A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma Karen L. Reckamp, MD, Vladislava O. Melnikova,

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A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma Karen L. Reckamp, MD, Vladislava O. Melnikova, MD, PhD, Chris Karlovich, PhD, Lecia V. Sequist, MD, MPH, D. Ross Camidge, MD, PhD, Heather Wakelee, MD, Maurice Perol, MD, Geoffrey R. Oxnard, MD, Karena Kosco, PhD, Peter Croucher, PhD, Errin Samuelsz, BS, Cecile Rose Vibat, PhD, Shiloh Guerrero, BS, Jennifer Geis, PhD, David Berz, MD, Elaina Mann, MS, Shannon Matheny, PhD, Lindsey Rolfe, MB, ChB, Mitch Raponi, PhD, Mark G. Erlander, PhD, Shirish Gadgeel, MD Journal of Thoracic Oncology Volume 11, Issue 10, Pages 1690-1700 (October 2016) DOI: 10.1016/j.jtho.2016.05.035 Copyright © 2016 International Association for the Study of Lung Cancer Terms and Conditions

Figure 1 Mutation (MT) enrichment next-generation sequencing. (A) Comparison between input ratio of mutant-to–wild-type (WT) EGFR copies and output ratio of mutant-to-WT EGFR sequencing reads for five to 500 input mutant copies of indicated EGFR variants diluted in 60 ng (∼18,180 genome equivalents) of WT DNA (mutation abundance of 0.028%–2.7%). Output sequencing reads are means of 18 replicates from six independent next-generation sequencing dilution series experiments performed on three different days by two operators on two MiSeq instruments. Percent mutant is calculated as a fraction of all copies or reads. (B) Data from (A) presented as mutation fold enrichment estimates. Fold enrichment is calculated as the percent of input mutant EGFR molecules divided by the percentage of output mutant EGFR sequencing reads. Journal of Thoracic Oncology 2016 11, 1690-1700DOI: (10.1016/j.jtho.2016.05.035) Copyright © 2016 International Association for the Study of Lung Cancer Terms and Conditions

Figure 2 Quantification of EGFR mutant and wild-type DNA blends by mutation enrichment next-generation sequencing. (A) Analysis of dilution series of indicated mutant EGFR variants spiked into 60 ng (∼18,180 GEq) of WT DNA. An analysis algorithm was applied to transform the mutant EGFR sequencing reads into the absolute mutant copies detected. The box-and-whisker plots show the median (center line), 25th, and 75th percentiles (box) with the connecting “whiskers” extending from the first quartile minus 1.5 of the interquartile range (the third quartile minus the first quartile) and the third quartile plus 1.5 of the interquartile range. (B) Interrun reproducibility of the EGFR exon 19 deletions, L858R, and T790M mutation enrichment next-generation sequencing assays for the dilution series shown in (A). Coefficient of variation percent (CV%) is presented. (C) Quantification of twofold or 2.5-fold differences between subsequent mutant copy input levels. The expected fold ratio was calculated as the ratio of the two input mutant copy levels. The observed fold ratio was calculated as the ratio of two means for two measured mutant copy levels with a 95% confidence interval (CI). Journal of Thoracic Oncology 2016 11, 1690-1700DOI: (10.1016/j.jtho.2016.05.035) Copyright © 2016 International Association for the Study of Lung Cancer Terms and Conditions

Figure 3 Contingency tables for the analysis of EGFR T790M mutation in matched tumor, urine, and plasma specimens from patients enrolled in the TIGER-X clinical trial. (A) Urine versus tumor analysis of T790M in 63 matched tumor and urine specimens. (B) Plasma versus tumor analysis of T790M in 60 matched tumor and plasma specimens. (C) Urine versus plasma analysis of T790M in 60 matched urine and plasma specimens. (D) Venn diagram showing T790M-positive status of 60 cases with available matched tumor, plasma, and urine specimens. Four cases not identified as T790M-positive by tumor, plasma, or urine are not depicted in the diagram. FFPE, formalin-fixed, paraffin-embedded. Journal of Thoracic Oncology 2016 11, 1690-1700DOI: (10.1016/j.jtho.2016.05.035) Copyright © 2016 International Association for the Study of Lung Cancer Terms and Conditions

Figure 4 Longitudinal dynamics of EGFR T790M signal in urine of patients treated with rociletinib. (A) A rapid decrease in urinary T790M signal from baseline was observed after one cycle of treatment (21 days) in all patients treated with rociletinib. (B) Clinical outcomes of patients in the longitudinal analysis. Best overall confirmed response was assessed by investigator. For patient 2, percent change in urine T790M from baseline was estimated at day 42. PR, partial response; SD, stable disease. Journal of Thoracic Oncology 2016 11, 1690-1700DOI: (10.1016/j.jtho.2016.05.035) Copyright © 2016 International Association for the Study of Lung Cancer Terms and Conditions