14983 results for "cancer studies using rna-seq"

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• Palbociclib resistance analyses on breast cancer bone metastasis PDX

  Identify mecanisms of metastatic breast cancer resistance to palbociclib by RNAseq analyses.

  Study EGAS00001006428

• NGS on cardiac samples in Hungarian patients of dilated cardiomyopathy

  Heterozygous (HET) truncating mutations in the TTN gene (TTNtv) encoding the giant titin protein are the most common genetic cause of dilated cardiomyopathy (DCM). We investigated 127 clinically identified DCM human cardiac samples with targeted sequencing using the TruSight Cardio panel on an Illumina MiSeq system with a special focus on TTNtvs.

  Study EGAS50000000049

• LCCC 1108: Development of a Tumor Molecular Analyses Program and Its Use to Support Treatment Decisions (UNCseqTM)

  The primary objective of this specimen correlative study was two-fold: to provide a mechanism for the association of known molecular alterations with clinical outcomes, and to provide rapid genetic profiling of alterations with known clinical utility using tumor and germline specimens to support treatment decisions.

  Study phs001713

• The Genomic Map of Poland in Open Access

  The main goal is to prepare and share WGS/WES of Polish population In this project NGS (next generation sequencing) was performed using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner was used. Shared BAM and BAM.BAI files Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Study EGAS50000000096

• Dataset of DNA methylation profiles of 189 pediatric central nervous system, soft tissue, and bone tumors

  The research of CNS tumors brought knowledge about the role of epigenetics in these tumors. Certain subgroups of tumors are defined solely by their epigenetic profiles. In this study we carried on epigenetic profiling using targeted methylation sequencing of aproximately 180 pediatric CNS and Sarcoma tumor samples.

  Study EGAS50000000051

• Visium CytAssist Spatial Gene Expression analysis for glioblastoma

  The glioblastoma spatial transcriptomics dataset was generated from 4 FFPE fixed adult glioblastoma samples, using the 10x Genomics Visium platform, producing raw FASTQ files, spatial feature matrices (.h5, .mtx, .tsv), and paired histology images (.tif). Spot-level transcript counts were aligned to tissue architecture and processed in Seurat, with results stored as .rds objects. Data visualization was performed using SpatialFeaturePlot, and quantitative analyses were supported by custom Matlab scripts. The dataset provides both raw and processed files, offering reproducible spatially resolved transcriptomic profiles of glioblastoma tissue sections

  Dataset EGAD50000001767

• Whole genome sequence: cardiomyopathy, 1 HCM patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000704

• Whole genome sequence: cardiomyopathy, 1 ARVC patient

  In this study, we analyzed the genomic information by whole genome sequencing using peripheral blood samples from patients with various cardiovascular diseases including severe heart failure to identify genetic variants related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions for cardiovascular disease.

  Study JGAS000705

• BAM file s of WGS data of Progressive supranuclear palsy patients

  BAM files of healthy controls (3) and Progressive supranuclear palsy (PSP) patients (4). Genomic DNA from donors was fragmented, end-polished, A-tailed, and ligated with Illumina adapters, followed by size selection. Libraries were PCR-amplified (unless PCR-free), purified with AMPure XP, assessed on the Agilent Fragment Analyzer, and quantified using Qubit and qPCR. Qualified libraries were pooled and sequenced on Illumina platforms, and low-quality reads or adapter-contaminated reads were removed. Clean data were then mapped to the hg38 reference genome using BWA.

  Dataset EGAD50000001758

• Investigation of 3D chromatin structure in clear cell renal cell carcinoma

  In order to investigation the 3D chromatin structure in clear cell renal cell carcinoma (ccRCC), we performed ultra high-resolution chromatin capture using MNase (Micro-C) in 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and the chromatin interactions in hic format. Data were processed using the Juicer pipeline.

