.

When generalizing OvaPrint to see if it could identify low-grade tumors, borderline tumors, and other histological subtypes, the test was able to identifying non-HGSOC histotypes and borderline tumors; however, sensitivity was lower in these subtypes. Additional studies are required to fully investigate the screening utility of OvaPrint for HGSOC subtypes.

The researchers concluded, “The focus on HGSOC highlighted the importance of not grouping all EOC into one category for biomarker development, a strategy that has likely hampered previous efforts…. The development of OvaPrint, which is an accurate, noninvasive preoperative test for ovarian cancer has the potential to improve diagnosis and cancer care for the almost 20,000 women diagnosed yearly.”

Reference

Buckley DN, Lewinger JP, Gooden G, et al. OvaPrint™ – a cell-free DNA methylation liquid biopsy for the risk assessment of high-grade serous ovarian cancer. Clin Cancer Res. Published online October 9, 2023. doi:10.1158/1078-0432.CCR-23-1197