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• EORTC RP1335 SPECTA Lung cancer data

  SPECTAlung has recruited patients with thoracic malignancies, collecting FFPE material for molecular analysis. Illumina TST170 NGS panel was used for sequencing. The goal was to identify patients for whom a personalized treatment was possible and build a clinically-annotated molecular database for thoracic patients.

  Study EGAS00001004485

• RNA-sequencing of adult T-cell leukemia/lymphoma samples

  Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive hematological malignancy derived from mature CD4+ T-lymphocytes. In this study, we performed RNA-sequencing (RNA-seq) analysis for ATL samples including 9 primary tumors and 1 ATL cell line to clarify gene expression profiles in this disease.

  Study EGAS00001003575

• Genetic dysregulation of gene expression and splicing during a ten-year period of human aging in the PIVUS study

  We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging.

  Study EGAS00001003583

• Post-zygotic germline mutations in sperm

  These data from sperm were generated to demonstrate detection of post-zygotic mutations in the male germline. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001700

• Human_Evolution_3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Study EGAS00001000315

• Copy number and mutation profiling of Stage 1 epithelial ovarian cancer biopsies

  This project aims at characterizing the genome-wide copy number profile and the variant profile of 139 genes om the five major histotytpes of early-stage (stage I) epithelial ovarian cancer (EOC), to provide insight in the the aethiology and development of the disease.

  Study EGAS00001004961

• Melanoma_brain_metastases

  This is a whole exome study of brain metastases in melanoma. We are studying the genomic evolution of primary cutaneous melanoma to brain met in patients with brain-only metastatic disease. We are also looking at the genomic heterogeneity in patients with temporally, anatomically and regionally separated brian metastases.

  Study EGAS00001002107

• Ensemble learning for classifying single-cell data and projection across reference atlases

  Single-cell data are being generated at an accelerating pace.How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types.

  Study EGAS00001004283

• 2015_AML_ETO

  This study includes 10 paired samples of 2015 Korean AML-ETO paitients.10 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002897

• 2015_AML_ETO_WGS_additional

  This study includes 2 paired samples of 2015 Korean AML-ETO paitients. 2 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002898

• Oesophageal_Adenocarcinoma_Organoid_ATAC

  ATAC Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger. This ATAC data will be combined with other sequencing data in order to generate

  Study EGAS00001003890

• Whole-exome sequencing of the transposition of the great arteries

  Transposition of the great arteries (TGA) is one of the most severe types of congenital heart diseases. Understanding the pathogenesis of TGA is urgently needed for patient management of this severe disease. We sought to systematically examine thegenetic etiology for isolated nonsyndromic TGA using whole-exome sequencing.

  Study EGAS00001004175

• Chemotherapy accelerates genomic aging of normal blood in children treated for cancer

  Whole genome sequencing (WGS) data obtained from clonally expanded hematopoietic stem and progenitor cells (HSPCs) from pediatric cancer patients before and after therapy exposure. In addition, WGS data of cord-blood derived HSPCs clones exposed to various chemotherapeutics and radiation was obtained.

  Study EGAS00001005141

• Paired healthy & tumor organoid Biobank _B16PON

  B16PON consists of a panel of organoids (three-dimensional cell cultures) of premalignant epithelial cells of the colon and rectum. These organoids are derived from adenomas that are resected during a colonoscopy procedure. These can be propagated indefinitely and can be used to answer different research questions.

  Study EGAS00001005937

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• Investigation of human variation in healthy individuals on gene and protein levels

  The study examines human variation in healthy individuals, with samples taken from peripheral blood mononuclear cells. The study is a part of a larger effort to understand variants better both on level of genes and proteins. Thus for each DNA sample, corresponding protein samples are available.

  Study EGAS00001003590

• Search for genetic variants influencing gestational weight gain in type 1 diabetes patients by genome wide association method

  Clinical data suggest that BMI and gestational weight gain (GWG) are strongly interconnected phenotypes, however the genetic basis of the latter is rather unclear. Here we aim to investigate the genetic factors associated with GWG from the perspective of the genetics of obesity.

  Study EGAS00001004408

• Primary_DIPG_expression_profiles

  In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

  Study EGAS00001007181

• Error-corrected targeted sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains error-corrected next-generation sequencing (ecNGS) data generated from 161 rectal mucus samples. These samples belong to colorectal cancer, adenoma, and control participants. Genomic DNA was extracted and processed using a hybrid-capture panel targeting 50 colorectal cancer–associated genes, incorporating unique molecular identifiers (UMIs) for duplex consensus error correction. Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp) producing paired-end FASTQ files. These data support analyses of DNA mutations in CRC detection and progression.

  Dataset EGAD50000002032

• cfDNA sWGS BAM — Healthy donors

  Paired-end shallow whole-genome sequencing (sWGS) of plasma cfDNA from healthy donors recruited at EFS Montpellier (France). Libraries: DSP (NEBNext Ultra II) and/or SSP (IDT/Swift Accel-NGS 1S Plus). Sequencing by IntegraGen (France, 2022–2024). Reads aligned to GRCh38 (hg38 canonical) with BWA-MEM; BAMs coordinate-sorted and indexed; submission contains primary mapped reads only (unmapped/secondary/supplementary/duplicates removed; typical filter “-F 3332”, MAPQ threshold as noted in analysis records). Each BAM/BAI pair is linked to its Sample and Experiment. Data Use: controlled access.

  Dataset EGAD50000001880

• RNA-sequencing of 82 pleural mesothelioma samples

  The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

  Dataset EGAD50000002131

• RNA Sequencing of Control and Myotonic Dystrophy Type 1 Cells During Myogenic Differentiation

  To investigate gene expression dynamics during myogenic differentiation in myotonic dystrophy type 1, RNA was collected from immortalized control, patient-derived, and CRISPR/Cas9-corrected myoblasts at proliferation (day -2) and at days 1 and 5 of differentiation. High-quality RNA was isolated and sequenced using poly(A)-enriched or rRNA-depleted protocols, yielding 100 bp paired-end reads with high coverage. A subset of samples at day 1 underwent deeper sequencing to enhance transcriptome resolution.

  Dataset EGAD50000001647

• RNA-Seq of Myeloid Cells in Dendritic Cell Therapy Response

  RNA libraries were prepared from 100 ng of total RNA using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, then sequenced (2×150 bp) on the Illumina NextSeq550. Transcript-level quantification was done with kallisto, followed by gene-level summarization (tximport) and differential expression analysis (DESeq2). Quality control included PCA, hierarchical clustering, and deconvolution with CIBERSORTx to exclude non-myeloid genes. Final analyses identified transcriptomic differences among healthy donors and three patient subgroups based on response to dendritic cell therapy.

  Dataset EGAD50000001681

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• Somatic L1 retrotransposition mapping in high-grade serous ovarian carcinoma using LDI-PCR/Nanopore-sequencing (part 2)

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from the same patient were utilised to understand L1-mediated intrapatient heterogeneity. Long-read data generated by LDI-Nanopore sequencing was aligned to the reference genome (GRCh38). This dataset contains the remaining file of this study.

  Dataset EGAD50000001757