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• Paired Exome sequencing of Sarcoma tumor and control

  Paired Exome sequencing of Sarcoma tumor and control of 10 samples (5 tumor/control pairs). The sequencing was done on Illumina Hiseq 4000 and Agilent Sureselect V5+UTRs kit.

  Dataset EGAD00001010278

• Single cell RNA sequencing of CD34+ CB and BM samples in SLE and healthy controls

  Single cell RNA paired-end sequencing was performed on CD34+ progenitor cells derived from 4 SLE patients, 6 healthy control samples and 2 umbilical cord blood samples using Illumina MiSeq/NextSeq 500.

  Dataset EGAD00001011277

• Spatial transcriptomics experiment

  This dataset include all spatial transcriptomics experiments. Samples coming from the same patient were sequenced on the same flowcell. Patients PTC4 to PTC9 were also sequenced on the same flowcell, as well as ATC1 and ATC2 on another one, and ATC3A and ATC3B on another one.

  Dataset EGAD00001011365

• Tel Aviv RNA-seq dataset of of BiPSCs and FiPSCs derived cells

  RNA-seq data obtained from directed differentiation of a subset of FiPSCs and BiPSCs cell lines towards islet-like cells. RNA was collected at two key developmental stages: definitive endoderm (DE) and pancreatic progenitors (PP).

  Dataset EGAD00001003780

• Genomic analysis of HPV-positive versus HPV-negative oesophageal adenocarcinoma

  Whole exome sequencing was performed to explore the mutational landscape and potential molecular signature of HPV-positive versus HPV-negative OAC. Four hr-HPV-positive and 8 HPV-negative treatment-naive fresh-frozen OAC tissue specimens and matched normal tissue were analysed to identify somatic genomic mutations

  Dataset EGAD00001001660

• EATL-II whole-exome sequencing profile

  Enteropathy-associated T-cell lymphoma (EATL), a rare and aggressive intestinal malignancy of intraepithelial T lymphocytes, comprises two disease variants (EATL-I and EATL-II) differing in clinical characteristics and pathological features. Here we report findings derived from whole exome sequencing of 15 EATL-II tumor-normal tissue pairs.

  Dataset EGAD00001002220

• RNA-sequencing

  Raw reads from RNA-sequencing of monocyte-derived macrophages from three individuals with heterozygous TET2 loss (Ly9, Ly11, Ly14) and two wild-type controls (Ly8 and an unrelated control). Libraries were prepared using ScriptSeq RNA-Seq Library Preparation Kit and Illumina sequenced with paired-end 75bp reads.

  Dataset EGAD00001004784

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  The cohort of 15 patients included ten patients with available tissue from the primary tumor and ≥1 metastatic site, four patients with pairs of metastases only, and one patient with an anastomotic recurrence five years after initial resection of the primary tumor

  Dataset EGAD00001005226

• Exome sequencing of 3 blood samples from tall man and his parents

  Exome sequencing was carried out in a tall male (height 3.5 SDS) and his parents (3 samples). The data was sequences on a Illumina Hiseq2000 and the library was prepared with Agilent SureSelect V4.

  Dataset EGAD00001007767

• miRNA and mRNA transcriptome data

  This dataset contains 278 miRNA and 20 mRNA transcriptomes generated as part of the study "miR-374a-5p regulates inflammatory genes and monocyte function in inflammatory bowel disease."

  Dataset EGAD00001008683

• Clinical data

  Clinical data from GO30140 group A and group F and IMBrave150 biomarker populations including gender, confirmed RECIST response by independent review forum (IRF), overall survival (OS), progression survival by IRF, treatment group and treatment

  Dataset EGAD00001008130

• Gastric Cancer Genetic Analysis of Metastasis

  To identify candidate drivers involved in oncogenesis and tumor evolution, we conducted an extensive genome sequencing analysis of metastatic progression in diffuse gastric cancer. This involved a comparison between a primary tumor from a Hereditary Diffuse Gastric Cancer Syndrome proband and its subsequent recurrence as an ovarian metastasis.

  Study phs000795

• Development of Precision Neoadjuvant-Adjuvant Therapies

  In clinical trials assessing neoadjuvant androgen deprivation therapy plus next-generation androgen receptor axis inhibitors, a subset of patients fail to demonstrate a complete pathologic response following treatment and radical prostatectomy. We performed exome and transcriptome analyses on laser capture microdissected foci of residual tumor from these patients.

