15041 results for "cancer studies using rna-seq"

in 19.47 milliseconds.

• Korean WGS

  We sequenced the genomes of 141 Korean never-smoker lung adenocarcinoma patients, excluding EGFR and ALK alterations. We utilized the TruSeq DNA Library Prep Kit and performed by the Illumina NovaSeq 6000 instrument, yielding sequencing paired reads of approximately 150 bp in size. Afterward, we processed the FASTQ files using the GATK Best Practice pipeline.

  Dataset EGAD50000000346

• Exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs

  This dataset contains exome sequencing data, phenotypic information, and somatic mutation analysis results for 44 diagnosis-relapse DLBCL pairs. Exon sequencing data were captured using the Agilent HaloPlex exon kit. bam files were obtained from illumina sequencing followed by BWA alignment.

  Dataset EGAD50000000049

• Moroccan Genome Project: Sequencing Data from 109 Whole Genomes of Moroccan Individuals

  This study is the first phase of the Moroccan Genome Project, which included the complete sequencing of 109 genomes from the Kingdom of Morocco. The sequencing was performing using the Illumina NovaSeq6000 platform, with a mean coverage of 30X.

  Dataset EGAD50000000750

• Cas9-targeted-based long-read sequencing for genetic screening of RPE65 locus

  The dataset includes sequencing data from five inherited retinal dystrophies (IRD) patients using three diferent platforms: Clinical Exome (CES), Long-read sequencing of RPE65 locus, and 3) whole genome sequencing.

  Dataset EGAD50000000847

• APS-1 TCR Sequencing

  Single cell TCR sequencing of expanded regulatory T cells (Tregs) in 9 APS-1 patients and 9 ange and gender matched controls. T-cell receptor (TCR) libraries were generated using the Single Cell Human TCR Amplification Kit and the Library Construction Kit from 10x genomics.

  Dataset EGAD50000000261

• HIV-phyloTSI: PANGEA (veSEQ-HIV)

  This dataset includes sample numbers TSI_0001 to TSI_0202 and TSI_0316 to TSI_0425 for the PANGEA (veSEQ-HIV) cohort of the study. Samples were sequenced using the Illumina NovaSeq system and the veSEQ-HIV method (see Bonsall, Golubchik et al 2020, DOI: 10.1128/JCM.00382-20). Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001309

• HIV-phyloTSI: PANGEA (PCR amplicon)

  This dataset includes sample numbers TSI_0426 to TSI_0527 for the PANGEA (PCR amplicon) cohort of the study. Samples were generated by pooling four overlapping PCR amplicons (see Gall et al 2012, DOI: 10.1128/JCM.01516-12). The sequencing was conducted using the Illumina NovaSeq system. Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001308

• Dataset for single cell transcriptome sequencing

  This datasets contains single cell transcriptome sequencing of 10 control samples. Sequencing has been performed on Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single Cell 5 Reagent Kits. Sequencing was always paired. This dataset additionally contains a .QS file from Seurat Analysis performed in R, generated as described in the related publication.

  Dataset EGAD50000001549

• Paired FastQ files from deep targeted DNA sequencing

  This dataset comprises paired-end and time-matched FastQ files from 356 cell-free DNA samples and 356 white blood cell DNA samples, derived from 299 patients with metastatic renal cell carcinoma or urothelial carcinoma. A baseline sample was available for all patients. Sequencing was performed using Illumina technology.

  Dataset EGAD50000001267

• Variant calling dataset from the whole-exome study of sepsis and acute distress respiratory syndrome in Spain

  Whole-exome sequence reads were obtained from a set of 934 unrelated individuals from the study of sepsis and acute distress respiratory syndrome in Spain (GEN-SEP study), using Illumina paired-end reads.

  Dataset EGAD50000001613

• PacBio Revio WGS on 10 carriers of ring and marker chromosomes

  Bam files containing PacBio HiFi reads from carriers of ring and marker chromosomes. The reads where genereated using the PacBio Revio platform. Each individual was sequenced to roughly 30X coverage on one flow cell per individual. The chromosome of interest is indicated in the file name.

  Dataset EGAD50000002111

• WGS of thymic epithelial tumors and paired normal

  Among the 20 newly sequenced cases, we conducted additional whole-genome sequencing (WGS) on five out of eight CN-type thymomas, excluding three with low tumor cell fractions (< 0.1). Libraries for WGS were prepared using the TrueSeq DNA PCR-free Prep Kit following standard Illumina protocols.

