Computational protocol: Extrachromosomal driver mutations in glioblastoma and low grade glioma

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Protocol publication

[…] The overall methodology was as previously described-. Briefly, DNA was extracted from the two distant fragments of frozen tissues, neurosphere cultures (spheres) and PBL using the QIAamp DNA Mini Kit (Qiagen) for 7 patients with glioblastoma. When little material was available (<0.5ug), Whole Genome Amplification (WGA) was performed using REPLI-g Mini Kit (Qiagen). Exome capture was conducted using the SureSelect Human Exon v3 50Mb (Agilent Technologies) reagents and sequencing was performed on Illumina HiSeq2000 instrument with paired-end 105 nt reads. Burrows–Wheeler Aligner (BWA) software was used to align the sequence reads to the human reference genome (NCBI build GRCh37/hg19). SAMtools was used to remove PCR duplicates and to call single-nucleotide variants (SNV). Detection of small insertions and deletions (smINDEL) was conducted with Pindel 0.2.2 software. The average sequencing coverage was 155× per DNA sample (). The search for somatic mutations was restricted to the regions covered at least 20-fold in both the normal and tumor samples. […]

Pipeline specifications

Software tools BWA, SAMtools, Pindel
Application WES analysis
Organisms Homo sapiens
Diseases Glioblastoma, Glioma, Neoplasms
Chemicals Tyrosine