1. Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing
- Author
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Jun Xian Liew, Swee Ho Lim, Raymond Ng, Iain Beehuat Tan, Benita Kiat-Tee Tan, Gek San Tan, Tony Kiat Hon Lim, Yoon Sim Yap, Danliang Ho, Chih Chuan Shih, Ann Siew-Gek Lee, Sarah Ng, Polly Suk Yean Poon, Dimitrios Kleftogiannis, Anna Gan, and Kiang Hiong Tay
- Subjects
Adult ,DNA Copy Number Variations ,lcsh:Medicine ,Breast Neoplasms ,Computational biology ,Biology ,Genome informatics ,DNA sequencing ,Article ,Circulating Tumor DNA ,chemistry.chemical_compound ,Breast cancer ,medicine ,Cancer genomics ,Biomarkers, Tumor ,Humans ,Copy-number variation ,Liquid biopsy ,Fragmentation (cell biology) ,lcsh:Science ,Gene ,Aged ,Multidisciplinary ,lcsh:R ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Middle Aged ,medicine.disease ,chemistry ,Mutation ,Next-generation sequencing ,Immunohistochemistry ,lcsh:Q ,Female ,DNA - 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.
- Published
- 2020