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• DO NOT USE - Whole genome sequencing of SI-NETs from six patients

  Small intestine neuroendocrine tumor (SI-NET), the most common cancer of the small bowel, often displays a curious multifocal phenotype with several intestinal tumors centered around a regional lymph node metastasis, yet the typical path of evolution of these lesions remains unclear. Here, we determined the complete genome sequences of 24 tumor and 3 adjacent normal tissue samples with their paired normal blood samples (totally 33 whole genomes) from 6 patients with multifocal SI-NETs, allowing elucidation of phylogenetic relationships between multiple intestinal tumors and metastases in individual patients.

  Study EGAS00001005009

• Immunosenescence: Immunity in the Young and Aged

  The study sequenced TCRB gene rearrangements from young versus elderly human subjects.

  Study phs000787

• Using RNA-sequencing to characterize the resistance to lirafugratinib

  In addition to Exome-sequencing, we used RNA-sequencing to also characterize resistance to lirafugratinib with whole exome sequencing in patients with FGFR2-driven cancers, treated in the phase 1/2 ReFocus trial (NCT04526106) and enrolled in the UNLOCK program at Gustave Roussy

  Study EGAS50000001370

• Screening of 2.5 million SNPs in 142 samples from the western Mediterranean area

  The analysis of 2.5 million SNPs in 142 samples from the western Mediterranean area, including southern Spain, Andalusia (Huelva: 35 samples, Granada: 35), southern Portugal (36 samples) and Moroccan Berbers (Asni: 15, Bouhria: 12 and Figuig: 9).

  Study EGAS00001003901

• Frequent mutation of the FOXA1 untranslated region in prostate cancer

  We sequenced the coding and untranslated regions of 72 prostate cancer driver genes in 712 plasma cell free DNA samples from 428 men with metastatic prostate cancer, in an effort to understand the role of untranslated region mutations in late stage prostate cancer.

  Study EGAS00001003113

• Aligned reads in the 2kb region centered on the HTT repeat expansion from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 58 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the HTT repeat expansion. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using bwa. Twelve of the samples used TruSeq Nano library preparation and 46 samples used TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003512

• RRBS analysis to characterize the epigenomic conservation between species in the context of Aging and Cancer.

  This dataset contains Raw Reduced Representation DNA bisulfite-sequencing data obtained from human brain samples corresponding to 3 Young and 3 Old individuals (aging context), and 3 normal and 3 Glioblastoma samples (tumor context). RRBS libraries were prepared at Diagenode SA and samples were sequenced using the Illumina Novaseq6000 sequencing platform.The accompanying samples from this study (mouse tissues) are located at the ENA database under the accession number PRJEB41460.

  Dataset EGAD00001006650

• Genomics of Pediatric Renal Medullary Carcinomas

  Version 1We derived faithful cancer cell lines from patients with a diagnosis of renal medullary carcinomas (RMC). These models have been sequenced with whole genome, exome and transcriptome technologies along with the patient's primary germline and tumor samples. We took these faithful models and performed loss-of-function genetic perturbation screens (e.g. RNAi and CRISPR-Cas9) along with an orthogonal small molecule screen. We identified the ubiquitin-proteasome system as an important target in RMC as well as other SMARCB1 deficient cancers.Version 2We have collaborated with the Children's Oncology Group and the study AREN03B2 to study the cohort of patients with a central diagnosis of RMC. Here, we used 10x linked read sequencing along with RNA-sequencing to profile these matched tumor-normal pairs.

  Study phs001800

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To clarify the biological difference between clear cell carcinoma and other histological subtypes in ovarian carcinomas by comparing copy number variants, and to identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing and RNA-sequencing. Then, characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes, prognostic factors and effectiveness of PARP inhibitor. Based on the results of whole-exome sequencing, an investigator-initiated, phase 2 clinical trial will be conducted to evaluate the efficacy and safety of the PARP inhibitor olaparib in HRD-positive cases.

  Study JGAS000789

• T cell receptor repertoire in cell-free DNA as a proxy for tumor infiltrates in patients treated with pembrolizumab

  Bulk TCR sequences from tumor, peripheral blood mononuclear cell (PBMC), and cell-free DNA (cfDNA) samples from 81 patients with solid tumors treated with pembrolizumab.

  Dataset EGAD50000001857

• Multiomic Dissection of Movement and Neurocognitive Toxicity Following BCMA-Targeting CAR T Cell Therapy

  Raw sequencing data (GEX, TCR, adn CSP libraries) for longitudinal cerebrospinal fluid and PBMC samples from a multiple myeloma patient treated with cilta-cel who developed MNT.

  Dataset EGAD50000002339

• BCR repertoir sequences from human buffy coat purified B-Cells with DIS3 and control ASO

  This dataset contains BCR sequences of buffy coat purified B-cells from 5 healthy donors. For each sample, sequences were obtained in two conditions : with control Aso and Dis Aso treatment.

  Dataset EGAD50000001601

• Guardant ctDNA variant analysis

  This table describes each variant detected using Guardant 360 for each sample included in this analysis.

  Dataset EGAD50000001340

• WGS FASTQ files studied in Allogeneic induced pluripotent stem (iPS) cell-derived cartilage transplantation for articular cartilage damage in knee joints: a phase I, first-in-human study

  This data set contains 5 paired fastq files (WGS).

  Dataset EGAD50000001666

• SIA Subtyping Shallow Whole Genome Sequencing (sWGS)

  Associated with Molecular classification of small intestinal adenocarcinomas. Shallow Whole Genome Sequencing (sWGS) generated 214 .fastq files from 127 small intestine adenocarcinomas from 125 patients. DNA libraries for shallow whole genome sequencing were prepared using TruSeq Nano kits (Illumina).

  Dataset EGAD50000001760

• Dataset for scRNA glioblastoma samples

  This dataset contains 5 scRNA samples of human glioblastoma samples, human cortical spheroid derived from hiPSC line 028-4 and 3 samples of mouse xenografts. Sequencing has been performed on Illumina NovaSeq 6000. Sequencing has always been paired.

  Dataset EGAD50000001117

• RNA-seq FASTQ files studied in A first-in-human clinical study of an allogenic iPSC-derived corneal endothelial cell substitute transplantation for bullous keratopathy

  This data set contains 18 paired fastq files (RNA-seq).

  Dataset EGAD50000000948

• Sample Sheet

  Sample sheet for aligning samples with patients.

  Dataset EGAD50000000484

• CRC Patient-derived-organoids Whole Genome Sequencing

  Whole Genome Sequencing raw paired-ends reads for 20 matched colorectal patient-derived-organoids (normal and tumor). Tumor samples were obtained from patients treated at Niguarda Cancer Center, (Milano, Italy) and Candiolo Cancer Institute (Candiolo, Turin, Italy).

  Dataset EGAD50000000617

• H3Africa ACEGID H3Africa Array Genotype

  SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina H3Africa array version 1

  Dataset EGAD00010002510

• Whole exome sequencing for primary lung adenocarcinoma samples

  We performed whole exome sequencing (WES) of 11 formalin-fixed paraffin-embedded lung tumour tissues and paired blood samples.

  Study EGAS00001003680

• Exome sequencing files for "Minimal functional driver gene heterogeneity among untreated metastases"

  Files from whole exome sequencing of 14 tumors from two cancer patients (endometrial and lung cancer) along with a matched normal tissue per patient.

  Dataset EGAD00001004212

• Meso RNA-seq data (SSA cell line study)

  RNA-seq data for mesothelioma cell lines after spliceostatin (SSA) or control (DMSO) treatment.

  Dataset EGAD00001001914

• WES and RNA-seq raw sequence data for HIFI project

  WES sequence data from 15 samples, RNA-seq sequence data from 19 samples, all sequence data are raw pair-end sequence data in fastq format, sequenced by Illumina platform.

  Dataset EGAD00001004799

• Indonesian Genome Diversity Project 2

  This dataset reports whole genome sequences for 82 individuals from different populations from Mentawai, New Guinea, Sumatra and Sumba islands.

  Dataset EGAD00001005059