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• Whole genome data for study EGAS00001000824 (Diverse modes of genomic alterations in hepatocellular carcinoma)

  Whole genome data (Complete genomics platform) for the study EGAS00001000824

  Dataset EGAD00001001034

• Exome sequencing of primary and relapse neuroblastoma

  In this dataset, 16 trios- primary tumor, relapse and corresponding normals- for patients with neuroblastoma are provided. For one patient, more than one relapse was available for the analyses.

  Dataset EGAD00001001607

• Illumina RNA sequencing data

  RNA sequence data for HKCI-2, HKCI-C1, HKCI-C2, HKCI-C3 and MIHA. RNA-seq data of all the 5 samples were stored in compressed fastq format.

  Dataset EGAD00001004476

• SCNA-Seq of plasma DNA samples

  Low coverage whole genome sequencing for the identification of somatic copy number alterations (SCNA) and focal amplification mapping in plasma DNA of prostate cancer patients

  Dataset EGAD00001002149

• Ovarian cancer sequencing dataset

  Sequencing data from patients with Ovarian cancer. Data utilised in the 'Enhanced detection of circulating tumor DNA by fragment size analysis' manuscript (Mouliere et al, 2018)

  Dataset EGAD00001004939

• 666PG genomic rearrangements

  Genomic rearrangement calls generated using Delly in VCF format from the CPCGene 666PG study

  Dataset EGAD00001006146

• ATAC-seq of spermatogonia

  Raw sequencing reads of ATAC-seq of spermatogonia in FASTQ format, comprising 6 samples sequenced on the Illumina HiSeq 4000 platform.

  Dataset EGAD00001007759

• Cell line sequencing data

  SmMIP libraries using bulk cell line DNA and DNA mixes were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)

  Dataset EGAD00001007790

• PrevANZ RNAseq dataset

  Whole blood samples collected at baseline and week 12 in PAXgene Blood RNA tubes. RNA sequencing on the Illumina NovaSeq 6000 System generated 150 base pair length paired end reads.

  Dataset EGAD00001011069

• Genetic architecture of male infertility in India

  The dataset consists of whole exome and genome sequencing data from infertile males and his parent(s) and/or sibling(s)

  Dataset EGAD00001015606

• Spatially resolved cellular and molecular drivers of cardiac remodelling in healthy and failing human hearts: Adult DNA (2025-10-16)

  Human Cell Atlas - WGS Adult Heart . This dataset contains all the data available for this study on 2025-10-16.

  Dataset EGAD00001015751

• Chromosome Segregation Errors Promote a Diverse Spectrum of Simple and Complex Genomic Rearrangements

  Cancer genomes are frequently characterized by numerical and structural karyotypic abnormalities. Here we combined an inducible centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy we term ‘CEN-SELECT’, and show that single-chromosome missegregation during cell division can directly drive a broad spectrum of structural rearrangement types. Cytogenetic profiling revealed that missegregated chromosomes are 120-fold more susceptible to developing seven major categories of structural variants, including translocations, insertions, deletions, and reassembly into chromothriptically rearranged chromosomes. Whole-genome sequencing of clones with genetically propagatable derivative chromosomes identified complex rearrangements and copy-number alterations that can result in gene inactivation or extrachromosomal gene amplification. We conclude that chromosome segregation errors are sufficient to drive extensive structural variation that recapitulates those commonly associated with human cancers.

  Dataset EGAD00001004163

• Genomic Profiling of Relapsed and Refractory Childhood Cancers

  Through clinical trials focused on molecularly guided therapy in pediatric cancers (NCT01355679, NCT01802567, NCT02162732), the Beat Childhood Cancer Consortium performed paired tumor/normal whole exome sequencing and/or tumor mRNA sequencing for 202 pediatric or adolescent young adult patients with rare, relapsed and refractory cancers (including neuroblastoma, Ewing sarcoma, osteosarcoma, rhabdomyosarcoma, ependymoma, glioma, and other rare solid tumors). A subset of these patients had multiple biopsies sequenced, including longitudinal profiling.

  Study phs002238

• Blood Gene Signatures Associated with Stiffness After TKA

  In this study, we used PAXgene Blood RNA tubes collected from patients undergoing total knee arthroplasty (TKA) for osteoarthritis. Samples were collected with IRB approval and patient consent. We identified 8 patients with knee stiffness after TKA (cases) and 10 patients without post-TKA stiffness (controls). We isolated RNA from cases and controls for RNA-seq analyses, comparing samples collected the day of surgery and samples collected at 24 hours after surgery.

  Study phs002927

• Whole-genome sequences of Korean populations generated by using long- and short-read sequencing technologies.

  We newly sequenced whole-genome of Korean participants by using long- and short-read sequencing platforms (n = 3 and n = 100 for long- and short-read sequencing, respectively). With these data, generated by Sequel II HiFi system (Pacific Bioscience) and DNBSEQ-T7 (MGI) sequencers, we identified a set of structural variations common in Korean population as well as the genetic features distinct from other ethnicities.

  Study EGAS50000000375

• Panel sequencing of endocrine-resistant breast cancer

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Study EGAS50000000236

• Testing the feasibility of genome scale sequencing in routinely collected FFPE cancer specimens versus matched fresh frozen samples

  Testing the feasibility of genome scale sequencing in routinely collected FFPE cancer specimens versus matched fresh frozen samples

  Dataset EGAD00001000255

• Colorctal cancer WES/WGS analysis in Dr. Liu’s group in Sun Yat-sen University Cancer Center.

  The samples include paired tumor and normal tissues from 106 patients . High-coverage WES sequencing or whole genome sequencing of DNA samples were performed on the Illumina HiSeq 2000 system

  Dataset EGAD00001003551

• Myeloma Genome Project Targeted Sequencing Panel - Oxford Data

  This dataset comprises the BAM files from targeted genome sequencing of CD138+ selected myeloma tumour samples from 21 individuals. In 5 cases there is only one tumour sample, but in the other 16 cases there are sequential samples, spanning treatment relapses. There are denoted Tumor A, B C etc. Therefore there are a total of 48 myeloma tumour samples. For each individual there is also a germline control samples, obtained either from peripheral blood or from CD138-selected bone marrow cells.

  Dataset EGAD00001008735

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - structural variation vcf files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - structural variation vcf files (Mutographs)

  Dataset EGAD00001015389

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - copy number variants (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - copy number variants (Mutographs)

  Dataset EGAD00001015390

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - sequence data (Mutographs)

  Dataset EGAD00001015386

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - patient metadata files (Mutographs)

  Dataset EGAD00001015387

• The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  The complexity of tobacco smoke induced mutagenesis in head and neck cancer - filtered vcf files (Mutographs)

  Dataset EGAD00001015388

• Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ

  Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed single cell sequencing on endometrial and ovarian tumours, and on organoids both treated with DBZ and normal and found both secretory-like and ciliated-like tumour cells.

  Dataset EGAD00001006280