Computational protocol: Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics

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Protocol publication

[…] DNA extraction was performed on frozen tissue as previously described [] and on FFPE tissue using Biochain’s FFPE Tissue DNA Extraction Kit (#K5019100). Library preparation and WES were performed at BGI Americas using the Agilent SureSelect Human All Exon V5 Kit and Illumina HiSeq 2500 using V3 chemistry, respectively. All samples were sequenced at an average depth of 100× (4 samples per lane generating 12 Gb of raw data per sample). The Burrows-Wheeler Aligner [] tool was used to map all reads to the human genome build GRCh37/hg19. The GATK variant calling pipeline was followed to identify single nucleotide polymorphisms. MuTect 1.1.4 was used to detect somatic single nucleotide variants (SNVs) in 46 candidate genes with clinical significance (Additional file : Table S1). Variants with sufficient coverage were further annotated using Annovar and SNPeff, giving RefSeq gene annotations, amino acid changes, ExAC SIFT, PolyPhen, LTR and MutationTaster scores. […]

Pipeline specifications

Software tools BWA, GATK, Variant Calling Pipeline, MuTect, ANNOVAR, SnpEff, PolyPhen, MutationTaster
Application WES analysis
Organisms Homo sapiens
Diseases Astrocytoma, Brain Neoplasms, Glioma, Neoplasms