Next-Generation Sequencing of Tissue and Circulating Tumor DNA: The UC San Diego Moores Center for Personalized Cancer Therapy Experience with Breast Malignancies

Abstract

Clinical-grade next-generation sequencing (NGS) of tissueand blood-derived circulating tumor DNA (ctDNA) allows assessment of multiple genomic alterations in patients with cancer. We analyzed ctDNA (54-70 genes) in 62 patients with advanced breast cancer (median ¼ five prior therapies); 38 also had tissue NGS (236-315 genes). Overall, 42 of 62 patients (68%) had detectable (characterized) ctDNA alterations (variants of unknown significance excluded), and 37 of 38 (97%) had tissue alterations. The median (range) number of characterized alterations in ctDNA was 1 (0-7), and in tissue, 4 (0-17). The most common alterations in ctDNA were in TP53 (37% of patients) and PIK3CA (23%), and for tissue, TP53 (37%) and PIK3CA (24%); EGFR amplification was seen in ctDNA (11%), but not in tissue. Concordance between ctDNA and tissue appeared higher if <6 months separated the sample acquisition, although small sample size precluded statistical validation. Overall, 32 of 67 tissue alterations (48%) were also detected in ctDNA; 35 of 72 ctDNA alterations (48%) were also in tissue. Excluding estrogen receptor and ERBB2, 41 of 62 patients (66%) had potentially actionable alterations in ctDNA, and 36 of 38 (95%), in tissue (with potential actionability based on either preclinical or clinical evidence). If !1 genomic alteration had ctDNA !5%, survival was shorter than if ctDNA was <5% (median, 6.7 vs. 17.9 months; P ¼ 0.01). In conclusion, tissue and ctDNA NGS reveal potentially actionable alterations in most patients. The genomic results of ctDNA and tissue NGS overlap, but there are differences, perhaps reflecting temporal spacing and tumor heterogeneity. ctDNA quantification also provides prognostic information.

Assessing the Concordance of Genomic Alterations between Circulating-Free DNA and Tumour Tissue in Cancer Patients

“…Due to logistic and safety limitations of taking multiple biopsies in patients [5], detection of SGAs in the peripheral blood has promising potential as a non-invasive alternative [62]. Regarding biopsy sampling intervals, minimising the collection intervals between cfDNA and tumour tissue enhances concordance rates [32,45,147]. Thompson et al, analysed EGFR mutations in advanced NSCLC patients and found that increasing timing intervals between tumour and cfDNA sampling from less than 2 weeks to more than 6 months, led to significantly lower concordance (p=0 .038) [15].…”

The paradox of cancer genes in non-malignant conditions: implications for precision medicine

“…In recent years, liquid biopsy to detect cfDNA or circulating tumor DNA (ctDNA) has emerged as an attractive non-invasive methodology to discern cancerspecific genomic aberrations in plasma. Numerous studies have reported the utility of ctDNA in advanced cancer [194][195][196][197]. In particular, ctDNA assays can capture a more global portrait of tumor heterogeneity than that provided by tissue DNA (which reflects the small piece of tissue that is biopsied rather than DNA shed from both primary and multiple metastatic sites [198]); therefore, ctDNA can be exploited to monitor tumor response and resistance.…”

<p>Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer</p>

“…42 Even so, several studies reported significant differences between the genomic results of tumor tissue biopsy and cfDNA in MBC patients. [43][44][45][46] Diverse analysis tools, temporal spacing between ctDNA analysis and tumor biopsy, and tumor heterogeneity due to the substantial selection pressure from therapies perhaps contribute to this inconsistency. 43,46,47…”

“…60 In one study by Shatsky et al, ABC patients with at least one alteration with 5% ctDNA had poorer median OS (6.7 months) vs. patients with less than 5% ctDNA (17.9 months) (P = 0.01). 43 The DNA Integrity…”