Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Circulating Tumor DNA in Breast Cancer

Abstract

While identifying genomic alterations in tumor tissue is the current gold-standard technique for molecular profiling, circulating tumor DNA (ctDNA) represents a noninvasive method of assessing genomic alterations using peripheral blood. The concordance of genomic alterations between two commercially available ctDNA and tissue biopsies was compared in 45 patients with breast cancer using paired next-generation sequencing tissue and ctDNA biopsies. Across all genes, concordance between the two platforms was 91.0% to 94.2%. When only considering genomic alterations in either assay (e.g., excluding wild type/wild type genes), concordance was 10.8% to 15.1% with full plus partial concordance of 13.8% to 19.3%. Concordant mutations were associated with significantly higher variant allele frequency. Over half of mutations detected in either technique were not detected using the other biopsy technique. Including variants of unknown significance, the average number of alterations per patient was significantly higher for tissue (4.56) compared with ctDNA (2.16). When eliminating alterations not detectable in the ctDNA assay, mean number of alterations for tissue and ctDNA was similar (2.67 for tissue, 2.16 for ctDNA). Across five representative genes (TP53, PIK3CA, ERBB2, BRCA1, and BRCA2), sensitivity and specificity were 35.7% and 95.0%, respectively. Concordance when genomic alterations was detected in either tissue or ctDNA was low with each technique detecting a significant amount of nonoverlapping mutations. Potential explanations for the lack of concordance include tumor heterogeneity, different sequencing techniques, spatial and temporal factors, and potential germline DNA contamination. The study indicates that both tissue and blood-based NGS may be necessary to describe the complex biology of breast cancer.

Clinical Application of Circulating Tumor DNA in the Genetic Analysis of Patients with Advanced GIST

“…Yao and colleagues (20) showed that the overall concordance rate of gene mutations between tissue DNA and ctDNA detection was 78.21% in patients with advanced non-small cell lung cancer. Another study indicated that the concordance of genomic alterations between tissue DNA and ctDNA was 91.0%-94.2% in breast cancer (21). Consistent with these previous studies, we obtained an overall concordance rate between ctDNA and tissue DNA detection of 71.9%, with moderate concordance.…”

Clinical factors associated with circulating tumor DNA (ctDNA) in primary breast cancer

“…Because tissue sequencing is still the 'gold standard' for molecular profiling of solid tumors, we evaluated the overall concordance of somatic alterations between tumor DNA and ctDNA. While a prior study demonstrated unsatisfactory correspondence, two limitations may have influenced the accuracy of these results: The median interval between the collection of tumor tissues and peripheral blood was 146 days, and ctDNA and tumor DNA were each sequenced using different platforms (Guardant360 and Foundation One) (Chae et al, 2017). Alternatively, Kaisaki et al analyzed genomic alterations of ctDNA and primary tumors in 21 melanoma patients and showed an ideal concordance between ctDNA and tumor DNA when samples were collected before treatment, confirming that the interval between sample of tissue and peripheral blood affects sequencing results (Kaisaki et al, 2016).…”

Liquid biopsy in breast cancer: A comprehensive review

“…Quantitative analysis of ctDNA using ddPCR assays is performed on the basis of the correlation between disease stage and ctDNA:cfDNA concentration ratio . On the other hand, qualitative studies use NGS to examine ctDNA for variations in cancer hotspots or the entire genome to examine early‐stage disease, response to treatment and prognosis . Detection of single‐nucleotide variations is generally performed through sensitive methods such as BEAMing, Safe‐SeqS, TamSeq and ddPCR assays, while WGS is used to detect copy number variations (CNVs) and chromosomal instabilities .…”

“…107 On the other hand, qualitative studies use NGS to examine ctDNA for variations in cancer hotspots or the entire genome to examine early-stage disease, response to treatment and prognosis. 108,109 Detection of single-nucleotide variations is generally performed through sensitive methods such as BEAMing, Safe-SeqS, TamSeq and ddPCR assays, while WGS is used to detect copy number variations (CNVs) and chromosomal instabilities. 102,110,111 Analysis of single-locus hotspots is achieved through ddPCR assays, 112,113 but this approach is limited when searching for a large number of variants or when looking for novel variants.…”