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• Sequencing of Plasma DNA from breast cancer patients

  Dataset contains plasma DNA whole genome sequencing on 4 breast cancer patients. It also includes matched germline and tumour whole genome sequencing data. Two benign cancer patients were also sequenced and their plasma DNA and matched germline whole genome sequencing data are included in the dataset. Samples were sequenced on Illumina HiSeqX Ten.

  Dataset EGAD00001006869

• Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases

  Dataset consisting of three WGS BAM files, representing the two dual lung metastases with matched germline control, for a 37 year old female patient, with primary adrenocortical carcinoma. Work conducted at Garvan Institute of Medical Research, Sydney, Australia.

  Dataset EGAD00001004833

• DKFZ-St.Jude Medulloblastoma - 8 MB cases, exome/WGS data

  Tumor/Control pairs for 8 medulloblastoma cases, MB cohort, mixed exome and whole genome data, sequenced on Illumina machines from the paper "Germline Elongator mutations in Sonic Hedgehog medulloblastoma" (Waszak et al. 2020 Nature).

  Dataset EGAD00001006660

• Common clonal origin of chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia in a patient with a germline CHEK2 variant

  Whole exome sequencing data obtained from sorted leukemic clones and a buccal swab as germline reference. The dataset contains raw sequencing data (paired-end reads) for 3 samples (2 leukemic, 1 buccal swab), for a total of 6 fastq files.

  Dataset EGAD00001007644

• MNM - 16S rDNA amplicon dataset of 20 dense timeseries of fecal samples from Belgian women

  Fastq files for the 16S rDNA amplicon library of 714 fecal samples of 20 time series (as described in Vandeputte et al. 2021, Nature Communications)

  Dataset EGAD00001008275

• IBD WES trio data-ALPI-P2

  This project focused on identifying rare coding variation that substantially increases risk of VEOIBD by exome sequencing of VEOIBD patients and some of their family members. Here you can find BAM files from an affected proband (P2) and his unaffected parents. In this study ALPI mutations were identified as a likely cause of the disease.

  Dataset EGAD00001004485

• The immunopeptidome landscape associated with T cell infiltration, inflammation and immune-editing in lung cancer

  WES sequencing of multiple regions per tumor from 8 lung cancer patients (LUSC, LCNEC and LUAD) and adjacent healthy lung tissue for each patient.

  Dataset EGAD00001008950

• GELATO clinical trial RNA-Seq data (primary tumors and local recurrences)

  RNA-Seq data of 10 lobular breast cancer primary tumors and 3 local recurrences obtained from 11 unique patients from GELATO clinical trial. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material.

  Dataset EGAD00001009835

• bulk RNA-Seq samples of CRC patients

  The dataset contains samples of 30 CRC patients (3 samples for each patient, tumor and 2 normal adjacent tissue sites, 90 samples in total). Dataset is composed by fastq file (paired end) type from bulk RNA-Seq.

  Dataset EGAD00001009635

• Ashkenazi Jewish Leukoencephalopathy Syndrome

  Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T>G (p.C846G), as the genetic cause of a leukoencephalopathy syndrome in two individuals from two unrelated Ashkenazi Jewish (AJ) families. Both patients exhibited highly concordant disease progression characterized by infantile onset leukoencephalopathy with brain white matter abnormalities, severe motor impairment, cortical blindness, intellectual disability, and seizures.

  Dataset EGAD00001002005

• Whole genome sequencing of patient IPSCs and tumors (organoids)

  This dataset contains whole genome sequencing data of a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) . This dataset further contains whole genome sequencing data of two tumors showing CNLOH. Tumors were isolated from organoids grown using the patient IPS cell line (Patient 1 TSC2+/- iPSCs )

  Dataset EGAD00001006333

• scRNA-seq of patient-derived PDAC organoids

  We derived PDAC organoids from primary tumors of 18 patients, together with two matched samples from liver metastases. By single-cell RNA sequencing, we show that PDAC organoids consist of ductal cells with patient-specific expression of several gene groups, including genes which encode cell surface proteins. We report ‘classical’ and ‘basal-like’ cells coexisting within single primary tumors or metastases, with greater intratumor subtype heterogeneity linked to higher tumor grade. Single-cell transcriptome analysis of PDAC organoids and primary PDAC identified distinct tumor cell states shared across patients, including a cycling progenitor cell state and a differentiated secretory state. We show that these cell states are connected by a differentiation hierarchy, with ‘classical’ subtype cells concentrated at the endpoint of this hierarchy.