  Study phs001399

• Familial Exome Sequencing in Rare Pediatric Phenotypes

  To discover novel candidate genes associated with rare Mendelian phenotypes, we will conduct individual genomic and phenotypic characterization using genome-wide array, pedigree exome sequencing, candidate genotyping, and pertinent clinical testing to define phenotype. Pedigrees included in this submission will have a variety of clinical pathological phenotypes.

  Study phs000553

• Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas

  The purpose of this study was to identify somatic (tumor-specific) mutations in endometrial carcinosarcoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 14 de-identified primary tumor DNAs and matched non-tumor DNAs.

  Study phs001152

• Single-cell RNA-seq, single-cell TCR-seq, single-cell BCR-seq, and CITE-seq of B and T cells

  To describe human tonsillar CD4+ T cells, especially IL10+ Foxp3- follicular CD4+ T cells (Tfr1, T follicular regulatory type 1), human tonsillar CD4+ T cells were analyzed with single-cell RNA-seq, single-cell TCR-seq, single-cell ATAC-seq, and CITE-seq.

  Study JGAS000827

• Whole-Exome Sequencing in Mexican Patients with Testicular Germ Cell Tumors

  In this study, we performed whole-exome sequencing in 40 clinically well-characterized Mexican patients with testicular germ cell tumors. Paired tumor and peripheral blood samples were analyzed to characterize the genomic landscape, including both single nucleotide variants (SNVs) and copy number variations (CNVs).

  Study EGAS50000001721

• Perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma: Primary phase 2 trial results with ctDNA residual disease analyses

  This data set includes sequence files from whole genome sequencing of tumor (n=28), normal (n=28), and blood (n=113) specimens from a phase 2 clinical trial of neoadjuvant nivolumab and nivolumab/ipilimumab in resectable diffuse pleural mesothelioma (NCT03918252).

  Study EGAS50000001195

• Investigating differential diagnostic and prognostic biomarkers in primary cutaneous follicle center lymphoma and follicular lymphoma using low-coverage whole-genome sequencing

  In this study, we analyzed 28 primary cutaneous follicle center lymphoma samples from 20 patients and compared the copy number profiles to a cohort of diagnostic samples of 64 nodal follicular lymphoma patients using low-coverage whole genome sequencing (lcWGS).

  Study EGAS50000000141

• Whole exome sequencing of preneoplasia lung adenocarcinoma

  Multi-region exome sequencing of 271 pulmonary nodules and matched adjacent lung tissue including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=49), adenocarcinoma in situ (AIS, N=42), minimally invasive adenocarcinoma (MIA, N=37), invasive lung adenocarcinoma (ADC, N=57) and adjacent lung tissues (Normal, N=88).

  Study EGAS50000000270

• WGS data of pediatric T-ALL acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two T-ALL patient (ALLK-126, ALLT-503). ALLT-503 sample has two diagnostic samples one extracted from the BM (ALLT-503D) and from the lymph node (ALLT-503lympD). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both diagnostic/relapse (90x) and remission (30x) samples were sequenced using Illumina NovaseqX Plus.

  Dataset EGAD50000002015

• Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

  This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

  Dataset EGAD50000002183

• Transrenal DNA Analysis

  The current sequencing dataset consists of 91 whole genome sequencing data files (Fastq files) of human cell-free DNA (cfDNA) obtained from plasma and urine samples. Specifically, we extracted 20 ucfDNA and 17 plasma DNA samples from healthy pregnant women, 11 ucfDNA samples from pregnant women with preeclampsia, 19 ucfDNA samples from healthy controls, and 24 ucfDNA samples from patients with proteinuria. These extracted cfDNA samples were then constructed into DNA libraries using the TruSeq Nano DNA Library Prep Kit (Illumina) and subsequently sequenced on the Nextseq2000 platform (Illumina).

  Dataset EGAD50000001127

• RNA-seq from Glioblastoma treated with Indisulam

  The dataset includes RNA-sequencing results from four patient-derived glioblastoma cell lines treated with DMSO (vehicle control) or the splicing modulating-drug indisulam (at 6 and 16 hours), resulting in 12 RNA-seq samples. Paired-end sequencing produced 24 FASTQ.gz files. The RNA libraries were prepared using PolyA selection and ERCC spike-ins and sequenced on a NovaSeq platform. This dataset supports the analysis of drug-induced transcriptomic changes and the prediction of subsequent non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline.

