Sureselect hybrid capture kit whole exome v4

42 pituitary adenomas underwent whole exome sequencing, along with DNA from matched normal blood, as previously described (13 (link)). DNA was sonicated to 250 bp fragments, size selected with Agencourt AMPure XP beads, and ligated to specific barcoded adaptors (Illumina TruSeq; Illumina Inc., San Diego, CA) for multiplexed analysis. Exome hybrid capture was performed using the Agilent SureSelect hybrid capture kit (Whole Exome_v4; Agilent Technologies, Santa Clara, CA) and sequenced on a HiSeq 2500 system (Illumina Inc., San Diego, CA). All samples achieved at least 80X coverage in exons (mean coverage = 108X).
Sequence data were aligned to the hg19 (b37) reference sequence using the Burrows-Wheeler Aligner (14 (link)). Sample reads were sorted, duplicate-marked, and indexed using SAMtools and Picard. Bias in base quality score assignments due to flowcell, lane, dinucleotide context and machine cycle were analyzed and recalibrated, and local realignment around insertions or deletions (indels) was achieved using the Genome Analysis Toolkit (GATK) (15 (link), 16 (link)). All paired samples underwent quality control testing to ensure accuracy of tumor-normal pairs. All sequencing files are available for download from the European Genome-phenome Archive (EGA) under accession EGAS00001001714.

A total of nine meningiomas underwent whole genome sequencing, and 57 meningiomas whole exome sequencing, along with DNA from matched blood or saliva, as previously described [6 (link)]. DNA was sonicated to 250 bp fragments, size selected with Agencourt AMPure XP beads, and ligated to specific barcoded adaptors (Illumina TruSeq; Illumina Inc., San Diego, CA) for multiplexed analysis. Exome hybrid capture was performed on 76 meningiomas using the Agilent SureSelect hybrid capture kit (Whole Exome_v4; Agilent Technologies, Santa Clara, CA) and sequenced on a HiSeq 2500 system (Illumina Inc., San Diego, CA). All samples achieved at least 80× coverage in exons (mean coverage = 108×).
Sequence data were aligned to the hg19 (b37) reference sequence using the Burrows-Wheeler Aligner. Sample reads were sorted, duplicate-marked, and indexed using SAMtools and Picard. Bias in base quality score assignments due to flowcell, lane, dinucleotide context and machine cycle were analyzed and recalibrated, and local realignment around insertions or deletions (indels) was achieved using the Genome Analysis Toolkit (GATK). All paired samples underwent quality control testing to ensure accuracy of tumor-normal pairs.