Donavan T. Cheng, Talia N. Mitchell, Ahmet Zehir, Ronak H

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Presentation transcript:

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) Donavan T. Cheng, Talia N. Mitchell, Ahmet Zehir, Ronak H. Shah, Ryma Benayed, Aijazuddin Syed, Raghu Chandramohan, Zhen Yu Liu, Helen H. Won, Sasinya N. Scott, A. Rose Brannon, Catherine O'Reilly, Justyna Sadowska, Jacklyn Casanova, Angela Yannes, Jaclyn F. Hechtman, Jinjuan Yao, Wei Song, Dara S. Ross, Alifya Oultache, Snjezana Dogan, Laetitia Borsu, Meera Hameed, Khedoudja Nafa, Maria E. Arcila, Marc Ladanyi, Michael F. Berger The Journal of Molecular Diagnostics Volume 17, Issue 3, Pages 251-264 (May 2015) DOI: 10.1016/j.jmoldx.2014.12.006 Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Uniformity of sequence coverage. A: Distribution of mean coverage values across all canonical exons in 341 genes targeted by MSK-IMPACT. Coverage values were computed using a panel of 10 diploid, normal formalin-fixed, paraffin-embedded samples, each run in duplicate. B: Coverage for canonical exons binned by percent GC content. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Selection of variant calling filters. Coverage and variant frequency values are plotted for false-positive variant calls generated by comparing experimental replicates of normal formalin-fixed, paraffin-embedded samples against each other. A: First-tier false-positive calls occurring in hotspot regions. B: Second-tier false-positive calls occurring outside hotspot regions. Dotted lines indicate decision boundaries for rejecting false positives based on thresholds on coverage (DP ≥20×), number of mutant reads (AD ≥8 reads for first-tier events, AD ≥10 reads for second-tier events), and variant frequency (VF ≥2% for first-tier events, VF ≥5% for second-tier events). AD, number of mutant reads; DP, coverage depth; Indel, insertion/deletion; SNV, single nucleotide variation; VF, variant frequency. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Distribution of tumor types among the 284 unique samples profiled for the clinical validation study. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Range of coverage depth values (A) and variant frequencies (B) for known variants detected in 47 exons of 19 genes tested. Gray indicates SNVs, red, indels. Bars indicate mean values, whiskers indicate SEM. indel, insertion/deletion; SNV, single nucleotide variation. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 Variant calling for unmatched tumors. A: Number of variants called on: i) 209 samples for which a matched normal was unavailable, 75 samples where matched normal samples were available; and ii) variant calling was performed against the matched normal; or iii) variant calling was deliberately performed using a generic pooled normal. B: Distribution of variant frequencies for somatic mutations (red line) and additional private germline mutations (black line) identified when a generic pooled normal is used. Bars indicate mean values, whiskers indicate SEM. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 6 Variant frequencies of known SNV (A) and indel (B) calls tracked across successive serial dilutions. indel, insertion/deletion; SNV, single nucleotide variation. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 7 MSK-IMPACT reveals copy number alterations. Log-ratios comparing tumor versus normal coverage values are calculated across all targeted regions for samples containing ERBB2 amplifications: breast cancer sample with ERBB2, GNAS, MAPK1 amplifications, and ATM loss (A), gastric cancer sample with EGFR, ERBB2, and PIM1 amplifications (B). The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 8 MSK-IMPACT reveals structural rearrangements. Integrated Genomics Viewer screenshot of EML4-ALK translocation in a lung adenocarcinoma sample known to be positive for this translocation. The Journal of Molecular Diagnostics 2015 17, 251-264DOI: (10.1016/j.jmoldx.2014.12.006) Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions