Evaluation of cfDNA as an early detection assay for dense tissue breast cancer

Abstract

A cell-free DNA (cfDNA) assay would be a promising approach to early cancer diagnosis, especially for patients with dense tissues. Consistent cfDNA signatures have been observed for many carcinogens. Recently, investigations of cfDNA as a reliable early detection bioassay have presented a powerful opportunity for detecting dense tissue screening complications early. We performed a prospective study to evaluate the potential of characterizing cfDNA as a central element in the early detection of dense tissue breast cancer (BC). Plasma samples were collected from 32 consenting subjects with dense tissue and positive mammograms, 20 with positive biopsies and 12 with negative biopsies. After screening and before biopsy, cfDNA was extracted, and whole-genome next-generation sequencing (NGS) was performed on all samples. Copy number alteration (CNA) and single nucleotide polymorphism (SNP)/insertion/deletion (Indel) analyses were performed to characterize cfDNA. In the positive-positive subjects (cases), a total of 5 CNAs overlapped with 5 previously reported BC-related oncogenes (KSR2, MAP2K4, MSI2, CANT1 and MSI2). In addition, 1 SNP was detected in KMT2C, a BC oncogene, and 9 others were detected in or near 10 genes (SERAC1, DAGLB, MACF1, NVL, FBXW4, FANK1, KCTD4, CAVIN1; ATP6V0A1 and ZBTB20-AS1) previously associated with non-BC cancers. For the positive–negative subjects (screening), 3 CNAs were detected in BC genes (ACVR2A, CUL3 and PIK3R1), and 5 SNPs were identified in 6 non-BC cancer genes (SNIP1, TBC1D10B, PANK1, PRKCA and RUNX2; SUPT3H). This study presents evidence of the potential of using cfDNA somatic variants as dense tissue BC biomarkers from a noninvasive liquid bioassay for early cancer detection.

Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes

“…SERAC1 encodes a phosphatidylglycerol remodeling protein mediating phospholipid change. Additionally, it is also a known biomarker of breast cancer 83,84 , but the mechanisms of regulating other genes in trans remains unknown. A third enhancer is located on chromosome 2.…”

Variant Characterization of a Representative Large Pedigree Suggests “Variant Risk Clusters” Convey Varying Predisposition of Risk to Lynch Syndrome

“…The MLH1 gene has been established as a causative gene for LS and presents the highest risk of CRC among individuals over 75 (46.6% of women and 51.4% of men) who are affected by the MLH1 variation. Rates range from 0% (at age 30) to 48.3% (at age 75) in females, and from 4.5% (at age 30) to 57.1% (at age 75) in males [ 22 , 23 ]. In another study, MLH1 variants were correlated with the highest risk of developing CRC in both heredity and sporadic cases [ 27 ].…”

“…The full bioinformatics variant analysis (BVA) is described in Figure 2 and the Supplemental Material . We used a novel functional implicated variant pipeline created in our previous work on breast cancer [ 23 ], modified to account for the pedigree relationship between subjects and familial and thus the risk-related nature of the detected variants. Briefly, for each subject’s high-throughput sequencing (HTS) sequence, alignment, poor-quality read filtering, single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants (SVs) were called and variant quality score recalibration and filtering, annotation and removal of common and likely non-functional variants, and assessment of cancer-associated genes were performed.…”