Determining Minimal Residual Disease Using ctDNA Deep Sequencing

Condition(s) studied

Investigational drug(s) / intervention(s)

NGS sequencing of mutations selected based on sequencing of primary tumors: Sequencing of the primary tumor will be performed on a MiSeq instrument using the Accel-Amplicon panel, which covers the most common mutations. For deep sequencing of ctDNA, 2-3 genomic regions carrying mutations in the primary tumor will be selected for the patient. For these regions, sets of universal primers will be designed to amplify the mutations most commonly found in solid tumors (RAS, BRAF, TP53, EGFR, APC, etc.). Another set of universal primers will contain a sequence for indexing individual samples, enabling the parallel sequencing of up to 96 samples simultaneously. The sequencing library will be analyzed on a NextSeq 500 instrument, which allows for up to 400 million reads in a single sequencing run. The sequencing results will then be correlated with the clinical course of the disease.

Study summary

Preoperative neoadjuvant chemotherapy is the standard treatment for locally advanced gastrointestinal tumours. However, not all patients respond to preoperative treatment. Early identification of progression during neoadjuvant chemotherapy or diagnosis of early disease relapse during adjuvant treatment is essential to modify the treatment strategy. The aim of this project is to validate ctDNA as a biomarker of molecular relapse/progression of disease.

Eligibility

Primary outcome measure(s)

• Sensitivity of targeted NGS assay for ctDNA mutation detection — Through study completion, an average of 24 months.
  Proportion of tumor-confirmed driver mutations detected in plasma cfDNA using the developed targeted NGS assay. Unit of Measure: Percentage (%)

Trial sites (1)

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