16767 results for "sec+and+unspecified+malignant+neoplasm"

in 35.93 milliseconds.

• Comprehensive genetic analysis of pediatric germ cell tumors

  Germ cell tumors (GCTs) are relatively rare tumors in children. Previous studies showed that adult testicular GCTs had some genomic alterations, but genetic basis of pediatric GCTs is still to be elucidated. We applied DNA methylation array analysis, whole-transcriptome sequencing, targeted capture sequencing, and SNP array analysis to fifty-one GCT samples.

  Study JGAS000204

• Somatic L1 retrotransposition dynamics in high-grade serous ovarian cancer

  Somatic L1 retrotransposition was mapped in high-grade serous carcinoma (HGSC) tumors using LDI-PCR/Nanopore-seq method. This method identifies somatic L1 insertions originating from two active L1 loci at chr22q12.1 and chrXp22.2. Multiple tumors from same patient were utilised to understand L1-mediated intrapatient heterogeneity.

  Study EGAS50000001198

• Chondrosarcoma_Targeted_Sequencing_Study

  This Study uses a focused bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these finding in a larger set of patients.

  Study EGAS00001000277

• GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

  This study introduces a novel scRNA-seq normalization method, which takes unobserved genes into account. To validate GTestimate we designed a cell targeted amplification strategy, enabling us to sequence a small set of cells twice, once at a "typical" sequencing depth and once at a "ultra-deep" sequencing depth.

  Study EGAS50000000915

• A distinct monocyte cellular state links systemic immune dysregulation to pulmonary impairment in long COVID

  This is an independent cohort of Long COVID patients recruited from a rehabilitation centre. These patients had Long COVID from 8 months to more than 2 years since their acute COVID-19 disease. PBMC from these patients were collected and single cell transcriptomics dataset was generated.

  Study EGAS50000001216

• Molecular classification of small intestinal adenocarcinomas

  In this study we analyzed genomic and transcriptomic data from 135 small intestinal adenocarcinoma (SIA) patients. Through this analysis, we identified three distinct subtypes based on gene expression patterns, revealing the diverse molecular characteristics among SIA patients. Our findings provide comprehensive insights into the unique features of each subtype.

  Study EGAS50000001238

• LongVar low-coverage data

  This dataset includes sequencing data from participants of the LongVar study. Specifically, it comprises low-coverage whole genome sequencing (WGS) data which was derived from cell-free DNA from blood samples. These data were generated to compare imputation accuracy. 133 individuals agreed to share their data, and are healthy volunteers.

  Study EGAS50000001114

• Identifying mutations in patient-derived melanoma DCC lines

  To identify mutations that cause resistance, we analyzed two patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). We employed targeted-panel sequencing to examine the coding sequences of 410 cancer-associated target genes.

  Study EGAS50000001225

• Repeated sampling

  Repeated sampling experiment – sample acquisition A repeated sampling experiment was set up to specifically evaluate the effect of increasing time after death on sample quality. Selected non-tumor and large tumor tissues (with enough material available to collect for this experiment beside routine sampling) were sampled repeatedly at 1.5-hour time intervals during the autopsy.

  Study EGAS50000000224

• Neversmoker lung adenocarcinoma

  Non-small cell lung cancer whole genome sequencing We performed whole genome sequencing of Korean never-smoker lung adenocarcinoma patients to discover novel pathway except EGFR and ALK patients. We identified estrogen signaling as a novel enriched signaling. Lastly we validated the elevated estrogen signaling through immunohistochemistry experiment in some patients which increased signaling.

  Study EGAS50000000232

• Duplex sequencing of selected breast cancer patients

  This study assessed the variant profiles of 22 samples from 11 breast cancer patients with adverse survival outcomes, including paired uninvolved mammary gland samples collected at various distances from primary lesions. Ultra-deep sequencing was performed to identify the presence of low-frequency pathogenic post-zygotic variants in PIK3CA and TP53 genes.

