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

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Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next- Generation Sequencing Bioinformatics and Variant Interpretation Kurtis D. Davies, Midhat S. Farooqi, Mike Gruidl, Charles E. Hill, Julie Woolworth-Hirschhorn, Heather Jones, Kenneth L. Jones, Anthony Magliocco, Midori Mitui, Philip H. O'Neill, Rebecca O'Rourke, Nirali M. Patel, Dahui Qin, Erica Ramos, Michael R. Rossi, Thomas M. Schneider, Geoffrey H. Smith, Linsheng Zhang, Jason Y. Park, Dara L. Aisner The Journal of Molecular Diagnostics Volume 18, Issue 4, Pages 572-579 (July 2016) DOI: 10.1016/j.jmoldx.2016.03.002 Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Sample characteristics. A: Of the 24 sample file sets used in the proficiency test, 20 were derived from formalin-fixed, paraffin-embedded (FFPE) processed clinical samples, one was derived from a Diff-Quik slide processed clinical sample, and three were derived from commercially available calibrators (NA12878, HD129, and HD200). B: Disease type distribution for the 21 clinical samples. C: Distribution of the total number of variants (summary of all variants called by all institutions) reported per sample, including calibrator samples. The Journal of Molecular Diagnostics 2016 18, 572-579DOI: (10.1016/j.jmoldx.2016.03.002) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Variant allele frequency (VAF) concordance. The range of VAF (highest reported minus lowest reported) was calculated for all variants reported by at least two institutions (66 variants total). The distribution of these ranges is shown. The VAF range was ≤5% for most variants (81.8%). The Journal of Molecular Diagnostics 2016 18, 572-579DOI: (10.1016/j.jmoldx.2016.03.002) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions