Figure 1 Overview of the IMPACT Analysis Pipeline

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Presentation transcript:

Figure 1 Overview of the IMPACT Analysis Pipeline From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Figure 2 Prediction algorithms on the deleterious variants From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Figure 6 Validation of the BRAF, NRAS, and CDKN2A mutations Figure 6 Validation of the BRAF, NRAS, and CDKN2A mutations. (A) By using qBiomarker Melanoma Somatic Mutation PCR array, we validated BRAF p.V600E is identified in the pre-treatment sample. NRAS p.Q61K was not detected and CDKN2A was detected in the pre-treatment sample. (B) In post-BRAFi/MEKi treatment, BRAF p.V600E and NRAS p.Q61K were detected, and CDKN2A was not detected. This confirms the IMPACT variants and copy number detection in these 3 genes. From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Figure 5 IMPACT tumor heterogeneity and clonal dynamic analyses Figure 5 IMPACT tumor heterogeneity and clonal dynamic analyses. (A) In the melanoma patient, allele frequency changes for BRAF (p.V600E) and NRAS (p.Q61K), and CDKN2A gene copy number changes between the 3 time points. (B) Allele frequency distributions of somatic mutations in pre-treatment, post-BRAFi-treatment, and post-BRAFi/MEKi treatment in the melanoma patient From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Figure 3 Venn diagram of the somatic variants identified by IMPACT in the 3 melanoma samples From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Figure 4 CDKN2A loss detection in the melanoma samples From: IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples J Am Med Inform Assoc. 2016;23(4):721-730. doi:10.1093/jamia/ocw022 J Am Med Inform Assoc | © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com