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• RNAseq data

  RNAseq data for 10 patients: 10 tumors and 10 cell lines

  Dataset EGAD00001002691

• Exome sequencing VCF files for glioma progression

  Exome sequencing VCF files describing mutations during glioma progression.

  Dataset EGAD00001001887

• Biomarker Data Subset

  This dataset contains data for CBC counts and absolute protein abundance measurements from ELISA experiments.

  Dataset EGAD00001011163

• Whole genome sequencing data of ccRCCs

  Whole genome sequencing data of ccRCCs were utilized for somatic variations calling.

  Dataset EGAD00001004588

• Phylogenetic reconstruction of breast cancer

  This dataset contains the fastq files used for this study

  Dataset EGAD00001006121

• Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes

  Head and neck squamous cell carcinoma (HNSCC) tumors were sampled from 88 patients. Samples were implanted subcutaenously into the flank of NOD/SCID/IL2R-/- mice. Mice were then monitored weekly for tumor growth and the time of initial palpation was recorded. Mice were euthanized when tumors reached 15 mm in diameter or after 6 months. If no tumor formed by 6 months, the patient tumor was defined as Non-engrafter (N). RNA-seq was performed on all primary tumor samples and successfully engrafted patient-derived xenograft (PDX) samples.

  Study EGAS50000000714

• Whole-genome sequencing of cell-free DNA from pancreatic and breast cancer cohorts for fragmentomic and tumor fraction analysis

  This project provides whole-genome sequencing data from cell-free DNA collected from patients with pancreatic ductal adenocarcinoma and breast cancer, alongside healthy and benign controls. The study aims to identify novel liquid biopsy biomarkers by exploring the relationship between per-base quality scores and fragmentomic signals like end-motifs and fragment length. Furthermore, the data supports the development of Bayesian deep learning frameworks for the uncertainty-aware estimation of tumor fraction and ploidy in low-concentration clinical samples.

  Study EGAS50000001620

• Comparison of single/pooled CTCs and bulk exome sequencing

  Single cell technologies allow the interrogation of tumor heterogeneity, providing insights into tumor evolution and treatment resistance. To better understand whether circulating tumor cells (CTCs) could complement metastatic biopsies for tumor genomic profiling, we characterized 11 single CTCs and 10 pooled CTC samples at the mutational and copy number aberration (CNA) levels, and compared these results with matched synchronous tumor biopsies from 3 metastatic breast cancer patients with triple-negative (TNBC), HER2-positive and estrogen receptor-positive (ER+) tumors. Similar CNA profiles and the same patient-specific driver mutations were found in bulk tissue and CTCs for the HER2-positive and TNBC tumors, whereas different CNA profiles and driver mutations were identified for the ER+ tumor, which presented two distinct clones in CTCs defined by mutations in ESR1 Y537N and TP53, respectively. Furthermore, de novo mutational signatures derived from CTCs described patient-specific biological processes. These data suggest that tumor tissue and CTCs provide complementary clinically relevant information to map tumor heterogeneity and tumor evolution.

  Dataset EGAD00001009052

• Size-tagged preferred ends in maternal plasma DNAshed light on the production mechanism and showutility in noninvasive prenatal testing

  Cell-free DNA molecules in the plasma of pregnant women exhibit nonrandom fragmentation with preferred end sites. We studied if such preferred end sites might bear any re- lationship with fragment lengths of plasma DNA. Short and long plasma DNA molecules were associated with different preferred DNA end sites. Analysis of size-tagged preferred ends could be used for measuring fetal DNA fraction and for facilitating fetal trisomy 21 detection. Fetal preferred end sites were generally located in the nucleosome cores, while the maternal ones were located in the linker regions. This con- ceptual framework provides an explanation of the relative shortness of fetal DNA in maternal plasma and brings us closer to understanding the biological mechanisms that influence plasma DNA fragmentation.

  Study EGAS00001002831

• UCSF Sebaceous Carcinoma DAC for review of sequence data release from manuscript in Nature Communications, based in the UCSF Departments of Dermatology and Pathology

  Dac EGAC00001000850

• DATA FILES FOR SJHYPO

  Hypodiploid acute lymphoblastic leukemia whole genome sequencing

  Dataset EGAD00001000260

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - side_cases_barretts

  Dataset EGAD00001001379

• TwinsUK_EpiTwin_DNA_Methylome

  MeDIP-seq RPM chromsome BED files for Peripheral Blood from EPITWIN Project (Columns 4-4353 represent samples)

  Dataset EGAD00010000983

• BLEMD (arrays set)

  Circulating tumor cells for comprehensive and multiregional non-invasive genetic characterization of multiple myeloma (arrays set)

  Dataset EGAD00010001857

• dataset_raw_NativesAmericans_LDGH_august2020

  Genome-wide data for 98 Native American individuals from Andes and Amazon

  Dataset EGAD00010001958

• Dataset for study EGAS00001004946 (Endothelium-derived stromal cells contribute to bone marrow niche formation)

  Dataset EGAD00001006914

• BreastCancer_Miroarrays

  Genotyping array data for breast cancer and matched normal mammary gland samples

  Dataset EGAD00010002251

• LOPEZ_2019.vcf.gz

  Genotype data for new samples in Lopez et al 2021

  Dataset EGAD00010002100

• Inherited Corneal Dystrophies - Institute of Ophthalmology, University College London (IoO, UCL)

  DAC created for access to data published by Dr. Alice E Davidson

  Dac EGAC50000000213

• ITER-FIISC Data Access Committee

  DAC for whole-genome variant calling data of individuals from the study of allergic diseases in the Canary Islands.

  Dac EGAC50000000180

• RNAseq for 190 AML patients

  This dataset contains 190 fastq files sequenced with Illumina HiSeq500.

  Dataset EGAD50000000490

• Mechanism of Decitabine response in MDS/AML patients

  Data access agreement for access to scRNASeq data of serial AML/MDS patients undergoing decitabine treatment.

  Dac EGAC50000000550

• Exome sequencing for identifying point mutations driving M haemophilum susceptibility

  To understand non tuberculous Mycobacterial susceptibility

  Study EGAS50000001076

• SiMSen‑Seq

  High resolution amplicon-bases sequencing o screen for PIK3CA hot spot mutations

  Dataset EGAD50000001668

• UROMOL 2020 - RNA-seq data for validation

  Total RNAseq data from 47 patients with NMIBC.

  Study EGAS00001005050