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• Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 90 cases

  Eccrine poroma (EP) and porocarcinoma (EPC) are rare benign and malignant adnexal neoplasms of the terminal sweat gland duct, respectively. Both can arise de novo, however, EPCs can also arise from a pre-existing EP. To-date, genetic investigation of these tumors has involved studies with small sample sizes and/or limited analyses. To comprehensively compare the driver events and mutational landscape of these tumors, we performed a retrospective multi-institutional whole-exome sequencing and RNA sequencing study on the largest cohort of EPs and EPCs to-date (n=90). We uncovered novel events and delineated different pathways of tumorigenesis underlying these tumors, with EPs driven largely by fusion genes, and EPCs driven largely by somatic mutations, with rare YAP1 and frequent PAK gene novel fusions.

  Dataset EGAD00001015379

• Transcriptomic consequences of complex rearrangements inv8p23.1 and inv17q21.31 associated with Autism Spectrum Disorders

  We have performed an RNAseq analysis in order to elucidate the transcriptomic consequences of two complex rearrangements associated with Autism Spectrum Disorder, including patients and controls (total n=24).

  Study EGAS00001005612

• Whole-exome sequencing data from breast cancer recurrence, endometrial cancer, and colon tumor samples harboring a rare germline BARD1 variant

  This dataset comprises whole-exome sequencing data from tumor and matched blood samples of a patient with breast cancer recurrence and endometrial cancer carrying a germline BARD1 p.(Gly753Val) variant, as well as from the colon tumor of the proband's father

  Dataset EGAD50000002412

• Whole-genome sequencing data of metastatic salivary gland cancer

  This dataset contains whole-genome sequencing data of three patients with metastatic salivary gland cancer who underwent autopsy to harvest tumor biopsies from spatially separated metastatic sites and biopsies from healthy skin as a control. Two patients had the subtype adenoid cystic carcinoma (patients 1 and 4) and one patient had the subtype myoepithelial carcinoma.

  Dataset EGAD50000002056

• Targeted DNA sequencing of TTFields-treated glioblastoma, IDH wildtype

  This dataset contains raw paired-end FASTQ files from targeted DNA sequencing using the TruSight Oncology 500 panel in patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. Tumour samples were collected at first surgery and are linked to pseudonymised clinical and molecular annotations described in the associated EGA study.

  Dataset EGAD50000002117

• Whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients

  This dataset contains whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients. Whole exome sequencing with a minimum coverage of 100x was performed using the Illumina Novaseq6000 platform and the Agilent SureSelect Human All Exon V7 kit.

  Dataset EGAD50000002264

• Spatial transcriptomics reveals immune and tissue remodeling, highlighting diverse host responses across mycobacterial granuloma types

  Granulomas are the hallmark of Mycobacterium infections, forming structured immune environments that drive disease persistence. However, their spatial and functional organization remains unclear. Using spatial RNA sequencing on 33 patient explants, we try to reveal the detailed gene expression and cell composition landscape of granulomas.

  Dataset EGAD50000001462

• MET amplification in gastric cancer

  WES sequencing of two cases of MET amplified gastric cancer. Six unfixed fresh frozen samples were obtained from the primary tumors (three samples from each) and three samples from corresponding non-neoplastic mucosa. In addition, formalin-fixed and paraffin-embedded (FFPE) samples were obtained from the primary tumors (n=2), lymph node metastases (n=7) and non-neoplastic mucosa (n=2).

  Dataset EGAD50000001099

• TN

  In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples.

  Dataset EGAD00001003351

• Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

  This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

  Dataset EGAD00001004565

• Illumina 5'end RNA sequencing

  The dataset contains 200 fastq files of Illumina 5'end RNA sequencing data of 50 PBMC samples. The paired-end data includes 100 fastq files (R1 and R2) of 50 full-length cDNA sequencing libraries and 100 fastq files (R1 and R2) of 50 HLA amplicon sequencing libraries.

  Dataset EGAD00001006838

• FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

  We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts such as misalignments or random pairing of transcript fragments and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including 8 cancers with and without known rearrangements.

  Study phs000311

• Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

  Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial). Panel sequencing data from baseline FFPE biopsies were used to perform a comprehensive genomic profiling of CUP metastases. Combined targeted next-generation sequencing of patient-specific hotsport mutations and shallow whole genome sequencing of baseline and follow-up liquid biopsy samples were used to analyze ctDNA and to evaluate response to immunei checkpoint inhibitor treatment. In some cases, whole exome sequencing of peripheral blood mononuclear cells was performed to screen for potential CHIP and germline mutations.

