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ICR_pHGG_Data_Access_Committee

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Chris Jones
chris.jones@icr.ac.uk

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This DAC controls 14 datasets

Dataset ID	Description	Technology	Samples
EGAD00001003563	Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)	Illumina HiSeq 2000	3
EGAD00001003762	Whole Exome sequencing of paediatric High Grade Gliomas	Illumina HiSeq 2000	99
EGAD00001004036	Whole exome sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. DNA from 86 cases was subjected to Illumina paired end whole exome sequencing using a customised SureSelect Human All Exon V6 capture set. Germline DNA from whole blood was sequenced for 83 cases. 26 cases were sequenced from both fresh frozen tissue and FFPE material, 10 were sequenced from only fresh frozen material and 50 from only FFPE. Data is provided as bwa aligned BAM files	Illumina HiSeq 2000	195
EGAD00001004070	RNA sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. RNA from fresh frozen surgical tissue in 20 cases was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files	Illumina HiSeq 2000	20
EGAD00001004114	The failure to develop effective therapies for paediatric glioblastoma (pGBM) and diffuse intrinsic pontine glioma (DIPG) is in part due to their intrinsic heterogeneity. Analysis of 142 sequenced cases revealed multiple tumour subclones, spatially and temporally co-existing in a stable manner as observed by multiple sampling strategies. This dataset provides multi region sequencing of high grade gliomas and diffuse intrinsic pontine gliomas from 15 patients. DNA was extracted from FFPE sections in 2-13 regions of each tumour and sequenced with Agilent SureSelect whole exome sequencing. Germline DNA was also sequenced in 14 cases. Data was aligned to hg19 with bwa and is provided as 79 separate BAM files.	Illumina HiSeq 2000	79
EGAD00001004116	RNA sequencing of paediatric high grade gliomas and diffuse intrinsic pontine gliomas. RNA was sequenced from fresh frozen surgical material or from primary cells cultured under stem cell conditions. RNA was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files	Illumina HiSeq 2000	16
EGAD00001004118	We have studied a unique case of astroblastoma arising in a 6 year-old girl, with multiple recurrences over a period of 10 years, with the pathognomonic MN1:BEND2 fusion 11 surgical samples from either fresh frozen of paraffin embedded material and 1 blood sample were subjected to Illumina short read whole exome sequencing using Agilent SureSelect whole exome v4. Data is provided as 15 BAM files aligned to hg19 with bwa.	Illumina HiSeq 2000	15
EGAD00001004119	Chromatin immunoprecipitation (ChIP) was carried out employing antibodies against H3K36me3 and RNA polymerase II using the HistonePath and TranscriptionPath assays by ActiveMotif. Whole genome sequencing was carried out using an Illumina HiSeq2000 and data is provided as 6 BAM files. H3K36me3 chipseq RNA polymerase II chipseq and input coverage for each cell line.	Illumina HiSeq 2000	6
EGAD00001004123	Whole genome sequencing of 5 paediatric glioma cells lines - KNS42, SF188, UW479, RES186 and RES259. Illumina paired end sequencing is provided as 5 BAM files aligned to hg19 with bwa.	Illumina HiSeq 2000	5
EGAD00001005246	Whole genome sequencing of infant high grade gliomas. BAM files of paired end reads aligned to GRCh37 with bwa	Illumina NovaSeq 6000	22
EGAD00001005247	Whole exome sequencing of infant high grade gliomas. BAM files of paired end reads aligned to GRCh37 with bwa	Illumina HiSeq 2000	13
EGAD00001005248	Targeted sequencing of infant high grade gliomas. BAM files of paired end reads aligned to GRCh37 with bwa. This targeted panel covers the exons of 435 genes commonly mutated in high grade gliomas in children.	Illumina MiSeq	16
EGAD00001008211	Whole exome sequencing of Diffuse intrinsic pontine gliomas, primary patient derived DIPG cell cultures and isogenic trametinib resistant clones	Illumina NovaSeq 6000	56
EGAD00001008212	RNA sequencing of Diffuse intrinsic pontine gliomas, primary patient derived DIPG cell cultures and isogenic trametinib resistant clones	NextSeq 500	28