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Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics  Maksym.

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Presentation on theme: "Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics  Maksym."— Presentation transcript:

1 Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics  Maksym Misyura, Tong Zhang, Mahadeo A. Sukhai, Mariam Thomas, Swati Garg, Suzanne Kamel-Reid, Tracy L. Stockley  The Journal of Molecular Diagnostics  Volume 18, Issue 6, Pages (November 2016) DOI: /j.jmoldx Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2 Figure 1 Variant allele frequency detection between the Ion Proton-Cancer Hotspot Panel (CHP) and the MiSeq-Amplicon Cancer Panel (ACP) was compared according to Bland-Altman (A) and linear regression (B) analyses of concordant calls. The values for degree of agreement (black dashed lines), bias (black dotted line), and systematic error (gray line) are shown, including the P values for the presence of bias and systematic error. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3 Figure 2 A total of 749 and 346 variants detected by the MiSeq-Amplicon Cancer Panel (A and B) and the Ion Proton-Cancer Hotspot Panel (C and D) were distributed across a range of genes and variant allele frequencies. Variants listed as other were detected in one of the following genes: RET, AKT1, CDH1, ERBB4, GNA11, IDH2, KIT, MLH1, NOTCH1, RB1, ABL1, FGFR2, HRAS, IDH1, MPL, SMARCB1, SMO, GNAQ, STK11, CSF1R, FLT3, KDR, PDGFRA, FGFR1, HNF1A, PTPN11, and SMAD4. The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4 Figure 3 Integration of the MiSeq-Amplicon Cancer Panel (ACP) and the Ion Proton-Cancer Hotspot Panel (CHP) sequencing platforms into a single workflow. Four hundred forty-two samples were sequenced by the MiSeq-ACP. Two hundred three cases were sequenced by the Ion Proton-CHP because of low quantity and/or quality, including 24 samples that yielded inconclusive results by the MiSeq-ACP because of borderline quality and/or quantity. DNA quantity: >40 ng/μL∗, 10–40 ng/μL†, <10 ng/μL‡. DNA quality: ΔCt >3.2§ and ΔCt <3.2¶. n = 179 (low quantity and/or quality). The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx ) Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

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