Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing

Abstract

Analysis of circulating cell-free DNA (cfDNA) has opened new opportunities for characterizing tumour mutational landscapes with many applications in genomic-driven oncology. We developed a customized targeted cfDNA sequencing approach for breast cancer (BC) using unique molecular identifiers (UMIs) for error correction. Our assay, spanning a 284.5 kb target region, is combined with a novel freely-licensed bioinformatics pipeline that provides detection of low-frequency variants, and reliable identification of copy number variations (CNVs) directly from plasma DNA. We first evaluated our pipeline on reference samples. Then in a cohort of 35 BC patients our approach detected actionable driver and clonal variants at low variant frequency levels in cfDNA that were concordant (77%) with sequencing of primary and/or metastatic solid tumour sites. We also detected ERRB2 gene CNVs used for HER2 subtype classification with 80% precision compared to immunohistochemistry. Further, we evaluated fragmentation profiles of cfDNA in BC and observed distinct differences compared to data from healthy individuals. Our results show that the developed assay addresses the majority of tumour associated aberrations directly from plasma DNA, and thus may be used to elucidate genomic alterations in liquid biopsy studies.

DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN

“…Although advances in sequencing technologies have reduced the cost of high read depth, the effective depth remains low in the case of prenatal fetal detection ( Alba et al, 2012 ), low purity tumors ( Wilkerson et al, 2014 ), and subclonal structures ( Al-Katib et al, 2020 ). For example, liquid biopsies that identify cancer mutations through blood material have been proposed as a transformative technology for early cancer screening and residual disease monitoring ( Kleftogianniss et al, 2020 ). However, the proportion of ctDNA (cell-free tumor DNA) in the overall blood DNA is relatively low, particularly in situations of low disease burden, such as early cancer detection, and residual disease surveillance after therapeutic intervention ( Underhill., 2021 ).…”

The Detection of Cancer Epigenetic Traces in Cell-Free DNA

“…Currently, these fundamental properties of cell-free DNA (cfDNA) analysis are translated to several applications in clinical oncology, generally termed as liquid biopsy, namely, molecular tumor profiling ( 4 – 6 ), therapy response monitoring ( 7 – 9 ), minimal residual disease (MRD) and recurrence detection ( 10 – 12 ), as well as early cancer diagnostics (representing a highly desirable but still elusive output) ( 13 ). Most of these clinical aims can be partially achieved through careful analysis of somatic mutations present in the tumor fraction of cfDNA (circulating tumor DNA, ctDNA) ( 14 – 16 ).…”