  Study EGAS00001004661

• WGS short read and 10X linked read sequencing of HR Deficient breast cancers

  A set of tumor/normal paired sequencing experiments, performed in short read WGS and 10X linked read whole genomes. BAM files aligned to hg19 are provided. Sample Alias number and Subject ID reflects patient of origin. T/N distinction discriminates between tumor and normal (peripheral blood) tissue.

  Dataset EGAD00001010326

• ovarian cancer sample RNA-seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to bulk RNA-sequencing on 17 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy. - Group C1, Epithelial Ovarian Cancer(EOC) patients with estrogen responsiveness : 6 samples - Group C2, Epithelial Ovarian Cancer(EOC) patients with estrogen non-responsiveness : 10 samples - non-classified 1-sample

  Dataset EGAD50000000613

• WTS data of patients diagnosed with angiosarcoma

  Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005367

• sWGS of OV04 patient samples for ACN rascal study

  This dataset contains 142 .bam files of shallow WGS data (~0.1X) from OV04 patient samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008121

• WTS data of patients diagnosed with NKTL

  Whole-transcriptome sequencing (WTS) of 36 samples from patients diagnosed with NKTL. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005230

• A clinically and genomically annotated Early onset colorectal cancer and late onset colorectal cancer

  This study aimed to identify genomic characteristics of early-onset colorectal cancer (EOCRC) compared to late-onset cases. Whole-genome sequencing (WGS) was performed on EOCRC and late-onset colorectal cancer (LOCRC) tissues and blood samples to analyze their genomic profiles.

  Study EGAS50000000544

• A Perioperative Study of Safusidenib in Patients with IDH1-Mutated Glioma

  10 participants with a radiological or pathological diagnosis of WHO Grade 2 lower-grade glioma (LGG) were recruited at a single center starting in December, 2022. Eligibility criteria permitted participants who had undergone prior surgery for WHO Grade 2 LGG, but excluded those with a history of prior radiation or chemotherapy.In Part A of the study, participants underwent an initial craniotomy with tumor biopsy and a lumbar puncture for cerebrospinal fluid (CSF) collection at study entry. Following sample collection, participants received safusidenib at the recommended phase 2 doses of 250 mg twice daily (b.i.d.) for a period of 22–36 days. This was followed by a second craniotomy for maximal safe tumor resection and a repeat lumbar puncture within 5 hours of the final pre-resection dose of safusidenib. Tumor, blood, and CSF samples were collected at both surgical time points for comprehensive translational research.Molecular analyses were performed on samples collected at both time points. These included pharmacokinetics (PK), targeted metabolomics, whole-genome sequencing (WGS) of tumor tissue, single-nucleus RNA sequencing (snRNA-seq), and DNA methylation profiling on all patients. Targeted metabolomics was conducted on samples from 9 participants, while spatial transcriptomics and spatial metabolomics were performed on tumor tissue from 3 participants each. Histone methylation profiling was conducted on samples from 8 participants.

  Study phs003976

• Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

  scGBS is a single-cell sequencing-based methodology to haplotype and copy-number profile single cells. Genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing of the restriction fragments. scGBS data serves as the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping (Zamani Esteki et al., 2015). We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells with the use of a HapMap cell line pedigree (7 single cells). A clinical validation of the methodology with a total of 14 single blastomeres and 3 trophectoderm samples biopsies from human preimplantation embryos for 6 PGT-M families were processed with scGBS and were previously haploptyped via SNP array.

