CAPP-Seq ctDNA Surveillance Protocol

The CAPP-Seq of ctDNA (10–50 ng) was performed using the AVENIO ctDNA surveillance kit (Roche Diagnostics, 197 genes) as recently described (18 (link)–20 (link)). The purified libraries were pooled and sequenced on an Illumina NextSeq 500 (Illumina) using the 300-cycle high output kit. Variants were called with the AVENIO ctDNA Analysis Software (Roche Diagnostics), which includes bioinformatics methods from CAPP-Seq (14 (link)) and integrated digital error suppression (15 (link)). Genetic variants previously cataloged by the Exome Aggregation Consortium at a frequency of ≥1% were excluded, and only non-synonymous single nucleotide variants (SNVs), insertions-deletions (Indels), copy number variations (CNVs), and gene fusions involving 197 cancer-related genes were extracted. Twenty plasma samples obtained from 10 patients treated with NAC were successfully analyzed by CAPP-Seq. The bTMB in each sample was evaluated as the number of non-synonymous mutations number per Mb.

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Noguchi T., Sakai K., Iwahashi N., Matsuda K., Matsukawa H., Yahata T., Toujima S., Nishio K, & Ino K. (2020). Changes in the gene mutation profiles of circulating tumor DNA detected using CAPP-Seq in neoadjuvant chemotherapy-treated advanced ovarian cancer. Oncology Letters, 19(4), 2713-2720.

Publication 2020

AVENIO ctDNA surveillance kit AVENIO ctDNA Analysis Software

Cancer genes Copy number variations Diagnostics Digital Exome Gene fusions Genes Genetic variants Indels Non synonymous mutations Nucleotide Patients Plasma Synonymous variants

Corresponding Organization :

Other organizations : Wakayama Medical University, Kindai University

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Variable analysis

independent variables

Quantity of ctDNA used for CAPP-Seq (10–50 ng)

dependent variables

Burden of tumor mutational burden (bTMB) in plasma samples, measured as the number of non-synonymous mutations per Mb

control variables

Patients treated with NAC
197 cancer-related genes analyzed
Genetic variants previously cataloged by the Exome Aggregation Consortium at a frequency of ≥1% were excluded

controls

Positive control: Not explicitly mentioned.
Negative control: Not explicitly mentioned.

Annotations

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