Use of liquid biopsies to monitor disease progression in a sarcoma patient: a case report

Abstract

BackgroundMany patients experience local recurrence or metastases after receiving potentially curative treatment, and early detection of these events is important for disease control. Recent technological advances make it possible to use blood plasma containing circulating cell-free tumour DNA (ctDNA) as a liquid biopsy. In this case report we show how serial liquid biopsies can be used to monitor the disease course and detect disease recurrence in a sarcoma patient.Case presentationA 55-year-old male presented with a rapidly growing, painful palpable mass in the left groin region, and a biopsy revealed a high-grade malignant spindle cell sarcoma. No metastases were detected on radiologic imaging scans. Using targeted resequencing with a custom 900 cancer gene panel, eight somatic mutations among them KRAS and NF1, were identified in the primary tumour. Targeted resequencing of plasma cell-free DNA (ctDNA) collected before and after surgery and at disease progression confirmed the presence of six of eight mutations at all three time points. The ctDNA level, estimated from the somatic allele frequencies of these six mutations, was high in plasma taken at the time of surgery, at levels similar to the primary tumour. Detection of low levels of ctDNA three days after surgery indicated persistent microscopic disease. Repeated radiologic imaging six weeks postoperatively showed widespread metastatic disease in the lungs, skeleton and the pelvic region. At this time point there was a dramatic increase in the ctDNA level, reflecting the disease progression of the patient. The patient had an unusually aggressive cancer, and succumbed to the disease 13 weeks after surgery.ConclusionsThis case report demonstrated that targeted resequencing of ctDNA from longitudinal collected plasma can be used to monitor disease progression in a soft tissue sarcoma patient, including manifestation of metastatic disease. The ctDNA represented the genomic profile of the tumour, supporting clinical use of liquid biopsies to identify tumour-specific mutations as well as recurrent disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-016-2992-8) contains supplementary material, which is available to authorized users.

Circulating tumour-derived DNA in metastatic soft tissue sarcoma

“…The second reported case evaluated the ctDNA characteristics of a patient with spindle cell sarcoma that developed disease recurrence soon after attempted curative treatment. Based on the detection of ctDNA both intra- and post-operatively, the authors of this study proposed that the persistence of microscopic disease post operatively explained this early relapse, and also highlighted a potential role for ctDNA as a marker of small volume disease in cases of STS [ 11 ].…”

“…In several malignant tumours, ctDNA characteristics correlate closely with tumour burden, disease recurrence and treatment resistance, highlighting ctDNA as an exciting potential source of biomarkers in cancer patients [ 6 – 9 ]. To date only two single case studies [ 10 , 11 ] have evaluated the presence (and so the potential clinical relevance) of cfDNA/ctDNA in STS patients. As a consequence very little is known about the circulating nucleic acid characteristics of STS patients, including what proportion of STSs shed DNA into the circulation.…”

Noninvasive Detection of ctDNA Reveals Intratumor Heterogeneity and Is Associated with Tumor Burden in Gastrointestinal Stromal Tumor

“…Blood was collected in Cell-Free DNA BCT tubes (Streck), and plasma and normal white blood cells were processed as previously described (19) and stored at À80 C. cfDNA, representing both normal and tumor DNA, was isolated from 2 to 4 mL (average 2.2 mL) plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen) and stored at À20 C. Normal genomic DNA from white blood cells was isolated using QIAamp DNA Mlood Mini Kit (Qiagen).…”

“…Raw reads were processed using the Illumina CASAVA (v. 1.8.2) to demultiplex data and filter out the low-quality reads. The mapping, alignment, quality assessment, and somatic variant calling were performed as previously described (19).…”

Preclinical Evaluation of Vemurafenib as Therapy for BRAFV600E Mutated Sarcomas

“…Three of the sarcoma cell lines (SA-4, SW872 and LPS510) were exome-sequenced at the Oslo University Hospital Genomics Core Facility using Agilent SureSelect XT Human All Exon v5 protocol and Illumina sequencing by synthesis technology on a HiSeq 4000 instrument (2 × 150 bp). Preprocessing, mapping of the reads and calling of variants was performed as previously described [ 44 ]. RNA-sequencing was performed at the Genomics Core Facility for three of the cell lines, SA-4, SW872 and LPS510, using the Illumina TruSeq Stranded mRNA Library Prep kit for NeoPrep following supplier’s instructions.…”