  Dataset EGAD50000001884

• WES

  Genomic DNA was extracted from PBMCs and whole blood using the Chemagic Prime DNA Blood 4k kit. DNA quality and integrity were assessed by Qubit and Tapestation, and only samples with sufficient quantity, DIN > 6, and confirmed sex were used. Whole-exome libraries were prepared with the SureSelect XT Human All Exon V8 kit (Agilent), covering all human protein-coding regions. DNA was fragmented, adapter-ligated, captured, and amplified following the manufacturer’s protocol. Libraries were quantified, pooled (95 samples), and sequenced on an Illumina NovaSeq 6000 using S4 flow cells, generating up to 12 billion paired-end reads per run.

  Dataset EGAD50000002037

• Building a Database of Genomic Structural Variants in Japanese population

  Epstein-Barr virus immortalized B-lymphoblast cell lines were obtained through the Japanese Collection of Research Bioresources (Japanese B cell DNA bank), National Institutes of Biomedical Innovation, Health and Nutrition, and cultured at UNITECH Co., Ltd. We extracted genomic DNAs, sequenced them using Nanopore PromethION, and analyzed genomic structural variations.

  Study JGAS000580

• Pediatric Papillary Thyroid Carcinoma Whole Exome Sequencing

  Exome libraries from 47 blood and tissue samples were prepared using Agilent SureSelect Human Exome Library Preparation V5 kit and the Agilent Bravo Automation System fExome libraries were pooled and sequenced with the TruSeq SBS sequencing chemistry using a V4 high throughput flowcell on a HiSeq 2500 platform following Illumina’s recommended protocol. Approximately 6-8 gigabases of raw paired end data of 126-bases were generated per exome library.

  Dataset EGAD00001007502

• Comprehensive copy number aberration analysis using digital Multiplex Ligation-dependent Probe Amplification (digitalMLPA) in pediatric B-cell precursor acute lymphoblastic leukemia

  In this study a next-generation sequencing based method was applied to comprehensively screen for recurrent, disease-relevant copy number aberrations in a cohort of Hungarian patients. Diagnostic bone marrow samples from 260 children with B-cell acute lymphoblastic leukemia as well as 72 control samples and were investigated by digital multiplex ligation-dependent probe amplification using the disease-specific D007 probemix. Whole chromosome gains and losses, as well as subchromosomal copy number aberrations were simultaneously profiled.

  Dataset EGAD00001010878

• 463 newly diagnosed patients paired samples (Tumor/Normal)

  463 newly diagnosed patients from the UK Myeloma XI clinical trial (NCT01554852) underwent whole exome sequencing plus targeted capture of the IGH/K/L and MYC loci. 200 ng of DNA were processed using NEBNext DNA library prepartion kit and hybridised to the SureSelect Human All Exon V5 Plus. Four samples were pooled and run on one lane of a HiSeq 2000 using 76-bp paired end reads. DNA from CD138+ selected bone marrow cells (myeloma tumour) as well as peripheral white blood cells were analysed and somatic mutations detected.

  Dataset EGAD00001001358

• Understanding_population_genetics_and_patterns_of_genome_wide_heterozygosity_in_a_sample_of_the_Croatian_isolated_populations__ESGIDalmatians_

  Using high-throughput sequencing technologies and analytical tools, we conduct an exome sequencing study that will help understand the populationgenetics of a Croatian island isolate, in a sample of 200 subjects from the Adriatic island of Vis who wereselected to reflect islanders with at least four known ancestors in grandparental line who are original islanders.

  Study EGAS00001000336

• Mutation_burden_in_sun_exposed_eyelid__MSSE_

  Eyelid skin from blepharoplasty surgery will be collected from patients of different ethnic origin (Chinese, Malay, Indian and Caucasion) exposed to tropical sunshine. 2mm2 biopsies will be collected and DNA sequenced using a specific bait capture set and at high depth. The aim is to try and see if different mutations expand in different ethnic populations.

  Study EGAS00001002512

• Validation_of_AML_Mutational_Screening

  We recently worked-up a pulldown protocol for studying 21 genes recurrently mutated in AML (Study1770). Our manuscript is currently under revision and to address the reviewers' comments we need to validate some mutations by re-sequencing. In this add-on study we will be using PCR followed by MiSeq for this purpose.

