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• DAC "Genotyping based on SNPs covered by targeted NGS"

  DAC for the dataset from the article "Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples"

  Dac EGAC50000000358

• H3Africa KDRN Phenotype

  The phenotypic data for 6431 samples of the KDRN Study from Ghana and Nigeria.

  Dataset EGAD00001009333

• ESGI - Whole Genome Sequencing of samples from the Croatian isolated populations (2017-11-22)

  Whole genome sequencing of sampels from isolated populations from Croatia. The samples are sequenced using the Illumina HiSeq X Ten system. This dataset contains all the data available for this study on 2017-11-22.

  Dataset EGAD00001003812

• Somatic mutation and selection at epidemiological scale - TwinsUK_ExomeNanoSeq_Buccal

  Exome NanoSeq in buccal swab samples obtained from patients with a wide range of clinical phenotypes. As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations. Some of these clones represent a first step towards cancer whereas others may contribute to ageing and other diseases. However, our understanding of the clonal landscapes of human tissues, and their impact on cancer risk, ageing and disease, remains limited due to the challenge of detecting somatic mutations present in small numbers of cells. Here, we introduce a new version of nanorate sequencing (NanoSeq), a duplex sequencing method with error rates of less than 5 per billion base pairs, which is compatible with whole-exome and targeted gene sequencing. Deep sequencing of polyclonal samples with single-molecule sensitivity enables the simultaneous detection of mutations in large numbers of clones, yielding accurate somatic mutation rates, mutational signatures and driver mutation frequencies in any tissue. Applying targeted NanoSeq to 1,042 non-invasive samples of oral epithelium and 371 samples of blood from a twin cohort, we found an unprecedentedly rich landscape of selection, with 46 genes under positive selection driving clonal expansions in the oral epithelium, over 62,000 driver mutations, and evidence of negative selection in some genes. The high number of positively selected mutations in multiple genes provides high-resolution maps of selection across coding and non-coding sites, a form of in vivo saturation mutagenesis. Multivariate regression models enable mutational epidemiology studies on how carcinogenic exposures and cancer risk factors, such as age, tobacco or alcohol, alter the acquisition and selection of somatic mutations. Accurate single-molecule sequencing has the potential to unveil the polyclonal landscape of any tissue, providing a powerful tool to study early carcinogenesis, cancer prevention and the role of somatic mutations in ageing and disease.

  Dataset EGAD00001015620

• Access to "A Spatially Resolved Single-Cell Atlas of the Human Fetal Olfactory System"

  The human nasal region arises from neural crest and placodal lineages, yet its early development remains poorly understood owing to limited fetal tissue access and structural complexity. Here we present an integrated single-nucleus and spatial transcriptomic atlas of the human fetal nasal region, generated from 10 fetuses (males and females) between 7 and 12 post-conceptional weeks. Single-nucleus RNA sequencing resolved 32 distinct cell types, while integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) enabled spatial and temporal mapping of gene expression dynamics across the olfactory epithelium (OE) and adjacent tissues. We identify novel markers of olfactory sensory neuron differentiation and pathways governing epithelial patterning and OE morphogenesis. Notably, spatially organized expression of 169 olfactory receptor genes reveals molecular evidence for the “one neuron-one receptor” principle during the first trimester. Together, this work establishes the first molecular and spatial framework of early human olfactory development and provides a foundational resource for studies of sensory neurogenesis and congenital disorders.

  Dac EGAC50000000688

• 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

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD37920__Targeted_

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003321

• The Study of Somatic LINE1 Activity in Cancers

  This study focuses exclusively on the quantification of LINE1 mobilization. We analyzed a recent whole genome sequencing data release from multiple Cancer Genome Atlas (TCGA) sub-projects. In addition to the somatic LINE1 insertions (present in tumor and having no support in the matched normal) there are "pseudo-germline" non-reference LINE1 elements identified in tumor tissue and having some support in the matched normal. This dataset reports such "pseudo-germline" LINE1 retrotranspositions. Individual level data for TCGA can be accessed by requesting access to phs000178.

  Study phs003888

• Hospital for Sick Children Infant Glioma RNA Sequencing

  Whole transcriptome (n=4) and targetted RNA sequencing (n=15) .bam files of infantile glioma samples reported on at the Hospital for Sick Children

  Dataset EGAD00001005092

• T-WGBS for Naive B Cell

  Tagged-WGBS for 3 Naive B Cell samples of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005966

• Human Origins array data for 1510 individuals

  Genotype data typed on the Human Origins array for 1510 individuals published in "Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture."

  Dataset EGAD00001010015

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• Isala Cross sectional Flow Meta Data

  This meta data contains extensive meta data from the cross sectional flow of the Isala Citizen Science project. The meta data file contains ENA Accession numbers for 16S Microbiome data, and cleaned responses to questionnaires.

  Dataset EGAD00001009890

• Data Access Commitee for the project : Methylome profiling of human mesenchymal chondrosarcoma

  Dac EGAC00001003217

• Data Access Committee for the Metastatic Breast Cancer Whole-exome sequencing study

  Dac EGAC00001000434

• DAC for the study of tumor-derived somatic mutation detection in cfDNA

  Dac EGAC00001001569

• Data Access Commitee of the Princess Maxima Center for Pediatric Oncology

  Dac EGAC00001001948

• tRCC UTSW 2024 Cohort

  This submission contains the WES and RNA-Seq raw data for the study titled 'Comparative Genomics of a Translocation Renal Cell Carcinoma Mouse Model Reveals Molecular Mechanisms of Tumorigenesis.

  Dac EGAC50000000105

• BROCA cancer panel sequencing for 15 samples

  BROCA panel sequencing using the BROCA-HR v8 and BROCA-GO v1 versions of the gene panel

  Dataset EGAD50000000035

• GR@ACE_StageI.CEL_files

  Intensity calculation on the pixel values of the DAT file for 7409 samples genotyped using Axiom 815K Spanish Biobank array (Thermo Fisher)

  Dataset EGAD00010001655

• Exome chip analysis file

  This data set includes the following summary level data file used for the exome chip analysis: exome_chip.sv.assoc.txt: results from single variant association analysis in exome chip

  Dataset EGAD00010001187

• Melanoma post mortem analysis

  We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient.

  Dataset EGAD00001005072

• Human Spermatogenesis Methylome

  The dataset contains the methylome EM-sequencing raw data (fastq) of different spermatogenic cells from 5 human males (three controls and two crypotzoospermic). The datasets correspond to the following cell types: undifferentiated spermatogonia, differentiating spermatogonia, 4C spermatocytes, and 1C spermatids (this cell type only for the control individuals)

  Dataset EGAD00001011180

• WGS of all Patients Listed within this Study

  This dataset contains WGS from whole blood of patients II.2, II.3, III.1-4 and WGS from fibroblasts of patients III.2 and III.3. All WGS was performed on an Illumina NextSeq2000 to a minimum depth of 250 million read pairs (2x150nts).

  Dataset EGAD50000002362

• RNA-seq dataset of salivary gland tumor samples

  This dataset contains paired-end RNA-seq data of salivary gland tumor samples from 94 patients. Sequencing was performed on Illumina HiSeq 2500, HiSeq 4000, HiSeq X Ten or NovaSeq 6000.

  Dataset EGAD50000001191