  Dataset EGAD50000000957

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Shotgun Proteomics; Glioblastoma samples from 11 patients were obtained at initial and recurrent tumor stages. Proteins were extracted, identified and quantified via tandem mass spectrometry based on a TMT isobaric labelling approach. Quatitative proteomics reveals 146 differentially abundant proteins using a patient-matched statistical modelling. Analysis of proteolytic processing reveals differential proteolytic patterns in recurrent tumors. Proteogenomics reveals the presense of 30 single-amino acid variants present in glioblastoma tumor and 1 of those as increased in recurrent tumor.

  Dataset EGAD00010002350

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four ETV6::RUNX1 patients (ALLT-388, ALLT-392, ALLT-394, ALLK-114) and from a second relapse sample of one ETV6::RUNX1 patient (ALLK-104). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002589

• MEC/SEF rhabdomyosarcoma mRNA sequencing

  This project was undertaken to sequence and analyze mRNA expression in these tumor subtypes. We intended to discover distinctive patterns of tumor subtype gene expression in these subtypes. In addition, we used this data to discover expression differences between ESWR fusion positive and fusion negative MEC tumors.

  Study EGAS50000000535

• Array-based DNA methylation analysis in blood from patients with Snijders Blok–Campeau syndrome (CHD3)

  DNA methylation array data generated using the Illumina Infinium MethylationEPIC BeadChip (v1.0 and v2.0) from whole-blood DNA of patients with Snijders Blok–Campeau syndrome (ORPHA:599082). Raw IDAT files were generated to identify differentially methylated regions in typical and atypical patients.

  Study EGAS00001008414

• Human_primary_melanoma_project

  Mutational burden and profiles to be studied in approx. 500 human primary melanomas with matched normal samples, part of the Leeds melanoma cohort. New custom design targeted capture panel covering melanoma-specific copy number alterations, promoter mutations, gene fusions, coding genes, HLA regions and IFNg/JAK/STAT pathway genes.

  Study EGAS00001002409

• Radiotherapy_induced_Sarcoma_exome

  Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000194

• Spatiotemporal genomic architecture informs precision oncology in glioblsatoma

  We characterized genomic and expression profiles across 127 multi-sector or longitudinal specimens from 52 glioma patients. We showed that, while samples from nearby geographical location shared similar genomic alterations (clonal or subclonal) and expression signatures, multifocal tumors were seeded from individual clones.

  Study EGAS00001001880

• Radiotherapy_induced_sarcoma

  Whole genome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000138

• Genomic analysis of Japanese gastric cancer (345 gastric cancers of NCC)

  As a contribution to the International Cancer Genome Consortium, whole exome sequencing of 345 Japanese gastric cancer (345 gastric cancers of NCC) with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer.

  Study EGAS00001002884

• High_powered_complex_trait_association_mapping_through_whole_genome_sequencing_of_a_selected_subpopulation_of_the_INGI_Val_Borbera_genetic_isolate

  The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.

  Study EGAS00001000398

• Molecular profiling of acinar cell carcinoma of the salivary glands

  Samples of acinar cell carcinoma (AciCC) of the salivary glands and paired normal salivary gland tissue were analyzed by whole transcriptome RNA-seq (n=10), whole genome sequencing (n=6), whole genome bisulfite sequencing (n=3) and ChIP-seq (H3K27ac, H3K4me3, H3K27me3, NR4A3, CTCF).

  Study EGAS00001002795

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient tumors and observed that mutation rates were drastically increased relative to MMR-proficient endometrial tumors.

  Study EGAS00001000182

• Paediatric_CNS_tumour_autopsy_DNA_WES

  Paediatric gliomas likely have their origins in embryogenesis. This WES extension to the WGS study seeks to estimate the occurrence of driver mutations within the normal tissues of patients which have developed lethal brain tumours and compare the incidence between those that have a germline predisposition and those that don't.

  Study EGAS00001005642

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• RSV infection of primary bronchial epithelial cells in asthma

  Primary bronchial epithelial cells derived from healthy donors and asthma patients were differentiated in Air-Liquid-Interface condition and infected with the respiratory syncytial virus. Single-cell RNA sequencing analysis of these cultures was used to study the transcriptomic response of the cells to RSV.

  Study EGAS00001007450

• Ither NB in Organoids WGS dataset - Exploring high-throughput drug sensitivity testing in neuroblastoma cell lines and patient-derived tumor organoids in the era of precision medicine

  Ither NB in Organoids WGS dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.