  Study EGAS00001000430

• Whole-exome sequencing of acute erythroid leukemia

  To clarify the genomic characteristics of acute erythroid leukemia (AEL), 24 AEL cases with matched controls were analyzed using whole exome sequencing. Based on the patterns of genetic alterations, AEL were divided into 4 subgroups. EPOR/JAK/STAT pathway are frequently affected in AEL and could be a therapeutic target.

  Study EGAS00001003696

• Growth Hormone (GH) -secreting Pituitary Adenoma

  We profiled the somatic landscape of 21 growth hormone (GH) -secreting pituitary adenomas using somatic copy-number alteration (SCNA), whole-genome sequencing (WGS), bisulfate sequencing, and transcriptome approaches. See details in Valimaki et al. Genetic and epigenetic characterization of growth hormone (GH) - secreting pituitary tumors. Manuscript in preparation, 2019.

  Study EGAS00001003488

• Single-cell TCR sequencing of gluten-specific T cells from 20 celiac disease patients uploaded on 2021

  To examine the T-cell receptors of the gluten-specific T cells in celiac disease, we isolated single CD4+ T cells from blood , gut biopsies or T-cell lines generated from gut biopsies using HLA-DQ2.5 tetramers and determined the sequences of rearranged TCRalpha and TCRbeta gene pairs.

  Study EGAS00001005047

• The genetic scenario of Mercheros: an under-represented population within the Iberian Peninsula

  In this work we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. We examine the demographic history and the genetic scenario of Mercheros by using genome-wide array data and whole mitochondrial sequences.

  Study EGAS00001005360

• The genomic landscape of serrated lesion of the colorectum

  Serrated lesions of the colorectum are the precursors of 15-30% of colorectal cancers (CRCs). These lesions have a peculiar morphological appearance, and they are more difficult to detect than conventional adenomatous polyps. In this study we sought to define the genomic landscape of these lesions using high depth targeted sequencing.

  Study EGAS00001005648

• Whole-genome sequencing of Tibetans from China

  Whole-genome sequencing of 27 Tibetan individuals from China using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001003500

• Characterization of Leukemic Stem Cells in DNMT3Amut and NPM1mut AMLs

  Trascriptomic profile of FACS-sorted LSCs from diagnostic DNMT3Amut and NPM1mut AML patients using a novel sorting strategy. Briefly, positive selection for GPR56 and a negative selection for NKG2DLigands were used to enrich for LSCs in both CD34+ and CD34- subpopulations. Primary samples were retrospectively collected based on their mutational profile.

  Study EGAS00001006527

• Whole-genome sequencing of Himalayan populations

  Whole-genome sequencing of 60 individuals from 15 Himalayan populations using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Study EGAS00001007269

• FFPE WGS for optimizing mutation signature extraction from archival HGSC samples

  HGSC cases were selected for which matched fresh frozen and FFPE samples were available from the same tissue specimens. Fresh frozen, FFPE and normal blood were subject to WGS for the purpose of assessing the possibility of using FFPE WGS in place of fresh frozen for somatic mutation calling

  Study EGAS00001007521

• EGAD00010000387

  Cambridge control samples using a 1.2M genotyping chip from Illumina

  Dataset EGAD00010000387

• Genomic Study of Gastric Cancer

  We perform whole exome sequencing of 50 pairs of gastric cancer and matched normal samples

  Study EGAS00001005032

• UK Biobank whole cohort directly genotyped and imputed data (~500,000 participants)

  Genotype data is available for all 500,000 participants in the UK Biobank cohort. Genotyping has been performed using the Affymetrix UK BiLEVE Axiom array on an initial 50,000 participants and the remaining 450,000 participants have been genotyped using the Affymetrix UK Biobank Axiom® array. The two arrays are extremely similar (with over 95% common content).Quality control and imputation (to over 90 million SNPs, indels and large structural variants) has been performed by a collaborative group headed by the Wellcome Trust Centre for Human Genetics.The following data are available:* A clean set of QC’ed genotype calls* Confidence values that a genotype call is correct* Intensity data to generate cluster plots* Extensive QC information regarding SNPs and samples including SNP metrics, batch effects, population structure and relatedness* Imputed dataFor further information, please refer to the UK Biobank website

  Study EGAS00001002399