Matched Whole-Genome Sequencing (WGS) and Whole-Exome Sequencing (WES) of Tumor Tissue with Circulating Tumor DNA (ctDNA) Analysis: Complementary Modalities in Clinical Practice

Abstract

Tumor heterogeneity, especially intratumoral heterogeneity, is a primary reason for treatment failure. A single biopsy may not reflect the complete genomic architecture of the tumor needed to make therapeutic decisions. Circulating tumor DNA (ctDNA) is believed to overcome these limitations. We analyzed concordance between ctDNA and whole-exome sequencing/whole-genome sequencing (WES/WGS) of tumor samples from patients with breast (n = 12), gastrointestinal (n = 20), lung (n = 19), and other tumor types (n = 13). Correlation in the driver, hotspot, and actionable alterations was studied. Three cases in which more-in-depth genomic analysis was required have been presented. A total 58% (37/64) of patients had at least one concordant mutation. Patients who had received systemic therapy before tissue next-generation sequencing (NGS) and ctDNA analysis showed high concordance (78% (21/27) vs. 43% (12/28) p = 0.01, respectively). Obtaining both NGS and ctDNA increased actionable alterations from 28% (18/64) to 52% (33/64) in our patients. Twenty-one patients had mutually exclusive actionable alterations seen only in either tissue NGS or ctDNA samples. Somatic hotspot mutation analysis showed significant discordance between tissue NGS and ctDNA analysis, denoting significant tumor heterogeneity in these malignancies. Increased tissue tumor mutation burden (TMB) positively correlated with the number of ctDNA mutations in patients who had received systemic therapy, but not in treatment-naïve patients. Prior systemic therapy and TMB may affect concordance and should be taken into consideration in future studies. Incorporating driver, actionable, and hotspot analysis may help to further refine the correlation between these two platforms. Tissue NGS and ctDNA are complimentary, and if done in conjunction, may increase the detection rate of actionable alterations and potentially therapeutic targets.

Analysis of the Whole-Exome Sequencing of Tumor and Circulating Tumor DNA in Metastatic Melanoma

“…We now report that ctDNA sequencing provides an accurate, albeit incomplete snapshot of the mutation profile and mutation burden of the patient-matched metastatic tumor. The SNVs found in the patient-matched melanoma gDNA and ctDNA overlapped by 22.7% to 77.6%, which is comparable to gDNA and ctDNA mutation concordance data reported for other cancers [9,10,12,31]. A major caveat of this work is the lack of patient-matched germline analyses, and although we applied a stringent bioinformatic filtering approach to enrich for somatic variants, the number of somatic variants and the concordance data may have been overestimated.…”

“…In our study, 9/10 patients received some sort of systemic treatment, and although melanoma has a very high TMB [38], the concordance between gDNA and ctDNA mutations was variable. Furthermore, although our cohort consisted of gDNA and ctDNA samples collected at different time points, the timing of sample collection was not associated with mutation concordance in our report and in another similar study [12].…”

“…One recent study found substantial discordance between NGS of matched gDNA and ctDNA in several tumor types (including one melanoma sample) and reported that ctDNA analysis may improve detection of hotspot and actionable mutations compared to gDNA alone [12]. Tissue and circulating DNA mutation concordance was reported to be higher in patients who had received systemic therapy and in cancers with high TMB [12]. In our study, 9/10 patients received some sort of systemic treatment, and although melanoma has a very high TMB [38], the concordance between gDNA and ctDNA mutations was variable.…”

“…The genomic profiling of ctDNA using whole genome, whole exome or targeted sequencing is feasible, but technically challenging due to the low quantities and fragmented nature of ctDNA [5][6][7][8]. Nevertheless, several reports have examined the value of sequencing patient-matched tumor gDNA and ctDNA and the results showed variable concordance in the mutation profiles of gDNA and ctDNA derived from patients with neuroblastoma, breast cancer, lung cancer or gastrointestinal malignancies [9][10][11][12]. The degree of concordance between circulating and tumor mutations appears to reflect tumor heterogeneity, which can be influenced by prior therapy, tumor stage and tumor mutation burden [12].…”

A comprehensive analysis of somatic alterations in Chinese ovarian cancer patients

“…Next-generation sequencing (NGS) technology has been widely used in molecular genetic research of various tumors 6 – 8 . Recently, a series of studies on the mutational landscape of ovarian cancer have been reported 9 , 10 .…”