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• Sequencing data for oesophageal and related samples - OACs release 2 (RNA)

  Dataset EGAD00001003839

• WES in muscle-invasive bladder cancer (MIBC) treated with durvalumab plus olaparib in the neoadjuvant setting: NEODURVARIB trial

  This submission contains the metadata derived from the whole exome sequencing of 70 samples from 26 patients who developed advanced urothelial carcinomas. The patients were enrolled in the Neodurvarib clinical trial, which compares the molecular profiles at diagnosis and after neoadjuvant treatment with Durvalumab and Olaparib. In this regard, the analyzed samples include: normal tissue and tumoral tissue obtained from the transurethral resection of the bladder (TURBT, a procedure performed prior to neoadjuvant therapy) from the 26 patients (52 samples), as well as tissue obtained from the radical cystectomy (a procedure performed after treatment with the aforementioned drugs; 18 samples).

  Study EGAS50000000791

• InsPIRE islets

  We explored the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using RNA-Seq and genotyping data from 420 islet donors and 26 FAC sorted beta-cells.

  Study EGAS00001003997

• Genetic analysis of HLA and immune escape genes in Diffuse Large B-cell Lymphoma

  We performed genetic analysis of HLA and immune escape genes in samples from 44 patients sequenced by whole exome sequencing (34 tumor samples, 32 normal samples) and whole genome sequencing (10 tumor samples, 12 normal samples). We also performed HLA targeted sequencing in 26/44 patients (26 tumor samples, 26 normal samples).

  Dataset EGAD00001007565

• Whole Exome Sequencing of gliomas

  Dataset EGAD00001001614

• Bladder cancer sequencing data

  Dataset EGAD00001001036

• COIN DAC

  Dac EGAC00001002190

• Single-Cell TCR/BCR Sequencing for Korean COVID-19 Vaccinated and Patient Samples

  We conducted longitudinal single-cell TCR/BCR sequencing for COVID-19 vaccinated cases (297 samples from 112 cases) and COVID-19 infected cases classified as Asymptomatic (26 samples from 12 cases), Mild (82 samples from 37 cases), Moderate (123 samples from 50 cases), Severe (216 samples from 58 cases), and Critical (142 samples from 41 cases) according to the NIH guideline.

  Study phs003341

• Low-pass nanopore whole genome sequencing of brain tumors

  Dataset EGAD00001003382

• Meningioma Exome

  Meningioma Exome

  Dataset EGAD00001000099

• RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial

  Study on RNA-seq data from tumor tissue samples of primary tumors of advanced clear cell renal cell carcinoma patients enrolled in the NIVOREN GETUG-AFU-26 trial who consented to and participated in the translational program. The goal of this study was to assess previously published gene expression signatures and evaluate their association with the benefit and/or resistance to nivolumab, as well as their association with circulating soluble factors.

  Study EGAS50000001057

• RNA-seq after drug perturbation of primary lymphoma samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dataset EGAD50000002166

• WGS datasets of pediatric glioblastoma

  WGS with linked reads of pediatric glioblastoma. For each patient, blood and tumor tissue were sequenced. For two patients, we also provide sequencing data for the blood of their parents.

  Dataset EGAD00001005212

• CPC-GENE Prostate Cancer Heterogeneity Study

  Raw sequence data, fastq format

  Dataset EGAD00001002885

• CRLF2 sequencing project Exomes

  CRLF2 sequencing project Exomes

  Dataset EGAD00001000077

• Functional characterisation of CpG islands in human tissues

  Functional characterisation of CpG islands in human tissues

  Dataset EGAD00001000212

• WGS

  Whole Genome Sequencing

  Dataset EGAD00001001120

• WES of melanoma tumors treated with combined immune checkpoint blockade

  This study of pre-treatment melanoma tumor samples from patients subsequently treated with combined anti-CTLA-4 and anti-PD-1 checkpoint blockade sought to identify genomic biomarkers of response to therapy. A total of 26 tumor and matched normal samples underwent whole exome sequencing.

  Study EGAS00001003857

• Anaplastic meingioma methylation

  Methylation of anaplastic meningiona samples

  Dataset EGAD00010001629

• Error-corrected sequencing of 26 driver genes

  387 swab samples were sequenced. The bam files contain consensus reads.

  Dataset EGAD50000000079

• WGS in insulinomas

  Whole-Genome Sequencing datasets of insulinoma samples and paired blood controls

  Dataset EGAD50000000464

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• Gut metagenomic data of 2,338 Pinggu adults

  Here we exploited a Han Chinese population-based cohort with extensive host metadata established in the Pinggu (PG) district of Beijing, and investigated gut microbiota from 2,338 adults (26-76 years) by metagenomic sequencing, revealing associations of the gut microbiota with sex, sex hormones, age, and a number of clinical and metabolic parameters.

  Study EGAS00001004820

• Pancreatic adenocarcinoma QCMG 20110901

  Pancreatic adenocarcinoma QCMG 20110901

  Dataset EGAD00001000049

• Error-corrected sequencing of 26 driver genes (additional cohort)

  An additional 320 swab samples were sequenced. The bam files contain consensus reads.

  Dataset EGAD50000000641

• RNAseq dataset

  RNAseq experiment after DIS3 ASO or Control ASO treatment on human cells under plasmablast differentiation.

  Dataset EGAD50000001243

• Data files for PCGP SJACT RNASEQ

  This dataset contains RNA-Seq files for the SJACT cohort associated with the paper "Genetic landscape of pediatric Adrenocortical Tumor". In this paper, we analyse 37 adrenocortical tumours (ACTs) by whole-genome, whole-exome and/or transcriptome sequencing.

  Dataset EGAD00001002680

• Somatic mutations in twin breast cancers (2019-04-03)

  The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004890

• ICGC PCAWG Dataset: ORCA-IN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN.

  Dataset EGAD00001002120

• Prostate cancer datasets WES

  WES: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (HiSeq)

  Dataset EGAD00001004467

• RNAseq

  RNAseq was performed on CDX, CDX-derived cell line and LNCaP cell line, with triplicates.

  Dataset EGAD00001006008

• alopecia areata

  exome sequencing files from 25 alopecia areata samples from spain.

  Dataset EGAD00001006370

• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• RNAseq SCLC Cell lines MYC

  RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

  Dataset EGAD00001003099

• Prostate cancer datasets WGS

  Low pass WGS: 48 samples (5 blood samples from 6 patient data): 22 Tumour cores and 26 normal/benign cores (Next Seq )

  Dataset EGAD00001004466

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Study EGAS00001001463

• Transcriptomic profiling of patient-derived xenografts and organoids in prostate cancer

  Dataset contains RNA-seq of 30 samples (normal prostate tissue, human prostate cancer, PDX and organoids).

  Dataset EGAD00001006404

• DAC-2020-03-26-Lemola (DAC-039))

  This is only the location. For the raw data and any check if the dataset may be relevant please refer to the Harvard Dataverse (https://dataverse.harvard.edu/dataverse/lemola).

  Study EGAS50000000635

• The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways

  A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.

  Study EGAS00001006631

• RNA sequencing from High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  RNA-seq for 26 newly added samples in High-grade B-cell lymphoma, not otherwise specified: an LLMPP study, and 32 samples from a previously uploaded dataset.

  Dataset EGAD50000001365

• Dedifferentiated Melanoma (2021-02-02)

  De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006931

• Detection of cancers three years prior to diagnosis using plasma cell-free DNA

  A major goal of early cancer detection is to identify subclinical disease when the tumor burden is low, so that treatments are more effective. But how early can cancers be detected prior to clinical signs or symptoms? This question can be answered only through the evaluation of participants whose clinical course has not been altered by the study itself. We here describe such an evaluation, performed on prospectively collected plasma samples from the Atherosclerosis Risk in Communities (ARIC) study, including 26 participants diagnosed with cancer and 26 matched controls. At the index time point, eight of these 52 participants scored positively with a multicancer early detection (MCED) blood test. All eight of these participants were diagnosed with cancer within 4 months after blood collection. In six of these 8 participants, we were able to assess an earlier plasma sample collected 3.1 to 3.5 years prior to clinical diagnosis. In four of these six participants, the same mutations detected by the MCED test could be identified, but at 8.6 to 79-fold lower levels. These results demonstrate that it is possible to detect circulating tumor DNA (ctDNA) more than three years prior to clinical diagnosis, and provide benchmark sensitivities required for the success of ctDNA-based tests for this purpose.