  Dataset EGAD00001011130

• Genetic heterogeneity and dynamics of transcriptional subtypes in matched primary and recurrent head and neck squamous cell carcinomas

  To get a better understanding of different HNSCC subtypes, whole-exome (matched tumor-normal paits) and whole transcriptome sequencing to to elucidate underlying molecular processes. Here, we present the matched whole-exome sequencing data from 28 patients (normal tissue, tumor tissue, relapse).

  Study EGAS00001005005

• Single Cell MK and HSC sequencing

  In the current understanding of adult bone marrow hematopoiesis, megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. Here, we use single cell RNA sequencing to characterize HSCs and MKs from human bone marrow, to investigate MK lineage commitment and maturation.

  Study EGAS00001004844

• Single nucleus mRNA sequencing of immune cells from diverse CNS regions in human health and diseases

  CNS nuclei were isolated from frozen specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with single nucleus RNA-seq. One batch of samples was also labelled with CMO and allows distinguishing indivudal samples within the analysis. A combined seurat object was generated to include all the analyses and samples were integrated using Harmony integration.

  Dataset EGAD50000001835

• Congenital mesoblastic nephroma and infantile fibrosarcoma

  The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.

  Dataset EGAD00001003885

• Longitudinal Single-Cell Profiling in Refractory Mantle Cell Lymphoma

  we performed sequential scRNA-seq of 21 specimens (discovery cohort) collected at baseline, during treatment, and/or at disease remission/progression from 3 ibrutinib-responsive (R) patients (Pt-V, C and D) and 2 non-responsive (NR) patients (Pt-B and E). In addition, the PBMC samples from two healthy donors (N1 and N2) were included as the normal controls.

  Dataset EGAD00001006994

• A complex chromosomal rearrangement (CCR) was resolved at the nucleotide level by whole genome long read sequencing using PacBio sequencing platform.

  A complex chromosomal rearrangement (CCR) involving 7 chromosomes and 11 breakpoints was resolved at the nucleotide level by whole genome long read sequencing using PacBio sequencing platform.

  Study EGAS00001008133

• The dataset of Detection and characterization of lung cancer using cell-free DNA fragmentomes on NovaSeq 6000 at 1-2x coverage

  The dataset contains 364 CRAM files from whole-genome next-generation sequencing on the Illumina NovaSeq 6000 at 1- 2x coverage. These are plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD50000001961

• LCM_WES__Thyroid_

  Whole exome sequencing through the low-input DNA pipeline in thyroid samples. Tissue will be processed either from laser capture microdissection or directly from bulk frozen/fixed/paraffin-embedded tissue. Insights will be gained here directly from the sequencing but also from using the data as a matched normal in Exome Nanoseq. Thyroid samples will be obtained from patients with and without thyroid disease.

  Study EGAS00001007772

• RNA-seq of der(1;7)(q10;p10) & control MDS patients

  The study examined the RNA profiles of MDS cases. This study utilized BAM files of RNA-seq of der(1;7)(q10;p10) MDS cases, -7/del(7q) MDS cases, and OTHER MDS cases to analyze gene expression. In particular, the study profiled der(1;7)(q10;p10) MDS cases compared to non-der(1;7)(q10;p10) MDS cases.

  Study EGAS50000000705

• Lothian Birth Cohort 1921 whole genome sequencing study

  297 members of the Lothian Birth Cohort 1921 (LBC1921) were sequenced using the Illumina HiSeq X platform. The LBC1921 are a relatively healthy cohort of 550 individuals who underwent cognitive and medical testing at a mean age of 79.1 (SD=0.6) years. They have since undergone four further waves of testing, approximately three years apart.

  Study EGAS00001003818

• Lothian Birth Cohort 1936 whole genome sequencing study

  1075 members of the Lothian Birth Cohort 1936 (LBC1936) were sequenced using the Illumina HiSeq X platform. The LBC1936 are a relatively healthy cohort of 1091 individuals who underwent cognitive and medical testing at a mean age of 69.5 (SD=0.8) years. They have since undergone four further waves of testing, approximately three years apart.

  Study EGAS00001003819

• Circulating RNAs prior to endometrial cancer diagnosis

  We analyzed circulating RNA levels using small RNA sequencing, targeting RNA in the size range 17 to 47 nucleotides, in samples collected prior to endometrial cancer diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1-11 years prior to diagnosis , and 316 matched controls, both from the Janus Serum Bank Cohort in Norway.

  Study EGAS50000000267