  Dataset EGAD00001007794

• Single_Cell_Targeted_Sequence_Capture

  This study is to ascertain whether it is feasible to extract single cell from a tumour, perform amplification, generate a library and sequence a targeted pulldown.

  Study EGAS00001000435

• Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors

  Large-cell neuroendocrine lung carcinomas (LCNEC) have similarities with other lung cancers, but their precise relationship has remained unclear. We conducted comprehensive genomic (n=60) and transcriptomic (n=69) analyses of 75 LCNECs and identified two molecular subgroups: “type I LCNECs” with bi-allelic TP53 and STK11/KEAP1 alterations (37%), and “type II LCNECs” enriched for bi-allelic inactivation of TP53 and RB1 (42%). Despite sharing genomic alterations with adenocarcinomas and squamous cell carcinomas, no transcriptional relationship was found; instead LCNECs form distinct transcriptional subgroups with closest similarity to SCLC. While type I LCNECs and SCLCs exhibit a neuroendocrine profile with ASCL1high/DLL3high/NOTCHlow, type II LCNECs bear TP53 and RB1 alterations and differ from most SCLC tumors with reduced neuroendocrine markers, a pattern of ASCL1low/DLL3low/NOTCHhigh and upregulation of immune-related pathways. In conclusion, LCNECs are comprised of two molecularly defined subgroups, and distinguishing them from SCLC may allow for stratified targeted treatments for high-grade neuroendocrine lung tumors.

  Study EGAS00001000708

• Single Cell Colony Whole Genome Sequencing Data From Individuals With Telomere Syndromes

  This is an observational study which examined the phylogenetic evolution of somatic clonal mutations in POT1 mutation carriers. Two individuals with telomere syndromes who carry a heterozygous germline POT1 p.R273Q variant and one related control who did not carry this variant were studied. Single cell hematopoietic colonies were derived from peripheral blood mononuclear isolates. These colonies were analyzed by whole genome sequencing (WGS) and phylogenetic trees were reconstructed accordingly. Phylogenetic reconstruction of somatic mutations show clonality is increased among POT1 p.R273Q mutation carriers and co-occurs with known clonal hematopoiesis driver mutations, including DNMT3A and/or JAK2.

  Study phs003207

• Understanding_hematopoietic_stem_cell_mobilization_and_engraftment_

  This study looks at patients undergoing gene therapy for genetic blood and immune disorders, in particular sickle cell disease. From each patient, single blood HSPC colonies are grown from patient blood mononuclear cells, bone marrow mononuclear cells, or CD34+ at multiple time points: pre gene transduction, post-transduction, and post-infusion (at several time points). Whole-genome sequencing will be performed on DNA from these colonies and somatically-acquired mutations will be called. Using these mutations, a phylogeny of these cells can be inferred and further inferences can be made about the gene therapy transduction and engraftment steps.

  Study EGAS00001004620

• Shallow whole genome sequencing and targeted sequencing of DLBCL patients treated in the HOVON84 trial

  Shallow whole genome sequencing and targeted sequencing of DLBCL patients treated in the HOVON84 trial

  Dataset EGAD00001008389

• Genomic analyses to identify metabolic vulnerabilities

  Genomic analyses to identify metabolic vulnerabilities on PDX samples

  Study EGAS00001007244

• Cancer Single Cell Sequencing

  This study is to ascertain whether it is feasible to extract a single cell form a Cancer cell line, amplify it and sequence it.

  Study EGAS00001000003

• Resistance to selective FGFR2 inhibitors across FGFR2-driven malignancies

  18 patients were biopsied at resistance to an FGFR inhibitor with tumor WES and/or WTS performed to identify resistance mechanisms to selective FGFR2 inhibitors across FGFR2-driven malignancies.

  Dataset EGAD50000000439

• Whole exome sequencing of 69 trios with bipolar disorder

  We performed whole exome sequencing to trios with bipolar disorder to elucidate genetic architecture of bipolar disorder including de novo mutations and transmitted variants.

