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• Picuris Pueblo Genomic Project (Ancient Data)

  Data Access Committee for the ancient dataset of the project "Picuris Pueblo oral history and genomics reveal continuity in US Southwest".

  Dac EGAC50000000525

• Whole Exome Sequencing Data

  This dataset includes: whole exome sequencing data for a total of 23 BCP-ALL patients - BAM files

  Dataset EGAD50000001519

• Sutherland Nine Ancient DNA DAC

  This Data Access Committee controls access for the genetic data from the Sutherland Nine. It consists of involved Scientists and Family respresentatives.

  Dac EGAC50000000529

• RNA-seq from melanoma biopsies

  RNA-seq data for melanoma biopsies at baseline and after treatment

  Dataset EGAD00001009059

• Genomic characterization of metastatic breast cancers

  This dataset contains all the .bam files used for the study.

  Dataset EGAD00001004772

• Genomic Analysis of Mucinous Tumours (GAMuT) - RNA

  RNASeq for Genomic Analysis of Mucinous Tumours (GAMuT)

  Dataset EGAD00001005190

• RNA sequence of HUB_5 cell culture

  RNA sequence data for conditionally reprogrammed cells from patient HUB_5

  Dataset EGAD00001001923

• CUT&RUN in G3-MB

  Aligned BAM files from CCUT&RUN sequencing for BRD4 and H3K27ac in Group 3 Medulloblastoma cell models.

  Dataset EGAD50000002301

• A Multimodal Atlas of Human Brain Cell Types

  "A multimodal atlas of human brain cell types" includes sample data targeting two cell types that show species differences between mouse and human. First, it includes a detailed transcriptomic, morphological, and electrophysiological characterization of cell types in layer 1 of human middle temporal gyrus, focusing primarily on different inhibitory cell types. This project also includes gene expression data collected from nuclei in layer 5 of human fronto-insula, with a goal of identifying transcriptomic signatures of Von Economo neurons. Control samples collected as part of the same experiment are also included in the data set. This study was conducted as part of a collaboration between the Allen Institute for Brain Science, the University of Szeged, and the J. Craig Venter Institute. Collaborators request that publications resulting from these data cite their original publication: Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type (PMID: 30150662).

  Study phs001791

• Recurrent CLTC::SYK fusions and CSF1R mutations in juvenile xanthogranuloma of soft tissue

  In this study, the genomic landscape of extracutaneous juvenile xanthogranuloma (JXG) was analyzed. By leveraging the Dutch Nationwide Pathology Databank (Palga), tumor samples were obtained from different academic medical centers in the Netherlands. The study was approved by the Palga Scientific Council and Privacy Committee (LZV-2016-183) and the Institutional Review Board of Leiden University Medical Center (B19.074). In addition, the study was approved by the Biobank and Data Access Committee of the Princess Máxima Center for Pediatric Oncology (PMCLAB2024.0512). Provided are whole transcriptome sequencing (WTS) data of 3 histiocytic tumors with CLTC::SYK fusions. WTS was performed in the routine workflow of the Princess Máxima Center for Pediatric Oncology (as described in Hehir-Kwa, et al. JCO Precis Oncol 2022). RNA was derived from formalin-fixed paraffin-embedded tumor tissue (n=1) or from frozen tumor tissue (n=2).

  Study EGAS50000000584

• Detection of brain cancer using genome-wide cell-free DNA fragmentomes

  Diagnostic delays in patients with brain cancer are common and can impact patient outcome. Development of a blood-based assay for detection of brain cancers could accelerate brain cancer detection. In this study, we analyzed genome-wide cell-free (cfDNA) fragmentomes, including fragmentation profiles and repeat landscapes, from the plasma of individuals with (n=148) and without (n=357) brain cancer. Machine learning analyses of cfDNA fragmentome features detected brain cancer across all grade gliomas (AUC=0.90, 95% CI: 0.87-0.93) and these results were validated in an independent prospectively collected cohort. cfDNA fragmentome changes in patients with gliomas represented a combination of fragmentation profiles from glioma cells and altered white blood cell populations in the circulation. These analyses reveal the properties of cfDNA in patients with brain cancer and open new avenues for noninvasive detection of these individuals.

