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• Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

  Normal-cell counterparts of solid and myeloid tumors accumulate mutations years before disease onset; whether this occurs in B-lymphocytes prior to lymphoma remains uncertain. In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma, a singular disease for studying lymphomagenesis because of high-prevalence of mutated MYD88.

  Study EGAS00001005656

• Sputum bacterial microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006721

• Genetic and Microenvironmental Analysis of Peripheral T-cell Lymphoma

  This study enrolled 129 patients diagnosed with PTCL, comprising 94 cases of nTFHL and 35 cases of PTCL-NOS. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) were performed using DNA and RNA of sufficient quality extracted from their tumor specimens. WES was conducted for all 129 cases, while RNA-seq was performed on 57 tumor samples.

  Study EGAS50000001258

• Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

  Splice-switching antisense oligonucleotides (AONs) are designed to modulate pre-mRNA splicing, thereby for instance restoring protein expression or modifying the eventual protein to restore its function or reduce its toxicity. To determine off-target effects, RNA from neuronally differentiated human induced pluripotent stem cells transfected with splice-switching AONs was sequenced.

  Study EGAS50000001222

• μSeq: Universal mutation rate quantification via deep sequencing of a single clonal expansion

  We use patient-derived colorectal cancer organoids to introduce µSeq, a universal framework for inferring mutation rates in diverse biological systems. Our approach extracts mutation rates from deep sequencing of single clonal expansions, with a time gain of tenfold or more compared to a mutation-accumulation line, at the cost of three billion read whole-genome sequencing.

  Study EGAS50000001761

• Sputum fungal microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006720

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• Whole genome sequencing data of paediatric ETV6::RUNX1 acute lymphoblastic leukemia

  ETV6::RUNX1 (E::R) subgroup is the second most frequent form of B cell acute lymphoblastic leukemia (B-ALL) in childhood. This subgroup of ALL generally presents with low-risk features and responds well to chemotherapy with ensuing favorable prognosis. Some patients, however, have a slow response to induction treatment and carry increased risk for relapse.

  Study EGAS50000001599

• RNA-sequençing of 21 inflammatory hepatocellular adenomas

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors.The present series corresponds to 21 RNA-seq of IHCA samples. Aligned bam files correspond to hg38 human reference.

  Study EGAS00001003685

• ICGC_Benchmarking_Exercise

  The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.

  Study EGAS00001000433

• Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study

  This is a case-control study in which differences in the gut microbiome of patients with bipolar disorder and schizophrenia spectrum disorders were assessed. The study contains the samples in this dataset, except for G002, G025, G041, G093, G106, G107, G120 and G123. These samples were not yet available at the time the study was performed.

  Study EGAS50000000969

• Investigating transcriptional changes in rapidly differentiated iPSC-derived neurons (i3Ns) harbouring the SNCA A53T mutation +/- RSL3

  In this study we performed bulk RNA sequencing of a iPSC-derived rapid neuronal model harbouring the Parkinson's disease associated A53T mutation in SNCA. These neurons were subsequently treated with a low dose of RSL3 (300nM) for 6 hours to establish the transcriptional impact of ferroptosis induction in the presence or absence of SNCA A53T mutation.

  Study EGAS50000001536

• Low_depth_whole_genome_sequencing_across_multiple_isolated_populations

  Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

  Study EGAS00001001597

• Investigating_the_impact_of_MBD4_on_the_mutability_of_the_germline

  We will be testing the hypothesis that MBD4 PTV germline carriers also show an increased number of C toT germline mutations in their offspring. 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 EGAS00001002861

• Whole_exome_sequencing_for_HELIC

  The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.

  Study EGAS00001000602

• SARS-CoV-2 induced alterations of the upper airway DNA methylome exert long-term impacts on ciliary genes involved in ciliary function

  Enzymatic DNA methylome (n=33) and single-cell RNA (n=24) sequencing were performed in nasal cells of COVID-19 patients and controls. In addition, we re-sampled a subset of patients for transcriptome analyses at 3 and 12 months post-infection and followed the expression of differentially regulated genes over time.

  Study EGAS50000000273

• Prostate_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331

  Study EGAS00001000427

• Longread sequencing of selected 12q-amplified osteosarcomas

  Longread sequencing of selected 12q-amplified osteosarcomas for verification of SV data. This was carried out in order to verify findings from mate-pair sequencing regarding the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification.

  Study EGAS50000000495

• ICARUS-BREAST01-RNAseq

  Efficacy, safety and biomarker analysis of ICARUS-BREAST01: a phase 2 Study of Patritumab Deruxtecan in patients with HR+/HER2- advanced breast cancer. RNA-squencing is available for 44 samples comprising 22 samples collected at entry into the trial and 22 samples collected during treatment (cycle 1 day 3, cycle 1 day 19, or cycle 2 day 3) from 22 patients.

  Study EGAS50000000543

• Targeted pancancer RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoeitic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood.The data is used for tumour driver identification. SNVs, indels and fusion detection.

  Study EGAS50000000700

• Single-Cell Profiling of the Human Endometrium in Polycystic Ovary Syndrome: Uncovering Disease Signatures and Treatment Responses

  We generated the first single-nuclei map of human endometrial biopsies from women with and without PCOS to identify cell-type-specific disease signatures, compositional variations, and transcriptomic reversibility after a 16-week intervention with metformin or lifestyle. Single nuclei were extracted from 27 frozen endometrial biopsies for snRNA-seq using the 10X Genomics protocol.

  Study EGAS50000000735

• DAC-2023-07-05-Ritz (DAC-007) - Diagnosis of tuberculosis infection in children with a novel skin test and the traditional tuberculin skin test: an observational study

  Diagnosis of tuberculosis infection in children with a novel skin test and the traditional tuberculin skin test: an observational study This is only the location for the raw data and any check if the dataset may be relevant please refer to the MF-DAC Zenodo community (https://zenodo.org/records/11237107).

  Study EGAS50000000780

• IL_10_signalling_and_macrophage_gene_expression

  Study to stimulate WT and IL-10RB mutant macrophages with LPS in presence or absence of recombinant IL-10 and compare their gene expression profiles by RNASeqThese data are 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 EGAS00001001283

• CAR_T_cell_Study

  CAR-T cell Study The aim of this study is to understand single cell transcription and chromatin accessibility in CAR-T cells. 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 EGAS00001004718

• Whole Exome Sequencing of High grade T1 non-muscle invasive bladder cancer

  High-grade T1 (HGT1) bladder cancer (BC) is the highest risk subtype of non-muscle-invasive BC with unpredictable outcome and poorly understood risk factors. Here we performed whole exome sequencing across 61 HGT1 samples to identify genomic predictors of good outcome, recurrence or progression. This study includes somatic mutation calls and clinical data for 61 HGT1 tumors.

  Study EGAS00001004603