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• Brain mets discovery cohort copy number calls

  These are the Sequenza copy number calls for the 30 brain tumour samples within the discovery cohort.

  Dataset EGAD00001005983

• ChIPseq data

  ChIPseq data for CLL patients

  Dataset EGAD00001008665

• Cancer Alliance RNA-Seq total RNA

  Total RNA transcriptome profiling by high-throughput for individualized cancer interpretation

  Dataset EGAD00001006235

• RNAseq metadata

  Meta-data/patient information for the bulk RNAseq data

  Dataset EGAD00001008815

• ChIPseq data

  ChIPseq data for H3K4me1 and H3K9me3 in HT29; H3K4me1, H3K27me3, H3K9me3, H3K36me3 in LoVo.

  Dataset EGAD00001003258

• Reference epigenome IPS06_X_ENeuron_WGBS data generated from KEP study

  A IPS06_X_ENeuron_WGBS paired end data for Early neuron cells(Tuj1)

  Dataset EGAD00001003478

• Reference epigenome OB56_N_PreA_mRNA-Seq data generated from KEP study

  A OB56_N_PreA_mRNA-Seq paired end data for Preadipocytes(fat)

  Dataset EGAD00001003486

• Reference epigenome IPS05_X_NPC_WGBS data generated from KEP study

  A IPS05_X_NPC_WGBS paired end data for Neural progenitor cells(Nestin)

  Dataset EGAD00001003477

• Modern Aboriginal Australians WGS

  BAM files for high-throughput whole genome sequence data of 17 modern Aboriginal Australians

  Dataset EGAD00001004492

• SSBP1 sample

  The dataset includes exome sequencing results for a patient with SSBP1 mutations that cause a complex optic atrophy spectrum disorder

  Dataset EGAD00001005475

• Germline snv g.vcf for EGAS00001004572

  Bulk Germline snv vcfs from haplotypecaller analysis in EGAS00001004572

  Dataset EGAD00001006910

• G3-MB WGS

  Whole genome sequencing BAM files for four samples of MYC-amplified Group 3 medulloblastoma cell models.

  Dataset EGAD50000002302

• Single cell sequencing in D425

  Single cell sequencing aligned BAM files for the D425 cell line

  Dataset EGAD50000002304

• G3-MB ATAC Sequencing

  ATAC sequencing for two MYC-amplified G3-MB cell models.

  Dataset EGAD50000002305

• cell-Free DNA Genomic Profiling and its Clinical Implementation in Advanced Prostate Cancer

  Sixty-eight patients with advanced prostate cancer in castration-resistant or castration-sensitive settings undergoing treatment at the University Hospital Basel or the St. Claraspital Basel (Switzerland) were selected for targeted parallel sequencing analysis on liquid biopsy (plasma cfDNA) and matched formalin-fixed, paraffin-embedded (FFPE) tumor tissue samples.

  Study EGAS50000000234

• Genetic and Genomic Stability Across Lymphoblastoid Cell Line Expansions

  This study was focused on exploring genetic and genomic stability across cell line expansions. We used DNA and cell lines sampled from six apparently healthy research participants. We assayed genome-wide genetic variants and inferred structural variants for DNA extracted from blood, from transformed cell cultures, and from three generations of expansions.

  Study phs001650

• Methylome of memory B cells with autoproliferation in MS

  Methylome of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 6 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Methylome libraries for 12 samples were constructed by applying the post-bisulfite adaptor tagging (PBAT) method on lysed cells and sequencing was conducted on Illumina NovaSeq 6000. CpGs with minimum 10X coverage were used for differential methylation position (DMP) analysis.

  Dataset EGAD50000001269

• Study of biomarkers implicated in radio-immunotherapy response in metastatic cancer

  Immuno-radiotherapy may improve outcomes for patients with advanced solid tumors, although optimized combination modalities remain unclear. Here, we report the analysis from the SABR-PDL1 (NCT02992912) trial that evaluated the PD-L1 inhibitor atezolizumab in combination with stereotactic body radiation therapy (SBRT) in patients with advanced cancer.

  Study EGAS50000000681

• Bulk TCRseq data from 149 patients with bladder cancer

  For this dataset we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive bladder cancer (n patients = 119, n blood = 209, n tumor = 28) or non-muscle invasive bladder cancer (n patients = 30, n blood = 56, n tumor = 19) for a total of 149 patients and 312 samples. Each sample consists of a paired fastq file. Sequenced on the Ilumina NovaSeq6000 platform using SP and S1 flow cells (v1.5, 2x101 cycles), with a mean yield of 42 million reads covering the CDR3β region.

  Dataset EGAD50000001382

• Study of biomarkers implicated in radio-immunotherapy response in metastatic cancer

  Immuno-radiotherapy may improve outcomes for patients with advanced solid tumors, although optimized combination modalities remain unclear. Here, we report the analysis from the SABR-PDL1 (NCT02992912) trial that evaluated the PD-L1 inhibitor atezolizumab in combination with stereotactic body radiation therapy (SBRT) in patients with advanced cancer.

  Study EGAS50000001149

• mRNA-seq data from ALL patients with NUP214::ABL1 disease

  Dataset contains mRNA-sequencing data (fastq files) from 2 patients with NUP214::ABL1 disease (one T-ALL and one B-ALL patient). Patient samples (peripheral blood or bone marrow) were taken at diagnosis (B-ALL) or relapse (T-ALL). mRNA was extracted from lymphoblasts and underwent paired-end sequencing (75bp) using the Illumina NextSeq platform. Transcriptomic data was used for identification of gene fusions, SNVs and InDels. mRNA-seq data for an additional B-ALL patient with NUP214::ABL1 disease utilised in this study has already been published (EGAS00001006460).

  Dataset EGAD50000001395

• The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

  The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

  Dataset EGAD50000001701

• WGS of Five Pancreatic Cancer Patients-Tumor and Normal

  We performed whole genome sequence on tumor-derived and normal cell lines from patients who had terminal pancreatic cancer and consented for rapid autopsy upon their death. The 5 samples are from Dr. Christine Iacobuzio-Donahue's rapid autopsy program as reported in Boland et al. (PLOSOne, 2024, In Press, PMID 38352348).

  Study phs003775

• The genetic scenario of Mercheros: an under-represented population within the Iberian Peninsula

  In this work we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. We examine the demographic history and the genetic scenario of Mercheros by using genome-wide array data and whole mitochondrial sequences.

  Study EGAS00001005360

• Whole-genome sequencing of Tibetans from China

  Whole-genome sequencing of 27 Tibetan individuals from China using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001003500