Additional file 3: Table S7 and Table S8. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

Table S7. Mean coverage achieved by Agilent SureSelect and Roche NimbleGen libraries within 90 PCR-capture amplicons. Mean coverage ± SD within 90 regions amplified by AmpliSeq Colon and Lung Cancer Panel v.1 (Thermo Fisher Scientific) from ‘FF’, ‘FFPE’ and ‘FF plus FFPE’ samples achieved by Agilent SureSelect and Roche NimbleGen libraries respectively. In each column, the mean coverage values are reported for each amplicon, and the heat map was created using two-color scale (lowest value is represented by dark blue and highest value by dark red). Table S8. Variant calling comparison between the two WES systems (Agilent SureSelect and Roche NimbleGen) and the AmpliSeq Colon and Lung Cancer Panel. List of FFPE and matched FF samples genetic variants called by VC v.4.2 plugin on Ion PGMTM data and GATK pipeline in both exome capture systems. All variants are annotated with gene ID, locus, reference sequence, variant allele according to the hg19 Reference Genome. The red bars show the variant allele frequency (%) detected by VC on Ion pipeline and GATK on both Agilent SureSelect and Roche NimbleGen WES (0* means variant not called but found by IGV visual inspection of BAM files). All variants are annotated for COSMIC or dbSNP (rs number) together with the codons involved and the amino acid change (AA). The 'Effect' column reports if the variant is in a coding region, discerning between nonsynonymous, synonymous and non-sense, or in an intron, downstream the gene or in a splicing region. The last four columns of the table reports the Minor Allele Frequency (MAF) reported in the 1000 Genomes Project, the prediction effect on the protein based on SIFT and Polyphen algorithms and the conservation score namely GERP. For SIFT prediction, the higher the number, the lower is the effect, whereas for Polyphen prediction is the opposite. Thus, a higher score for GERP indicates a higher conservation of the gene across 34 mammalian species. Abbreviation: - not available data. (XLSX 44 kb)