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• Exome Sequencing of Clear Cell Endometrial Tumors and Paired Non-tumor Samples

  The purpose of this study was to identify somatic (tumor-specific) mutations in clear cell endometrial tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 16 de-identified primary tumor DNAs and matched non-tumor DNAs.

  Study phs000967

• De novo detection of somatic variants

  The Tumor Profiler Study is an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease. This dataset contains scDNA-seq data for 3 ovarian cancer samples from the Tumor Profiler Study used to validate LongSom. LongSom is a computational workflow leveraging high-quality long-read scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), and gene fusions, to reconstruct tumor clonal heterogeneity.

  Dataset EGAD50000001292

• SF3B1 splicing signature

  We describe individuals with de novo pathogenic variants in SF3B1. SF3B1 is a core component of the U2 snRNP complex that ensures accurate branchpoint and 3′ splice-site recognition, and its mutations induce aberrant splicing that contributes to tumorigenesis, notably in myelodysplastic syndromes. We aim to study splicing defects associated with constitutional pathogenic variants.

  Study EGAS50000001473

• Intellectual Disability cases with parents (trios) or affected sibs (sibpairs)

  Samples from ID cases negative for CNV through array-CGH were submitted to exome sequencing. Families with one affected individual underwent trio exome sequencing for identification of de novo variants. Families with more than one affected child underwent sibpair sequencing for identificatio of shared recessive or x-linked variants.

  Study EGAS00001003968

• Multi-omics of Richter syndrome

  Richter syndrome (RS) is the aggressive transformation of Chronic Lymphocytic Leukemia, mostly with Diffuse Large B-Cell Lymphoma histology. While histologically similar, RS and de novo DLBCLs present with different clinical courses. We characterized the RS epigenome by combining genome-wide DNA methylation with transcriptome-sequencing on a large RS cohort.

  Study EGAS00001005495

• Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Dataset EGAD00001003306

• BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

  RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000808

• Exome Sequencing in Moebius Syndrome

  Möbius syndrome (MBS; MIM 157900) is a neurological disorder that is characterized by paralysis of the facial nerves and variable other congenital anomalies. The etiology of this syndrome has been an enigma since the initial description in 1880 by von Graaefe and in 1888 by Möbius, and it has been debated for decades whether MBS has a genetic or a non-genetic etiology. Here, we reveal various de novo mutations affecting two genes, PLXND1 and REV3L. The finding that de novo mutations can cause Möbius syndrome will have considerable impact on further research, as well as in diagnostics. PLXND1 and REV3L represent totally unrelated pathways involved in hindbrain development: neural migration and DNA translesion synthesis, essential for the replication of endogenously damaged DNA. However, analysis of Plxnd1 and Rev3l-mutant mice revealed that both genetic defects converge at the facial branchiomotor nucleus, affecting either motoneuron migration or proliferation.

  Study EGAS00001001250

• Exome sequence data from DNMT3A microcephalic dwarfism patients.

  Exome sequence data from microcephalic dwarfism patients with de novo DNMT3A variants

  Dataset EGAD00001004470

• 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

• 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

• Neuroblastoma_MP-PCR_MultiplexPCR_TargetedSequencing_BAMs

  This dataset contains raw sequencing data (BAM/BAI files) generated from human neuroblastoma patient samples. The data were produced using targeted high-throughput next-generation sequencing and are intended to support genomic analyses of tumor-associated alterations. All files are provided under controlled access in accordance with EGA data protection requirements.

  Dataset EGAD50000002260

• Mutation analysis of 17 genes in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit

  Mutation analysis of 17 genes (ALK, APC, BRAF, BRCA1, BRCA2, DPYD, EGFR, ERBB2, KIT, KRAS, MET, NRAS, PDGFRA, RET, ROS1, TP53, UGT1A1) in plasma DNA of CRC patients using the AVENIO ctDNA Targeted Kit.

  Dataset EGAD00001006103

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 8a)

  Whole genome sequencing data of 26 high-grade serous carcinoma (HGSC) patients (87 samples) sequenced with MGISEQ-2000 and HiSeq X Ten.

  Dataset EGAD00001011304

• Verification of BCR reconstruction from single-cell RNA-seq using BraCeR

  This dataset was made to verify the computational reconstruction of B cell reseptors from single-cell RNA-seq using BraCeR. The dataset contains BCR-derived reads from single-cell RNA-seq from 13 cells using the Smart-seq2 protocol, as well as targeted BCR-sequencing data from the same cells.

  Dataset EGAD00001004199

• Childhood arthritis DNA (2020-01-15)

  The aim of this study is to describe the transcriptome of single arthritic cells. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005785

• Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Whole genome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Dataset EGAD00001003115

• MutWP1: CRUK Grand Challenge Mutographs of Cancer: pancreas_LCM (2020-01-15)

  Samples prepared by LCM - 5 cases for pilot study. Bulk DNA not available. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005789

• RNA sequencing of PTCL-NOS

  This dataset contains raw .fastq files of a paired-end RNA-seq experiment on 15 PTCL-NOS samples. Samples were prepared with Truseq stranded mRNA library kit.

  Dataset EGAD00001006925

• Bulk RNAseq fastq files

  RNAseq FASTq files from 15 samples from patients with ovarian cancer, 5 samples for each of the 3 tumor immune phenotypes (Infiltrated, Excluded and Desert).

  Dataset EGAD00001006975

• Dataset SNP tumours

  This dataset contains 30 idat files each from 15 SNP array runs on patient colitis-associated colorectal cancer tumours. All phenotypes are cancer. See Baker et al. 2018 Supplementary Table 2 for patient details of 12 tumours used in the analyses in the publication.

  Dataset EGAD00010001587

• Multi-omics characterisation of the response to stimulation in Long Covid patients

  We stimulated immune cells of 15 patients (5 timepoints) with Long Covid with RPMI or P. Aeruginosa strains (4h stimulations).

  Study EGAS50000000143

• Whole exome sequencing of melanomas from a Braf mutant mouse model UV radiation study

  Whole exome sequencing of 41 melanomas and normal DNA from Braf mutant mice: 15 tumours from UV exposed mice, 15 tumours from non-exposed mice and 11 from UV exposed, sunscreen-protected mice.

  Dataset EGAD00001000775

• Dataset for transcriptome sequencing of chordoma cells

  This dataset contains transcriptome sequencing for 15 samples from chordoma cells. The sequencing was performed on Illumina HiSeq 4000 and Illumina NovaSeq 6000. The sequencing was always paired.

  Dataset EGAD00001015642

• NiCOL Study RNA-seq dataset

  15 samples sequenced in RNA-seq. This dataset contains their raw FASTQ data and the raw count table and the TPM count table.

  Dataset EGAD00001010912