Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation.

摘要: Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and revolutionizing molecular testing. However, the large amounts of raw data produced by next-generation assays need for complex bioinformatics analyses present unique challenges. Proficiency testing has traditionally been designed to evaluate their entirety; however, it can be alternatively applied separate assay components. We developed implemented a multi-institutional proficiency approach directly assess custom variant interpretation processes. Six laboratories, all which use same commercial library preparation kit analysis tumor specimens, each submitted (FASTQ files) from four samples. These 24 file sets were then deidentified redistributed five institutions according clinically validated approach. Among there was high rate concordance calling single-nucleotide variants, particular those we considered significant (100% concordance). discordance insertions/deletions, with only two seven being called participating laboratories. Missed calls addressed laboratory improve Thus, through our alternative approach, identified bioinformatic detection insertions/deletions as an area concern performing