  Study EGAS50000000986

• Revealing active mutational processes in tumours using DigiPico/MutLX at unprecedented accuracy

  Active mutational processes in a tumor result in genetic micro-heterogeneity that can determine the tumor’s evolutionary trajectory. Identification of these processes by studying micro-heterogeneity can unveil novel aspects of tumor evolution with potential therapeutic implications. Such studies, however, are inherently problematic because of the discovery of excessive false positive mutations. Here we report the optimization and validation of a robust whole genome sequencing and analysis pipeline (DigiPico/MutLX) that virtually eliminates false positive results. Using our method, we identified, for the first time, a sub-clonal local hyper-mutation (kataegis) event in a recurrent ovarian carcinoma, which was unidentifiable from the bulk WGS data of the same tumor. Overall, we propose DigiPico/MutLX method as a powerful framework for the reliable study of genetic micro-heterogeneity in tumor and normal tissues.

  Study EGAS00001003555

• Hereditary Cancer Diagnostics with I2HCP gene panel

  This dataset contains targetted DNA sequencing data generated in the context of genetic diagnostics of hereditary cancer. Target enrichment was performed with the I2HCP, a custom hereditary cancer gene panel based in Agilent SureSelect and developed by the Germans Trias i Pujol Research Institute (IGTP, Badalona, Catalonia, Spain) and the Catalan Institute of Oncology (ICO, L'Hospitalet de Llobregat, Catalonia, Spain). After the enrichment, 108 samples were sequenced in Illumina HiSeq machines and 130 in MiSeq machines. Some of the samples were sequenced on both platforms. The dataset also includes MLPA validation data for all identified copy-number alterations, annotated with exon resolution and information about negative MLPA results. All this data was generated in the context of routine diagnostics and compiled together with MPLA validation data for a genetic diagnostics oriented benchmark of germline CNV calling tools.

  Study EGAS00001004316

• Gene copy number variation in pediatric mental illness in a general population

  We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health, and cognitive biomarkers in a community sample of 7,100 unrelated European, and East Asian children and youth (Spit for Science). Diagnoses of mental health disorders were found in 17.5% of participants and 27.6% scored in the highest 10% on either or both ADHD and OCD trait measures. Clinically relevant CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of ADHD (p=5.0×10-3), on a cognitive biomarker of mental health (response inhibition (p=1.0×10-2)), and on prevalence of mental disorders (p=1.9×10-6, odds ratio: 3.09). With a rise of mental illness, our data establishes a baseline for delineating genetic contributors in paediatric-onset conditions.

  Study EGAS00001006659

• cqmuGWAS1

  DNA for 1546 individuals from Chongqing was extract from peripheral blood and genotyped by Illumina Omni Zhonghua-8 version 1 gene chips.

  Dataset EGAD00010001527

• PMBCL IL4R DASL

  Expression data for 42 PMBCL patient samples (32 IL4R WT cases and 10 cases with mutations in IL4R)

  Dataset EGAD00010001542

• Copy number profiling of primary samples and cell lines of retinoblastoma

  Illumina SNP-arrays for matching retinoblastoma-blood pairs and retinoblastoma cell lines.

  Dataset EGAD00010000908

• Serum Proteomics of Aortic Diseases

  Comparative proteome-based analysis of different autologous bone entities used for alveolar onlay grafting

  Dataset EGAD00010002314

• SNParray_PGT_samples_scGBS

  PGT samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002169

• SNParray_HapMap_samples_scGBS

  HapMap samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002168

• scRaCH-seq data targeting BTK and SF3B1

  Data set for scRaCH-seq manuscript. We base call the fast5 using guppy.

  Dataset EGAD50000000235

• HMO-microbiome study dataset, 16S sequencing

  This dataset contains 16S sequencing of fecal and milk samples for HMO-microbiome Lifelines NEXT study

  Dataset EGAD50000000532

• Cancer Genomics, ICR, summary data

  DAC for summary level data from the Cancer Genomics group, Division of Genetics and Epidemiology at the Institute of Cancer Research, Sutton, UK.

  Dac EGAC50000000050

• Foundation Medicine Binary Calls

  Binary calls for all available samples in 4 Atezo trials.

  Dataset EGAD50000000709

• Picuris Pueblo Genomic Project (Modern Data)

  Data Access Committee for the present-day dataset of the project "Picuris Pueblo oral history and genomics reveal continuity in US Southwest".

  Dac EGAC50000000526