1. Molecular Diagnostic Profiling of Lung Cancer Specimens with a Semiconductor-Based Massive Parallel Sequencing Approach 
Volker Endris, Roland Penzel, Arne Warth, Alexander Muckenhuber, Peter Schirmacher, Albrecht Stenzinger, Wilko Weichert 
The Journal of Molecular Diagnostics 
Volume 15, Issue 6, Pages (November 2013)
DOI: /j.jmoldx
Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Tumor/normal titration. Sample VLR010 was mixed with matching normal tissue DNA, yielding total tumor DNA contents of 80% (with no admixed normal DNA), 60%, 40%, 20%, and 10%. Independent libraries for all tumor DNA titration samples were sequenced using the Ion AmpliSeq cancer panel. Three SNPs were detected in the tumor, in EGFR (p.L858R), TP53 (p.R273L), and PDGFRA (p.Y671∗). Although all SNPs were detectable in titrations with ≥40% tumor-cell content, the SNPs in TP53 and PDGFRA fell below the detection limit of the variant caller in the two lower titrations.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

3. Figure 2
EGFR amplification detection. A: Normalized relative read counts of the eight amplicons covering the EGFR gene in a subset of samples. Increased read counts were observed for samples VLR011, VLB012, and VLx025 with variation in distribution and coverage of EGFR exons. B: Validation of EGFR exon 19 amplification in sample VLx025 using a qPCR copy number assay. Both qPCR and MPS show a similar degree of exon 19 amplification in sample VLx025, but not in sample VLB012, in which only exon 20 was found amplified in the MPS reads. VLB004 and VLB005 are control samples, without sign of amplification in the MPS data. NGS, next-generation sequencing.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

4. Figure 3
Detection of ERBB2 amplification. Additional sequencing of seven breast cancer samples (positively screened for ErbB2 immunoreactivity) demonstrated increased relative read counts across the four analyzed ERBB2 amplicons in the Ion AmpliSeq cancer panel, similar to sample VLB003. No amplification of ERBB2 was detected in any other control samples analyzed.
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions