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• Genome and transcriptome sequence data from a metastatic pleomorphic sarcoma patient

  Genome and transcriptome sequence data from a metastatic pleomorphic sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010969

• WGS dataset of Mutational Mechanisms in Multiply Relapsed Pediatric Acute Lymphoblastic Leukemia

  Pediatric acute lymphoblastic leukemia (ALL) is marked by low mutational load at initial diagnosis, which increases at relapse. The elevated mutational load at relapse can partly be explained by at least two therapy-related effects and a combination of therapy and underlying mismatch repair deficiency. However, our understanding of the type and timing of mutational mechanisms in relapsed ALL is limited, and it is unclear to what extent mutational processes contribute to disease progression. We collected a cohort of 29 Dutch ALL patients across multiple treatment protocols who had multiple relapses. Using whole genome sequencing of the sequential tumor samples of each patient we were able to distinguish the mutational processes active in relapsed ALL and could track the activity of mutational processes over time. This allowed us to investigate whether subtype-specific mutational processes at diagnosis can continue in relapse or emerge at relapse if absent in initial diagnosis. Furthermore, we assessed whether the activity of mutational processes contributed to disease development and relapse.

  Dataset EGAD00001015401

• A Pilot Study Using Next Generation Sequencing in Advanced Cancers: Feasibility and Challenges

  In this study, we used NGS to identify somatic events in advanced stage cancer patients to demonstrate the feasibility for using this approach to improve patient treatment.

  Study phs000657

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

  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.

  Dac EGAC50000000468

• Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens

  Data for 1) hiPSC-derived macrophages across a polarization time course from the naive M0-state to the M1- and M2-states, 2) Primary T-cells differentiated to helper subtypes, and 3) spontaneous differentiation of hiPSCs upon perturbation of GATA2, NR4A2 or SOX17

  Dac EGAC50000000485

• Cancer Affected Patients - Data Access Committee

  Access to the cancer cohort is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use. Individuals requesting access to the data need to comply with the terms of a Data Access Agreement (DAA) and are requested to use the data only in approved and ethical ways.

  Dac EGAC50000000037

• Etiology of congenital thyroid dysfunction in Down Syndrome: a multi-omics investigation

  The goal of this study was to investigate dfiferences in the thyroid DNA methylome and transcriptome between fetuses with Down syndrome and fetuses with no genetic/developmental abnormality.

  Study EGAS50000000264

• Deciphering novel TCF4-driven mechanisms underlying a common triplet repeat expansion-mediated disease

  short and long read data generated from cultured corneal endothelial cells (CECs) of unaffected controls, expansion positive Fuchs Endothelial Corneal Dystrophy (FECD) and expansion negative FECD individuals.

  Study EGAS50000000303

• Pediatric UBA1-mutated MDS Single-Cell Sequencing DAC

  This DAC oversees controlled access to single-cell DNA and protein sequencing data generated from a pediatric MDS patient with somatic UBA1 mutation. Access is restricted to researchers who have appropriate ethical approvals and intend to use the data for studies related to pediatric blood disorders, immunology, or VEXAS pathogenesis. The DAC evaluates requests for compliance with these conditions.

  Dac EGAC50000000947

• Whole-exome sequencing of intrahepatic cholangiocarcinoma tumors with matched normal tissue from the Medical Center – University of Freiburg

  This dataset contains raw whole-exome sequencing data from 40 samples of intrahepatic cholangiocarcinoma patients, including tumor and matched normal tissue. Samples were sequenced on the NovaSeq platform. The cohort is part of a proteogenomic profiling study integrating genomic and proteomic data.

  Dataset EGAD50000001926

• Variant calling dataset from the whole-exome study of sepsis and acute distress respiratory syndrome in Spain

  Whole-exome sequence reads were obtained from a set of 934 unrelated individuals from the study of sepsis and acute distress respiratory syndrome in Spain (GEN-SEP study), using Illumina paired-end reads.

  Dataset EGAD50000001613

• Targeted capture sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Targeted capture sequencing for 366 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study and 29 samples from a previously uploaded dataset.

  Dataset EGAD50000001364

• Whole genome sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Whole genome sequencing for 10 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 6 samples from a previously uploaded dataset.

  Dataset EGAD50000001366

• HIV-phyloTSI: PANGEA (veSEQ-HIV)

  This dataset includes sample numbers TSI_0001 to TSI_0202 and TSI_0316 to TSI_0425 for the PANGEA (veSEQ-HIV) cohort of the study. Samples were sequenced using the Illumina NovaSeq system and the veSEQ-HIV method (see Bonsall, Golubchik et al 2020, DOI: 10.1128/JCM.00382-20). Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001309

• HIV-phyloTSI: PANGEA (PCR amplicon)

  This dataset includes sample numbers TSI_0426 to TSI_0527 for the PANGEA (PCR amplicon) cohort of the study. Samples were generated by pooling four overlapping PCR amplicons (see Gall et al 2012, DOI: 10.1128/JCM.01516-12). The sequencing was conducted using the Illumina NovaSeq system. Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001308

• CHIP panel sequencing of rheumatoid arthritis patients

  Targeted NGS sequencing data (bam and index files aligned to hg38) a total of 573 newly diagnosed, untreated RA patients and 163 healthy controls. The sequencing panel included 65 genes recurrently mutated in myeloid malignancies, to capture clonal hematopoiesis of indeterminate potential (CHIP) mutations. The median target coverage was 1700x across samples.

  Dataset EGAD50000001300

• Paired FastQ files from deep targeted DNA sequencing

  This dataset comprises paired-end and time-matched FastQ files from 356 cell-free DNA samples and 356 white blood cell DNA samples, derived from 299 patients with metastatic renal cell carcinoma or urothelial carcinoma. A baseline sample was available for all patients. Sequencing was performed using Illumina technology.

  Dataset EGAD50000001267

• WES for CNV-verified CTCs from 2 patients with metastatic prostate cancer

  This dataset contains 4 paired fastq files sequenced by illumina Novoseq 6000. WES analysis (illumina platform, PE150, 100x coverage) was performed on a pool of CNV-verified CTCs that were enriched using high-throughout microfluidic device from entire leukopak from patients with metastatic prostate cancer (GU-1 and GU-2).

  Dataset EGAD50000001005

• Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

  Dataset with eQTL and e2QTL metadata. The analyses were performed using CD8+ T cells from 461 healthy European participants stimulated with high doses of 5 different carcinogens to induce early apoptosis. These include Methyl-methanesulfonate (MMS), tert-butyl-hydroperoxide (TBOOH), benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE), 4-hydroxycyclophosphamide (HC) and UVC radiation.

  Dataset EGAD50000000941

• Early and Late Onset Colorectal Cancer Genomic Data

  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.

  Dataset EGAD50000000774

• BAM files from capture-based targeted sequencing of 4 agressive B-cell lymphoma tumour samples (DLBCL-panel)

  This dataset contains BAM files from capture-based targeted sequencing of 4 agressive B-cell lymphoma tumour samples for cases 2, 3, 4 and 13. The sequencing panel used is a DLBCL-oriented panel containing 136 genes, described in Mozas P. et al., Hematol Oncol 2023.

  Dataset EGAD50000000802

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Dataset EGAD50000000199

• Transcriptome atlas of brain organoid developent

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. We used scRNA-seq to profile transcriptome. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000223

• Single-cell RNA-sequencing of peritoneal fluid from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peritoneal fluid (PF) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000251

• Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA

  sEVs were isolated from postmortem human brain tissue. RNA was extracted from the source brain tissue and the sEVs and prepared for RNA sequencing. cDNA was sequenced on the Illumina HiSeq using a 2x150 paired-end read configuration.

  Dataset EGAD50000000042

• DNA methylation-based classification of sinonasal tumors [Proteomics data]

  This dataset includes raw label-free mass spectrometry proteomics data of different sinonasal tumor entities as well as normal sinonasal tissue. 72 samples were processed on a Q Exactive HF-X instrument coupled to an easy nanoLC 1200 system using one microgram of peptides and an 110 minutes gradient.

  Dataset EGAD00010002381

• Set_of_human_mesenchymal_CSA

  51 DNA methylation arrays of human samples initially diagnosed as mesenchymal chondrosarcoma. Microdissection of the cartilage and/or the small round cell component from the same sample may have occurred. As mentioned in the sample descriptions, the diagnoses of four samples have been revised. Additional molecular investigations were conducted for a subset of samples as described in the related publication.

  Dataset EGAD00010002515

• Panel based plasma sequencing data for patients with NSCLC in TRACERx cohort

  Ultrasensitive circulating tumour DNA (ctDNA) detection can stratify clinical risk in early-stage non-small cell lung cancer (NSCLC). Here, we applied a whole-genome, tumour-informed approach to study ctDNA in more than 400 NSCLC of the TRACERx project. This study captures the plasma sequencing data from the project.

  Dataset EGAD50000002534

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10345i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003107

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003108

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10592i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003109

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10679iA

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003110

• Single cell mRNA sequencing of CD11b cells from a primary GBM - SF 10360i

  We collected fresh tissue from an untreated GBM directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine after selection of CD11b+ cells using magnetic beads.

  Dataset EGAD00001003111

• RNA-seq iNKT, T and C1R cells

  RNA-seq (Ribodepleted Directional -75 PE- Hiseq 4000) data of purified and expanded iNKt and T cells from normal donor, and RNA-seq (poly-A 100-PE Hiseq 2500) data from C1R cell line. Data set consist of 3 pairs of fastq files, one pair per sample

  Dataset EGAD00001004331

• Chromosomally integrated HHV6 data of parent-infant pairs

  Raw data used in the analysis of chromosomally integrated HHV6 genomes in parent-infant pairs, generated by means of full viral genome sequencing by SureSelect target enrichment, in the context of a larger study investigating the relationship between HHV6 and adverse pregnancy outcome.

  Dataset EGAD00001004592

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW4_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_M

  Dataset EGAD00001001834

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW49_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_M

  Dataset EGAD00001001831

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW49_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW49_C

  Dataset EGAD00001001829

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW47_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_M

  Dataset EGAD00001001828

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW47_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_F

  Dataset EGAD00001001827

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW47_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW47_C

  Dataset EGAD00001001826

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW46_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_M

  Dataset EGAD00001001825

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW46_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_F

  Dataset EGAD00001001824

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW46_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW46_C

  Dataset EGAD00001001823

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW3_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_M

  Dataset EGAD00001001822

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW3_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_F

  Dataset EGAD00001001821

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW3_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW3_C

  Dataset EGAD00001001820

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW38_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_M

  Dataset EGAD00001001819

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW38_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_F

  Dataset EGAD00001001818

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW38_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW38_C

  Dataset EGAD00001001817