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• Genomic characterisation of SDH deficient renal cell carcinoma - RNA

  SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

  Dataset EGAD00001008470

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Dataset EGAD00001010156

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (WG) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 40 women who underwent mastectomies due to breast cancer. LCM and sequencing will be conducted on both normal, unaffected breast, and, where possible, tumour tissue. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue, and compare findings between the normal and associated cancer tissues. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those who are BRCA carriers. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005922

• ChIP-seq of primary AML patients with t(3;3)/inv(3)

  ChIP-seq was conducted in blasts from patients with t(3;3) AML to assess differences of the GATA2 super-enhancer between the translocated allele and the non-translocated allele. The dataset includes 2x H3K27ac ChIP-seq and 1x MYB ChIP-seq. ChIP samples were processed according to the Illumina TruSeq ChIP Sample Preparation Protocol (Illumina) or Diagenode Library V3 preparation protocol (Diagenode) and either sequenced single-end (1x 50 bp) on the HiSeq 2500 platform (Illumina) or paired-end (2x100 bp) on the Novaseq 6000 platform (Illumina). Briefly, reads were aligned to the human reference genome build hg19 with bowtie for single-end runs and bowtie2 for paired-end runs.

  Dataset EGAD00001006821

• European Prospective Investigation into Cancer and Nutrition BAMs

  516 DNA samples were collected from individuals upon enrollment into the European Prospective Investigation into Cancer and Nutrition study between 1993 and 1998 across 17 different centers. 126bp pair-end reads sequencing data from the Illumina platform were converted to fastq format, the 2bp molecular barcode information at each read of the pair was trimmed and was written in the reads name. The Thymine nucleotide required for ligation was removed from the sequences. Burroughs-Wheeler Aligner (BWA-mem) was used for alignment of the processed fastq files to the reference hg19 genome, following indel-re-alignment using GATK. An in-house algorithm was written to collapse read families that share the same molecular barcode sequence

  Dataset EGAD00001003583

• Whole Genome, RNA, and ChIP Sequencing of matched brain tumor-normal pairs (ICGC)

  Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x

  Dataset EGAD00001000664

• Inherited Predisposition to Cancer Projects Data Access Committee

  Dac EGAC00001001565

• Board considering access to BELOB RNA-seq data

  Dac EGAC00001001686

• DAC related to monozygotic twins discordant for ALS

  Dac EGAC00001003524

• Whole_Exome_Sequencing_for_Characterization_of_Disease_Causing_Mutations_in_two_Pakistani_Families_Suffering_from_Autosomal_Recessive_Ocular_Disorders_

  We propose to use whole exome Agilent solutionprobes and paired end Illumina sequencing to sequence 4 individualsfrom two families suffering from novel autosomal recessive disease[microphthalmia, MOP (OMIM %251600) and non-syndromic persistenthyperplastic primary vitreous, PHPV (OMIM %611311)]. Selectedcandidate variants will subsequently be genotyped in the remainingfamily members in Pakistan with the aim of identifying the rarehomozygous recessive mutations responsible for the disease phenotype. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001000026