Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation
Autor: | Charles E. Hill, Julie Woolworth-Hirschhorn, Linsheng Zhang, Mike Gruidl, Philip H. O'Neill, Jason Y. Park, Midori Mitui, Rebecca O’Rourke, Nirali M. Patel, Dahui Qin, Anthony M. Magliocco, Geoffrey H. Smith, Heather Jones, T. Schneider, Kenneth L. Jones, Erica Ramos, Midhat S. Farooqi, Kurtis D. Davies, Michael R. Rossi, Dara L. Aisner |
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Jazyk: | angličtina |
Rok vydání: | 2016 |
Předmět: |
0301 basic medicine
FASTQ format Laboratory Proficiency Testing Computer science Concordance Library preparation Bioinformatics DNA sequencing Pathology and Forensic Medicine 03 medical and health sciences 0302 clinical medicine Proficiency testing medicine Humans Genetic Testing Genetic testing medicine.diagnostic_test Computational Biology High-Throughput Nucleotide Sequencing 030104 developmental biology Health Care Surveys 030220 oncology & carcinogenesis Molecular Medicine Laboratories Raw data |
DOI: | 10.17615/5nnt-6558 |
Popis: | Next-generation sequencing is becoming increasingly common in clinical laboratories worldwide and is revolutionizing clinical molecular testing. However, the large amounts of raw data produced by next-generation sequencing assays and the need for complex bioinformatics analyses present unique challenges. Proficiency testing in clinical laboratories has traditionally been designed to evaluate assays in their entirety; however, it can be alternatively applied to separate assay components. We developed and implemented a multi-institutional proficiency testing approach to directly assess custom bioinformatics and variant interpretation processes. Six clinical laboratories, all of which use the same commercial library preparation kit for next-generation sequencing analysis of tumor specimens, each submitted raw data (FASTQ files) from four samples. These 24 file sets were then deidentified and redistributed to five of the institutions for analysis and interpretation according to their clinically validated approach. Among the laboratories, there was a high rate of concordance in the calling of single-nucleotide variants, in particular those we considered clinically significant (100% concordance). However, there was significant discordance in the calling of clinically significant insertions/deletions, with only two of seven being called by all participating laboratories. Missed calls were addressed by each laboratory to improve their bioinformatics processes. Thus, through our alternative proficiency testing approach, we identified the bioinformatic detection of insertions/deletions as an area of particular concern for clinical laboratories performing next-generation sequencing testing. |
Databáze: | OpenAIRE |
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