  Study EGAS00001008068

• Young Boost Trial for Breast Cancer patients

  The Young Boost Trial (YBT, YOUNG BOOST / BOOG 2004-01 (Borstkanker) | Kanker.nl investigated the optimal radiation dose for breast cancer patients aged 50 years or younger, treated with breast-conserving therapy (BCT). In this randomized study, participants were assigned to receive either a 26 Gy or a 16 Gy radiation boost, with the primary endpoint being local recurrence. To explore potential predictive biomarkers of treatment response in this patient group, whole exome sequencing (WES) was performed on tumor samples to identify genetic factors that could guide personalized treatment strategies and improve clinical outcomes for these young breast cancer patients.

  Study EGAS50000000797

• Clinical utility of combined low-pass whole genome and targeted sequencing in liquid biopsies for diagnosis and monitoring of pediatric solid tumors

  Low-pass whole genome sequencing samples from pediatric solid tumor patients who are deceased

  Dataset EGAD00001009972

• WES dataset of a TIL-ACT metastatic melanoma cohort

  Whole-exome sequencing (WES) data from 13 patients with metastatic melanoma in a TIL-ACT cohort, generated to characterize tumor genomics and neoantigen landscapes relevant to adoptive T cell therapy.

  Dataset EGAD50000001731

• Short-read (RNA-seq)

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Dataset EGAD00001006596

• Exome Sequencing of Esophageal Adenocarcinoma

  The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. When coupled to the five-year survival rate of only 15% for this disease, identification of new therapeutic targets for EAC is of great importance. Here, we analyze the mutational spectra identified from the whole genome sequencing of 16 EACs and complete exome sequencing of 149 EAC tumors and matched germline samples. We identify a novel mutation signature marked by high prevalence of A to C transversions at AA*(N) trinucleotides. Notably, the development of EAC is preceded by pathologic intestinal metaplasia of the lower esophagus, Barrett's esophagus, itself a response to injury from gastric-esophageal reflux disease (GERD). Thus, we hypothesize to represent these AA*(N) mutations to a novel signature of GERD-induced mutagenesis. Analysis of the exome data identified 26 genes subject to statistically significant recurrent mutation. Of these 26 genes, only TP53, CDKN2A, SMAD4, and PIK3CA had been previously implicated in EAC. Novel mutations include those targeting chromatin modifying factors and novel candidate contributors to EAC: SPG20, TLR4, ELMO1 and DOCK2. Of these, ELMO1 and DOCK2 are notably direct dimerization partners that act to activate Rac1 to enhance cellular invasiveness, thus generating new hypotheses about the potential for the Rac1 pathway to be a novel target for therapy of EAC. "Reprinted from 'Unraveling the mutational complexity of esophageal adenocarcinoma', with permission from Nature Genetics."

  Study phs000598

• Breast Cancer Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of 26 primary breast cancers from Wu et al. (2021) study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001007495

• RNA-Sequencing and Somatic Mutation Status of Adrenocortical Tumors: Novel Pathogenetic Insights

  To investigate the relationship between transcriptome profile and genetic background in a large series of adrenocortical tumors and to identify new potential pathogenetic mechanisms, we performed transcriptome profiling by high-throughput sequencing. We collected snap-frozen tissue from patients with adrenocortical tumors (n = 59) with known genetic background: 26 adenomas with Cushing syndrome, 17 adenomas with mild autonomous cortisol secretion, 9 endocrine-inactive adenomas, 7 adrenocortical carcinomas. Additionally, we sequenced 4 control samples.

  Study EGAS00001004533

• DIPG WES and RNA-Seq

  We characterised H3K27M-mutant diffuse intrinsic pontine glioma (DIPG, n=21) and RNA-Seq (n=26 DIPG, 12 normal brain)

  Dataset EGAD00001006450