Additional file 2: Table S1, Table S2, Table S3, Table S4, Table S5, and Table S6. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

Table S1. Sequencing metrics for libraries prepared with both Agilent SureSelect XT v.5 and Roche NimbleGen v.3.0 kits starting from five matched FF and FFPE tumor samples. Table S2. Variant detection comparison between matched FF-FFPE pairs. For each matched FF-FFPE pair, the number and the percentage of both SNVs and InDels common to both sample types, and unique to either FF or FFPE sample are reported. Table S3. Genotype CR and NRDR between matched FF-FFPE pairs at increasing coverage thresholds. For each matched FF-FFPE pair, the genotype CR was computed as the ratio between the sum of concordant genotypes and the sum of all genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both samples (a). For each matched FF-FFPE pair, the NRDR was computed as the ratio between the sum of non-concordant genotypes and the sum of all non-reference genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both samples (b). Table S4. Genotype CR and NRDR between matched FF-FFPE pairs computed for each transition type at increasing coverage thresholds. For each matched FF-FFPE pair, the genotype CR for each transition type was computed as the ratio between the sum of concordant genotypes and the sum of all genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both samples; p-values for two-tail t-test for each comparison between two transition types are reported at the bottom of the table (a). For each matched FF-FFPE pair, the NRDR for each transition type was computed as the ratio between the sum of non-concordant genotypes and the sum of all non-reference genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both samples; p-values for two-tail t-test for each comparison between two transition types are reported at the bottom of the table (b). Table S5. Variant detection comparison between exome libraries prepared with both Agilent SureSelect and Roche NimbleGen kit. The table reports the total number and the percentage of SNVs and InDels common to both library prep types for each sample, and unique to either Agilent SureSelect and Roche NimbleGen kit. The comparison was performed considering both the whole kit-specific target region and the 42 Mb of common target region. Table S6. Genotype CR and NRDR rates within the shared 42 Mb target region between Agilent SureSelect and Roche NimbleGen at increasing coverage thresholds. For each sample, the genotype CR was computed as the ratio between the sum of concordant genotypes and the sum of all genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both Agilent SureSelect and Roche NimbleGen libraries (a). For each sample, the NRDR was computed as the ratio between the sum of non-concordant genotypes and the sum of all non-reference genotypes called at genomic positions covered at least a certain coverage threshold (from 1 to 50×) in both in both Agilent SureSelect and Roche NimbleGen libraries (b). (XLSX 54 kb)