  Dataset EGAD00001010282

• Chondrosarcoma Validation Study

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Dataset EGAD00001000392

• Identification of low frequency variants associated with ulcerative colitis using whole-genome sequencing

  2000 ulcerative colitis cases drawn from the UKIBD Genetics Consortium cohort and whole-genome sequenced at 2X depth. A case control association study using control samples whole-genome sequenced by UK10K will be undertaken to identify common, low-frequency and rare variants associated with ulcerative colitis. Data will be combined with similar data across 3000 Crohn's disease cases from the same cohort to identify inflammatory bowel disease (IBD) loci and better understand the genetic differences and similarities of the two common forms of IBD.

  Dataset EGAD00001000409

• Dataset Plasma-seq

  We performed low coverage whole genome sequencing of plasma DNA from prostate cancer patients to establish copy number profiles on both a genome-wide and a gene-specific level. The data include plasma samples from prostate cacner patients (n=13), non-malignant controls (males, n=10 and females, n=9), plasma samples from pregnancies with aneuploid and euploid fetuses (n=4). Furthermore, we sequenced different tumor samples (n=6) of one patients and a serial dilution of HT29 in a background of normal DNA (n=9).

  Dataset EGAD00001000364

• DCM-cases

  DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003390

• DCM-controls

  DCM-controls (113 human non-DCM samples) human heart biopsies from 113 non-diseased controls were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003391

• 33 Paired (Normal-Tumor1-Tumor2) MM whole-exome data

  Samples were sequenced from 33 multiple myeloma patients including tumor presentation and relapse samples and a matched patient control sample. Tumor DNA was isolated from CD138-positive plasma cells. Control DNA originated from peripheral blood leukapheresis products collected after induction therapy. Libraries were prepared using the SureSelectQXT sample prep kit and the SureSelect Clinical Research Exome kit (Agilent), with additional baits covering the Ig and MYC loci. Paired-end sequencing was performed to an average sequencing depth of 118× on a HiSeq2500 (Illumina).

  Dataset EGAD00001002165

• Genomic and Transcriptomic Profile of Paired Primary-Metastasis Colorectal Tumors

  Samples encompass primary colorectal tumors, adjacent normal colonic mucosa and metastasis of 12 patients, collected by Medical Pathologists from surgically removed specimens. Normal mucosa samples were taken more than 2 cm away from the tumor. Tissues were embedded in optimal cutting temperature (OCT) medium, snapshot frozen in liquid nitrogen within 40 minutes of collection and preserved at -80ºC. Samples were collected between June 2010 and October 2017 as part of a prospective biobanking project.

  Dataset EGAD00001007686

• Transcriptome analysis of iPSC-derived hepatocytes from Wilson's Disease patients and healthy controls

  To identify the differences in global gene expression patterns in WD-specific hepatocytes, we performed RNA-seq analysis. Six WD-specific hepatocytes and 6 healthy-donor (HD) hepatocytes were compared in total. The data suggested that our RNA-seq data were partially validated in the context of ATP7B deficiency and that these overlapped genes might be regulated by ATP7B deficiency among mammalian species in common.

  Study JGAS000382

• Clonal Evolution and Blastic Plasmacytoid Dendritic Cell Neoplasm - Two Cases

  Here we present two case studies of sequential whole exome sequencing (WES) in patients, who both developed BPDCN throughout their medical history but primarily presented with lymphoid cancers (clonally related ALK-negative anaplastic large-cell lymphoma (ALCL) and T-lymphoblastic lymphoma (T-LBL)) and whose bone marrow at remission exhibited a CMML phenotype, from which in both cases BPDCN clones arose that subsequently became treatment refractory.

  Study EGAS50000000214

• Single-cell multi-omics reveals clonal evolution and T-cell dynamics underlying differential responses to ibrutinib in Waldenström macroglobulinemia.

  To elucidate the molecular basis underlying differential response and resistance to ibrutinib in Waldenström’s macroglobulinemia (WM), we conducted a prospective phase II trial (NCT02604511) of ibrutinib monotherapy in treatment-naïve patients. Seventy-four sequential bone marrow (BM) aspirates from 17 patients, collected from baseline through 48 treatment cycles, were profiled using single-cell RNA and V(D)J sequencing.

  Study EGAS50000001596