  Dataset EGAD50000001160

• 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

• Exome-sequencing of H3-K27M glioma.

  Fastq or bam files are deposited for 28 patient H3-K27M diffuse midline gliomas. UMPEDD65 was profiled by targeted exome-sequencing using the TSO500 Illumina assay, while all other samples were sequenced by whole-exome sequencing.

  Dataset EGAD00001009269

• Low-coverage whole-genome sequencing (lcWGS) data of Genome in a Bottle (GIAB) reference samples

  This dataset contains low-coverage whole-genome sequencing (lcWGS) data generated from three GIAB reference samples (HG001–HG003) for method benchmarking and concordance analysis in FFPE-GWAS workflows. The data were generated using Illumina NovaSeq with paired-end 150bp reads and downsampled to 2x coverage.

  Dataset EGAD00001015533

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• Whole genome sequencing of GM09237 cells with and without folate depletion

  Two DNA samples extracted from GM09237 cell line cultured with either normal medium or medium with no folic acid for 5 days were sequenced using the BGISEQ500 platform (BGI whole genome 100 bp paired-end sequencing 60x) as well as PacBio Sequel long read sequencing.

  Dataset EGAD00001007732

• Whole exome sequencing of patient derived cell lines

  Whole exome sequencing of 3 patients derived cell lines and patient blood (N = 6 samples), performed using Agillent SureSelect All Exon V5 and Illumina HiSeq 4000. Data is in raw fastq format (N = 10 fastq pairs, 20 files total), as some samples were split between two lanes.

  Dataset EGAD00001007738

• Exome sequencing of control DNA samples from patients with BPLL

  DNA extracted from sorted CD3+ cells (16 patients) was used for exome capture with the SureSelect V5 Mb All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments.The files are in FASTQ format.

  Dataset EGAD00001004411

• Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients

  Metagenomics data for "Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients". Samples were sequenced on NovaSeq6000(NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 151nt (Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using ‘NovaSeqXp’ workflow in ‘S4’ mode flow cell.

  Dataset EGAD00001008142

• Pleomorphic invasive lobular carcinoma targeted exome sequencing

  Fifteen pleomorphic invasive lobular carcionoma samples and their matched normal controls were subjected to targeted exome sequencing using the Beijing Genomics Institute TumorCare gene panel. Genomic DNA samples were randomly fragmented and captured libraries of each exome were sequenced on an Illumina Hiseq2000 system. CRAM files are provided for each tumor and normal pair.

  Dataset EGAD00001003995

• Germline variants in childhood melanoma

  Whole-exome sequencing was performed on DNA extracted from blood samples of 50 children diagnosed with cutaneous melanoma prior to 18 years of age. Patients were all diagnosed in Queensland, Australia, and self-reported as of European descent. Sequencing was done the Illumina platform using SureSelct V7 Post capture kits.

  Dataset EGAD00001010039

• sWGS of matched patient and PDX ovarian tumour tissues

  This dataset contains 8 .bam files of shallow WGS (~0.1×) from fresh frozen tumour tissues of four matched patients and first generation PDX models. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008650

• Exome sequencing of tumor DNA samples from patients with BPLL

  DNA extracted from sorted CD19+ tumor cells (16 patients) was used for exome capture with the SureSelect V5 All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments. The files are in FASTQ format.

  Dataset EGAD00001004410

• WGS profiling of pediatric osteosarcoma

  Primary pediatric osteosarcoma samples were collected and profiled using WGS. When possible, germline and tumor samples were collected. For some patients, multiple tumor tissues were collected and sequenced. Some of the samples were used to derive PDTX models, which were also profiled with WGS. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

  Dataset EGAD00001004537

• Achilles tendinopathy exome data

  Exemplar asymptomatic controls (n=10, 6 males) and exemplar cases with chronic Achilles tendinopathy (n=10, 6 males), representing divergent extremes of the phenotype spectrum were selected for WES. Individual samples were sequenced at paired ends on the Illumina HiSeq 2000/2500 platform at 30X coverage using the Agilent V5+UTR (71Mbp) capture kit.

