Comprehensive Genomic Profiling of ctDNA

We analyzed the mutation profile and TMB as previous study^{11 (link)}; A maximum of 50 ng of DNA was used for the CAPP-Seq ctDNA analyses using the AVENIO ctDNA surveillance kit (Roche Diagnostics, 197 genes). The purified libraries were pooled and sequenced on an Illumina NextSeq. 500 sequencing system (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-Seq2^{12 (link)} and integrated digital error suppression^{13 (link)}. Germline mutations were excluded with the use of the Human Genetic Variation Database (http://www.genome.med.kyoto-u.ac.jp/SnpDB) and the ExAC database.

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Ishii H., Azuma K., Sakai K., Naito Y., Matsuo N., Tokito T., Yamada K., Hoshino T, & Nishio K. (2020). Determination of Somatic Mutations and Tumor Mutation Burden in Plasma by CAPP-Seq during Afatinib Treatment in NSCLC Patients Resistance to Osimertinib. Scientific Reports, 10, 691.

Publication 2020

AVENIO ctDNA surveillance kit NextSeq. 500 sequencing system AVENIO ctDNA Analysis Software

A dna Diagnostics Digital Genes Genetic variation Genome Germline mutations Human Mutation

Corresponding Organization :

Other organizations : Kurume University, Kindai University, Koga Hospital

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Variable analysis

independent variables

DNA amount (maximum of 50 ng) used for CAPP-Seq ctDNA analyses

dependent variables

Mutation profile
Tumor Mutational Burden (TMB)

control variables

Germline mutations excluded using the Human Genetic Variation Database and the ExAC database

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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