Section IV: Non–small cell lung cancer and malignant melanoma

Fisher, Kevin E.; Pillai, Rathi N.; Kudchadkar, Ragini R.; Rossi, Michael R.

doi:10.1016/j.currproblcancer.2014.08.007

Cited by 2 publications

(1 citation statement)

References 158 publications

(125 reference statements)

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“…Patients with activating mutations in KRAS do not benefit from targeted therapies and are typically treated with standard chemotherapeutic regimens or enrolled in clinical trials. 43 One melanoma sample that was tested for codon V600 mutations harbored a BRAF p.S616F mutation (MEL-11), which is described in melanoma. 44 Also, all four NSCLC patients with EGFR exon 19 deletions harbored concomitant TP53 mutations, and there are data to suggest that TP53 is involved in resistance mechanisms leading to EGFR tyrosine kinase inhibitor treatment failure.…”

Section: E42mentioning

confidence: 99%

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies

Fisher

Zhang

Wang

et al. 2016

The Journal of Molecular Diagnostics

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We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated !500Â coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at !5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n Z 27), deletions (n Z 5), insertions (n Z 3), and multinucleotide variants (n Z 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/ 80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines. (J Mol Diagn 2016, 18: 299e315; http:// dx

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Section: E42mentioning

confidence: 99%