  Dataset EGAD00001004362

• CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

  Single cell sequencing analysis for Dengue patients using Smart-seq2 and 10X platforms

  Dataset EGAD00001007656

• Ashkenazi Jewish Leukoencephalopathy Syndrome

  Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T&gt;G (p.C846G), as the genetic cause of a leukoencephalopathy syndrome in two individuals from two unrelated Ashkenazi Jewish (AJ) families. Both patients exhibited highly concordant disease progression characterized by infantile onset leukoencephalopathy with brain white matter abnormalities, severe motor impairment, cortical blindness, intellectual disability, and seizures.

  Dataset EGAD00001002005

• Whole genome sequencing of patient IPSCs and tumors (organoids)

  This dataset contains whole genome sequencing data of a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) . This dataset further contains whole genome sequencing data of two tumors showing CNLOH. Tumors were isolated from organoids grown using the patient IPS cell line (Patient 1 TSC2+/- iPSCs )

  Dataset EGAD00001006333

• A Comprehensive Genetic Study of Classical Hodgkin Lymphoma Using Circulating Tumour DNA

  This study on classical Hodgkin lymphoma (cHL) used advanced methods to analyse circulating tumour DNA (ctDNA) in 297 cases, offering insights into its genetic landscape and linking it to disease pathophysiology and clinical progression. Key findings include the identification of whole genome duplication as a predictor of poor chemotherapy response. Additionally, a highly recurrent somatic expression quantitative trait locus of the BCL6 gene was discovered, implicating regulatory mutations in cHL pathophysiology and highlighting BCL6 as both a vulnerability and therapeutic target. Consensus clustering identified two cHL subtypes distinguished by the underlying mechanisms of genetic instability, rather than by specific genetic mutations or EBV infection. The study also linked the number and clonality of neoantigens with tumour microenvironment and response to checkpoint blockade. Finally, our results suggested ctDNA analysis as a tool to distinguish ambiguous PET/CT-positive lesions persisting after treatment, aiming to reduce unnecessary medical interventions.

  Study EGAS50000000873

• Molecular diagnosis of albinism (2018-03-14)

  Albinism is genetically heterogeneous rare genetic condition affecting 1:17000 in the Western world (but more frequent in Africa) whose main feature is a profound visual impairment, characterised by foveal hypoplasia, abnormal chiasmatic connections, nystagmus and photofobia. All these features result in severly altered visual acuity (&lt;0,1), absent depth perception and poor night vision. People with albinism are primarily visually handicapped. In addition, for some types of albinism, the visual phenotype can be presented with partial or total hypopigmentation, hence resulting in a secondary phenotype which can lead to skin cancer if skin is not adequately protected. Recently a new syndrome has been described, FHONDA, with the same visual abnormalities of albinism but without pigment alteration. The traditional classification differentiates Oculoculatenous albinism (OCA), where hypopigmentation involves hair, skin and eyes versus Ocular Albinism (OA), where hypopigmentation only affects the eyes. These are non-sydrimic types of albinism. Some syndromic forms (Hermansky-Pudlak=HPS, Chediak-Higashi=CHS) affect cells beyond pigment cells, present in the lungs, immune system, platelets and intestines, resulting in more severe phenotypes that can be fatal. Mutations in at least 19 genes are assocaited with the corresponding types of albinism. Most hospitals will only diagnose the most frequent cases using traditional Sanger, MLPA approaches. Some will use CGH arrays. We aim to diagnose all cases of albinism through the Albinochip proposal, which combines a Sequenom first step of known mutations combined with subsequent NGS approaches. In some cases we fail to find a second mutation, these are good candidates for further full exome analyses. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-03-14.

  Dataset EGAD00001004039

• Lobular Carcinomas In Situ Display Intra-Lesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Disease

  This study comprises prospectively accrued, microdissected fresh frozen samples of multifocal lobular carcinoma in situ (LCIS), ductal carcinoma in situ (DCIS), invasive lobular carcinoma and invasive ductal carcinoma from patients undergoing prophylactic or therapeutic mastectomies after a diagnosis on LCIS diagnosed and managed at Memorial Sloan Kettering Cancer Center (MSKCC). Microdissected samples were subjected to paired-end whole exome sequencing on an Illumina HiSeq 2000. The data generated were used to define the landscape of somatic genetic alterations of LCIS, DCIS, invasive lobular carcinoma and invasive ductal carcinoma, to define clonal relatedness of these lesions and to investigate the clonal shifts in the progression from in situ to invasive breast cancer.

  Study phs001006