16474 results for "sec+and+unspecified+malignant+neoplasm"

in 31.46 milliseconds.

• 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

• Rheumatoid Arthritis Finger Stick RNA Sequence Data

  This is a longitudinal study of 355 blood samples collected weekly from 5 patients with Rheumatoid Arthritis with varying disease activity over the course of one to five years. Blood samples were self collected from finger sticks and mailed from home. RNA was extracted, purified and sequenced.

  Study phs003179

• 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

• Understanding the Biology of Language Impairment through Whole Genome Sequencing

  This study involves the whole genome sequencing of a cohort of 390 individuals assessed for language ability, IQ, and behavior as schoolchildren. The primary goal of the study is to identify genes, regulatory elements, and pathways which may underlie variation in language ability within an average population. 

  Study phs002255

• 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

• Genetics of Fuchs Corneal Dystrophy

  This grant proposal continues to expand our understanding of the clinical presentation of Fuchs corneal dystrophy, and its underlying genetic basis, which will lead to the development of better therapeutic models and treatment for a common corneal dystrophy that affects 4% of the US population over age 40.

  Study phs001834

• Genome-Wide Association Study on Calcific Aortic Valve Stenosis in Quebec (QUEBEC-CAVS)

  Calcific aortic valve stenosis (CAVS) is a common and life-threatening heart disease with no drug that can stop or delay its progression. A genome-wide association study (GWAS) on 1,009 cases and 1,017 ethnically-matched controls was performed to identify susceptibility genes for CAVS.

  Study phs001492

• 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

• Multi-omics analysis of CUD in the VS

  The aim was to molecularly characterize the human ventral striatum in CUD. For this, we generated epigenomic, transcriptomic, and proteomic datasets at the bulk-level, performed integrative multi-omics analyses and further analyzed CUD-associated transcriptomic changes at a cell type-specific level using snRNA-seq.

  Study EGAS50000000623

• Non-invasive prediction of immunotherapy response (NIPIT) project

  This project aims to find transcriptomic biomarkers for immunotherapy response prediction in several cancer types. So far, we have performed poly-A RNA-seq using whloe blood and peripheral blood mononuclear cells from 33 non-small cell lung cancer patients, collected before and after the start of immunotherapy.

  Study EGAS50000000266

• 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

• RNA-Seq Brest Patient-derived Tumor Organoids

  This dataset includes 14 RNASeq samples from 8 patients. For some patients, organoids at different passages have been profiled. They can be identified by their alias, composed of the following structure: <subjectId>_O<organoid_number>_<passage>_RNA. For example, ICSBCS002_O1_1_RNA indicates the earlier passage of organoid 1 for subject ICSBCS002, and ICSBCS002_O1_2_RNA indicates the later passage. Additionally, WCM2137_O1_RNA and WCM2137_O2_RNA indicate two organoids (O1 and O2) derived from different tissues. More information about the passages and tissues can be found in the sample information table.

  Dataset EGAD50000000960

• Cohort A spatial transcriptomics sequencing

  Cohort A includes glioma tumors of varied grading and pathology from male and female individuals. Fresh frozen glioma tissues for each sample in cohort A were analyzed with the 10X Genomics Visium Spatial Gene Expression protocol. Processed data is available on the NCBI Gene Expression Omnibus database with accession GSE242352.

  Study EGAS50000000954

• Genetic differences between primary colorectal cancer and its paired synchronous and metachronous metastases

  This study contains data obtained from 210 CRC samples (87 pairs and 36 singletons for whom only one of the sample pair was available). Our sample set consisted of 105 primary tumor and 105 metastatic samples. Data are analysis-ready BAM files. Sequencing libraries were prepared with the SureSelect Human All Exon V8 kit by Agilent. Sequencing was done on NovaSeq X Plus instrument (Illumina, San Diego, CA, USA) using 150-bp paired-end reads.

  Dataset EGAD50000001460

• CD79B expression in DLBCL

  This study proposes a novel association between CD79B expression and cell-of-origin subtypes of DLBCL. Integrative single-cell analyses also revealed a distinct association between germinal center B-cell physiology and the pattern of CD79B expression, which is potentially a key explanation for the variable CD79B expression in DLBCL.

  Study EGAS50000000363

• (RNA-seq) Shifted assembly and function of mSWI/SNF family subcomplexes underlie targetable dependencies in endometriod carcinomas

  Raw and processed RNA-seq data from a patient-derived xenograft (yielding 18 samples) and the VOA1066 undifferentiated endometrial carcinoma cell-line (yielding 15 samples). PDX samples were treater with either compound-14, dBRD9, or were untreated. VOA1066 samples were treated with either compound-12, dBRD9, or were untreated. Samples were sequenced on an Illumina NextSeq 500 using 37-bp single-end sequencing. Raw fastq files and gene count tables are included for each sample.

  Dataset EGAD50000001471

• RNASeq Whole Transcriptome Expression Profiles of NFE2 and PF4 as Translational Biomarkers for BET Inhibition-Induced Thrombocytopenia in Preclinical and Clinical Studies

  Longitudinal blood samples for exploratory biomarker analysis were collected from 51 out of 83 patients enrolled in CA011-001 (NCT02419417) study of BMS-986152, totaling 425 samples collected on three different dosing schedules (A, B, and C). Whole transcriptome expression profiling was performed on the collected blood samples using RNASeq, with Illumina TruSeq library preparation and paired sequencing. Gene expression data was quantified as transcripts per million (TPM).