  Study JGAS000273

• Unravelling the contribution of HIF pathway and its therapeutic potential in human AML leukemia-initiating cells

  We performed single cell RNA sequencing (scRNA-seq) from bone marrow on 11 pediatric (0-14 years-old) and adolescent and young adult (AYA) (15-39 years-old) de novo AML samples (Dx) (4 inv(16), 3 t(8;21) and 4 rMLL). In addition, for some patients also relapse sample was sequenced (2 inv(16), 2 t(8;21) and 3 rMLL). Cells were sorted into CD34+/CD38- and CD34-/CD38+ and sequenced separately.

  Dataset EGAD00001008514

• 16S rRNA gene V4 region sequencing data, ASV profiles, and sample metadata of human faecal samples predominantly from the Estonian population

  This dataset comprises 16S rRNA gene V4 region amplicon sequencing data generated from 1,826 human faecal samples, predominantly from the Estonian population. The dataset includes raw sequencing reads and processed amplicon sequence variant (ASV) outputs, consisting of ASV abundance tables, representative ASV sequences, and taxonomic assignments. In addition, a sample metadata table is provided, containing sample and host information, including sample identifier, sequencing run identifier, date of sampling, sex, age, height, weight, nationality, disease status, and Bristol stool type. Sequencing was performed using the Illumina MiSeq and iSeq 100 platforms. The cohort includes individuals with no reported disease (n = 889), gastrointestinal diseases (n = 217), allergies and asthma (n = 194), thyroid gland disorders (n = 117), cardiovascular diseases (n = 103), various general health conditions (n = 139), cancer (n = 28), diabetes (n = 20), gynaecological issues (n = 7). Disease status was unavailable for 112 samples.

  Dataset EGAD50000002306

• Genome-wide identification of distinct miRNA-mRNA target regulation pairs in Non-Hodgkin lymphomas: a report from the ICGC MMML-Seq consortium

  We obtained miRNA profiles by miRnome sequencing from ICGC MMML-Seq patients diagnosed with Burkitt lymphoma, diffuse large B-cell lymphoma and follicular lymphoma and provide evidence of subtype-specific miRNA expression differences. We describe differentially expressed, mutated, edited and not previously annotated miRNAs. Addditionally, by performing argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) experiments, we obtained a set of biochemically-validated miRNA binding sites and identified miRNA-mRNA interaction pairs with a negative correlation in patient RNASeq data.

  Study EGAS00001001394

• Whole exome sequencing of pretreatment gastric and gastroesophageal junction tumors

  This set contains 40 bam files with whole exome sequencing data from 20 patients included in the PANDA study treated with 1 cycle of monotherapy atezolizumab and 4 cycles atezolizumab plus chemotherapy (docetaxel, oxaliplatin and capecitabine). Tumor DNA was isolated from tumor samples and germline DNA was isolated from PBMCs, which was used for whole exome sequencing.

  Dataset EGAD50000000242

• H3Africa CAfGEN Exome

  Whole Exome Sequencing data from a retrospective paediatric HIV-disease progression cohort defined on the World Health Organization's criteria for paediatric HIV progression. Data comprises of BAM and VCF files for 314 participants from 2 countries: Botswana and Uganda. DNA and RNA samples are linked in bio-repository.

  Dataset EGAD00001006224

• mUM patient biopsies bulk RNAseq

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system

  Dataset EGAD50000001225

• M116 Whole Genome Bisulphite Sequencing

  DNA fragmentation from M116 blood sample (350 bp), library preparation, bisulfite conversion, and paired-end-150 whole genome bisulfite sequencing was conducted by Novogene®. Sequencing was carried out with a 10X coverage (approximately 60 Gb and 200 million reads per sample) using the NovaSeq X Plus platform (Illumina). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001285

• Myeloid cancer sequencing data

  SmMIP libraries using DNA from patients diagnosed with myeloid malignancies were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)

  Dataset EGAD00001007791

• WholeGenomeSeq-EGAS00001001306

  Whole Genome sequencing. 2 μg of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3.

