We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 @entity406 -fixed, @entity982 -embedded (FFPE) @entity5 samples. Forty @entity1149 ( @entity1149 ), 30 @entity320 , and 30 gastrointestinal (12 colonic, 10 gastric, and 8 @entity788 ) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina @entity5 ( @entity5 ) 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. @entity5 generated >= 500* 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. @entity5 detected 112 variants overall, and confirmed all known single- @entity4334 variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). @entity5 detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. @entity876 was the most frequently mutated gene in @entity1149 (13  variants; 13/32 samples), @entity344 (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). @entity817 mutations were most common in @entity320 (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid @entity5 specimens using @entity5 , benchtop instruments, and vendor-supplied bioinformatics pipelines.

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, XXXX , and @entity344 .

@entity788 :: ('MESH:D010190', 'Disease') :: ['pancreatic adenocarcinoma'] @entity5 :: ('MESH:D009369', 'Disease') :: ['tumor', 'TST', 'TruSight tumor'] @entity1149 :: ('MESH:D002289', 'Disease') :: ['NSCLC', 'non-small cell lung carcinoma'] @entity406 :: ('MESH:D005557', 'Chemical') :: ['formalin'] @entity344 :: ('MESH:D005767', 'Disease') :: ['gastrointestinal malignancies'] @entity876 :: ('7157', 'Gene') :: ['TP53'] @entity982 :: ('MESH:D010232', 'Chemical') :: ['paraffin'] @entity817 :: ('673', 'Gene') :: ['BRAF'] @entity4334 :: ('D009711', 'Chemical') :: ['nucleotide'] @entity320 :: ('MESH:D008545', 'Disease') :: ['melanoma']
@entity320 :: (MESH:D008545,Disease) :: ['Melanoma']