  Dataset EGAD50000001659

• RIP-SeqRaw data

  This dataset contains 15 paired FASTQ files from the PTBP1 project. Sequencing data were generated using bulk directional RNA-seq and RIP-seq experiments performed on a NovaSeq 6000 platform (2×100 bp paired-end reads). The dataset comprises two groups of samples: controls and patients. For each group, both input and immunoprecipitated samples are available. Patient samples correspond to skin biopsies from individuals affected by a neurodevelopmental disorder associated with variable skeletal dysplasia and disproportionate short-limbed short stature.

  Dataset EGAD50000001723

• Genomic analysis of high-risk prostate cancer.

  Whole genome sequencing analysis of high risk localised primary prostate cancer samples including metastatic samples was performed across 153 tumour samples with matching germline sequencing (whole blood). Samples were all fresh frozen frozen section confirmed tumour specimens and associated clinical and pathological metadata is available for these specimens.

  Study EGAS00001003088

• De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

  Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

  Dataset EGAD50000001673

• 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

• 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

• RNA-seq data for proximal and distal human LHBT UZH (CH)

  This dataset contains bulk RNA-seq data from 15 patients who underwent rotator cuff repair surgery, yielding paired proximal and distal samples of the long head of the biceps tendon (30 samples total). The submission includes 90 files, consisting of R1 and R2 FASTQ files for each sample as well asprocessed .TXT files containing gene-level counts generated after genome alignment. Raw sequencing reads were generated on an Illumina platform, aligned to the human reference genome GRCh38.p13, and quantified at the gene level.

  Dataset EGAD50000002095

• Single cell RNA sequencing of human cord Blood CD34 Cells

  We performed single cell RNA sequencing and ATAC e valuation of human umbilical cord blood. To explore the differentiation pathway for human lymphoid lineage, our target cells contain CD34-positive cord blood. That population is evaluated by single cell RNA sequencing and single cell ATAC.

  Study JGAS000528

• 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

• 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

• 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

• Data Access Committee for the DNA sequencing data included in the study "Multifocal cohort analysis unveils cell types associated with regional lymph node seeding in prostate cancer".

  A data transfer agreement (DTA), based on the example DTA provided by UZ Gent, is to be filled out by the requester and Multifocal RNA-seq and tNGS data from primary and metastatic tissues of locally advanced and de novo metastatic cohorts - Data Access Committee. https://www.uzgent.be/nl/over-uz-gent/organisatie/data-access-comite/wat-zijn-de-opdrachten-van-het-data-access-comite Coordinator: Muriel Fouquet E-mail: dataaccesscommittee@uzgent.be

  Dac EGAC50000000930

• ESGI___Molecular_diagnosis_for_mitochondrial_disorders_

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients.

  Study EGAS00001000164

• 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

• 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

• 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

• WGS-Lung Cancer sample 30 pair

  This study includes 30 paired samples of Korean Lung Cancer paitients. 30 Lung Cancer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001001474

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Study EGAS00001000575

• 2018_ETO_WGS

  This study includes 12 paired samples of Korean AML-ETO paitients.12 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002804

• 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

• 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

• ENGAGE___Amendment__500_genes_exon_sequencing_

  The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes

  Study EGAS00001000137

• Paired whole exome sequence of subcutaneous panniculitis-like T-cell lymphoma.

  Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare subtype of peripheral T-cell lymphoma affecting younger cases and associated with hemophagocytic lymphohistiocytosis. To clarify molecular pathogenesis of SPTCL, we analyzed paired tumor and germline DNAs from 13 patients by whole exome sequencing.

  Study EGAS00001003282

• 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

• Korean Lung Cancer - 36 pair WES data

  This study includes 36 paired samples of Korean Lung Cancer paitients.36 Lung Cnacer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WES study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002843

• 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

• MDS Sequencing Project_Cancer Cell

  Myelodysplastic syndromes (MDS) are uncommon entities, heterogeneous clinically and cytogenetically. The aim of the present study is to determine genetic alteration in this subset of patients. Expected results: Identification of new aberrations and genetic markers in order to detect novel genes involved in MDS 5q-response to Lenalidomide's treatment.

  Study EGAS00001001011

• Highlighted samples from the BCH CRDC

  These exomes are from some of the patients and family members detailed in our forthcoming publication, Children’s Rare Disease Cohorts: an integrative research and clinical genomics initiative. While this paper details an institutional collection of exomes, the samples here were specifically highlighted as having significant findings.

  Study EGAS00001004436

• Integrated molecular analysis of adult T-cell leukemia/lymphoma

  This study is an integrated molecular study of adult T-cell leukemia/lymphoma which includes whole-exome (n = 81), whole-genome (n = 48), and transcriptome sequencing data (n = 57) as well as methylation (n = 109) and SNP array data (n = 426)

  Study EGAS00001001296

• 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

• Australia_and_New_Guinea_haplotype_phasing_

  Whole-genome sequencing and phasing of admixed Aboriginal Australian genomes and Papua New Guinean genomes using 10x Genomics Chromium technology. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001853

• Keratinocyte_CRISPR_screens

  Immortalised HaCaT keratinocytes were transduced with Cas9 and the CRISPR-KO v1.1 genome-wide gRNA library. The gRNA library was prepared from genomic DNA isolated 14 days post library transduction. gRNA representation will be compared to the original CRISPR-KO v1.1 library to reveal genes essential for HaCaT survival and growth.

  Study EGAS00001002714