  Dataset EGAD00001001466

• Whole Exome PC9 and A375 (2019-04-03)

  Drug resistant population of PC9(human non-small cell lung cancer) or A375 (human melanoma) cell lines were used for this study. By exome sequencing, we will analyse mutations of cells in drug tolerent state and after drug holiday. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004891

• scATAC sequencing of FACS sorted CD4+ T and CD25+ T from isolated tissues

  T cells were isolated from human blood and tissues: skin and fat. Subsequently, CD4+ T cells and CD25+ T cells were FACS sorted. scATAC libraries were prepared using the 10x Genomics Kit (CG000168_ChromiumSingleCell_ATAC_ReagentKits_UserGuide_RevD.pdf) and sequenced on an Illumina NextSeq550. In total 15 samples were prepared

  Dataset EGAD00001006779

• SPATC1L variants associated with age-related and hereditary hearing loss.

  The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

  Dataset EGAD00001004147

• single-cell RNA-Seq samples of CRC patients

  The dataset contains samples of 11 CRC patients (2 samples for each patient, tumor and normal adjacent tissue site, 22 samples in total). Dataset is composed by fastq file (paired end) type from 10x single-cell RNA-Seq.

  Dataset EGAD00001009634

• Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections

  Advamced Visium Spatial Gene Expression assay for FFPE tissues with human and SARS-CoV-2 whole transcriptome (WT) information at a 55 µm resolution. The dataset consists of 13 tissue sections from 5 patient lung tissue samples, 3 from COVID-19 patients and 2 from control patients.

  Dataset EGAD00001008701

• RNAseq in ASD patients and controls

  RNA sequences of a total of 24 samples, including 13 unrelated ASD patients (13 males) and 11 adult individuals of Spanish origin as controls (4 males, 7 females). The RNAseq study was conducted on a HiSeq 4000 (Illumina) and paired-end sequences were obtained (fastq files).

  Dataset EGAD00001008160

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples used in the PCSI mismatch repair study

  Dataset EGAD00001006261

• Somatic variant calls from whole-exome sequencing of three tumor–normal matched cell lines

  This dataset comprises matched tumor–normal cell line samples. Whole-exome sequencing data are available for three matched pairs, and targeted deep sequencing–based somatic variant calls are provided for them as well in the form of VCF files.

  Dataset EGAD50000002392

• DNA whole-exome sequencing data from patients with metastatic basal cell carcinoma

  Whole-exome sequencing data in fastq format of matched tumour and germline DNA from 8 patients with metastatic basal cell carcinoma. Samples are labeled as Primary, Local or Metastasis: Primary: Sample was obtained from primary tumour. Local: Sample was obtained from local recurrence of primary tumour. Metastasis: Sample was obtained from a metastatic site. Germline: Sample was obtained from normal adjacent tissue. DNA was isolated from FFPE tissue sections of the tumor biopsies using the AllPrep DNA/RNA FFPE Kit (Qiagen) and quality controls conducted using the Qubit fluorometer (Thermo Fisher Scientific). Library preparation was performed using the Agilent SureSelect Human All Exon v7 XTHS2 probes and sequenced on a NovaSeq 6000 S2 2x100bp

  Dataset EGAD00001008675

• Gene expression profile of mesothelial-derived carcinoma-associated fibroblasts

  RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process.

  Study EGAS00001003747

• Exome and transcriptome sequencing of Desmoplastic Small Round Cell Sarcoma

  To conduct exome and transcriptome profiling to identify secondary recurrent mutations, multi-site phylogenetic analyse and immune characterization of Desmoplastic Small Round Cell Sarcoma.

  Study EGAS00001004575

• Sequencing data for CLL patients

  Single-cell RNA-sequencing and other genome-wide approaches were applied to a cohort of CLL patients receiving Venetoclax treatment to study mechanisms of resistance.

  Study EGAS00001005815