WES was performed by first fragmenting 1 μg of DNA (Bioruptor, diagenode, Liége, Belgium). The DNA fragments were then end-repaired and adaptor-ligated with sample index barcodes. Following size selection, the SeqCap EZ Human Exome Library version 2.0 kit (Roche NimbleGen, Madison, WI, USA) was used to enrich for the whole exome. The DNA libraries were then sequenced with a paired-end 2 × 100 bp protocol aiming for an average coverage of 90× and 120× for the normal and tumor DNA, respectively. The primary data were filtered for signal purity with the Illumina Realtime Analysis software.
WGS was performed with a read length of 2 × 100 bp. The samples were processed to provide 110 Gb of sequence, thus amounting to a mean coverage of 30× for both tumor and matched normal.
For RNA-seq, cDNA libraries were prepared from PolyA + RNA following the Illumina TruSeq protocol for mRNA (Illumina, San Diego, CA, USA). The libraries were sequenced with a paired-end 2 × 100 bp protocol resulting in 8.5 Gb per sample, and thus in a 30× mean coverage of the annotated transcriptome.
Whole genome, whole exome and transcriptome sequencing reactions were performed on an Illumina HiSeq 2000 sequencing instrument (Illumina, San Diego, CA, USA).
WGS was performed with a read length of 2 × 100 bp. The samples were processed to provide 110 Gb of sequence, thus amounting to a mean coverage of 30× for both tumor and matched normal.
For RNA-seq, cDNA libraries were prepared from PolyA + RNA following the Illumina TruSeq protocol for mRNA (Illumina, San Diego, CA, USA). The libraries were sequenced with a paired-end 2 × 100 bp protocol resulting in 8.5 Gb per sample, and thus in a 30× mean coverage of the annotated transcriptome.
Whole genome, whole exome and transcriptome sequencing reactions were performed on an Illumina HiSeq 2000 sequencing instrument (Illumina, San Diego, CA, USA).