  Study EGAS50000000538

• 3D genome topology distinguishes molecular subgroups of medulloblastoma

  Medulloblastoma (MB) has four molecular subtypes, but their 3D genome architecture differences are unclear. We used in situ Hi-C on 28 surgical specimens and a patient-derived xenograft to reconstruct the 3D genome architecture of MB subtypes, finding that topologically associating domain (TAD) insulation scores could distinguish MB subtypes.

  Study EGAS50000000540

• Ex vivo modeling of precision immuno-oncology responses in lung cancer

  Single-cell RNA-sequencing (scRNA-seq) data from paired lung cancer organoids and immune cells. The experiment was performed using the Single Cell 5' solution of 10X Genomics. The dataset includes 15 samples from 4 multiplexed experiments. The multiplexing was performed using the Feature Barcoding technology of 10X Genomics.

  Study EGAS50000000593

• WGS data of conditional knockout mouse model mammary tumours

  Deposited here are 56 whole-genome sequencing BAM files from 15 Trp53f/w, 12 Trp53f/f, 14 Brca1f/f Trp53f/w, and 15 Brca1f/f Trp53f/f mouse mammary tumor samples sequenced on Illumina NovaSeq PE150. An additional 6 whole genome sequencing BAM files from corresponding normal tissues of mice are also included as controls (BPC_D666, B1PC_D840, BPTC_D992, PC_D503, PC_D720_Kid, PTC_H531). All samples were used in the study “Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors, Huo et al., 2026.”

  Dataset EGAD50000002036

• Broad utility of ultrasensitive analysis of circulating tumor DNA (ctDNA) dynamics across solid tumors treated with immunotherapy

  Here, we applied a whole-genome, tumor-informed approach to study ctDNA in more than 202 advanced-stage cancer patients treated at VHIO. This study demonstrates the efficacy of ultrasensitive ctDNA as a broad biomarker in a large pan-cancer discovery and validation cohort, spanning 24 tumor types treated with diverse immunotherapy modalities. It demonstrates ctDNA’s potential for early response assessment, survival prediction, and distinguishing true progression from pseudoprogression, enhancing its clinical relevance. This dataset captures the plasma sequencing data from the project.

  Dataset EGAD50000001813

• RNA-Seq Profiles from the CheckMate-577 Clinical Trial

  The dataset contains RNAseq profiles of 386 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNA was analyzed using the Illumina TruSeq RNA Access method for library preparation, followed by sequencing on the Illumina NovaSeq platform with a 50bp paired-end strategy and a target read depth of 50M per sample. Fastq files are included.

  Dataset EGAD50000002394

• LongRNA_Monocytes

  This dataset consists of bulk RNA sequencing profiles generated from monocytes isolated from peripheral blood mononuclear cells (PBMCs) collected from 315 patients enrolled in the ImmunAID consortium. Each sample corresponds to a unique patient, providing a resource to investigate transcriptional variation in circulating monocytes across the cohort. PBMCs were isolated from whole blood, and monocytes were subsequently enriched using standard immunological protocols. Total RNA was extracted and libraries were prepared using the SMART-Seq mRNA Library Preparation Kit with Unique Molecular Identifiers (UMIs). Sequencing was performed on an Illumina NovaSeq 6000 platform following manufacturer-recommended protocols.

  Dataset EGAD50000002341

• WES for 45 patients with pleural mesothelioma (Matched)

  The dataset contains WES data (bam files) for 45 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002128

• WES for 42 patients with pleural mesothelioma (Not matched)

  The dataset contains WES data (bam files) for 42 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002127

• EM-seq datatset of primary human thymocyte subsets

  FASTQ-files of EM-seq experiments of 6 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-). Samples were sorted from 1-2 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001600

• The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

  The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

  Dataset EGAD50000001701

• PanelSeq IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using an Agilent SureSelect custom 0.5-2.9Mb kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC025, IDC026, IDC029, IDC031, IDC032, IDC038, IDC057, IDC062, IDC065, IDC069, IDC072, IDC090B, IDC092, IDC097, IDC099, IDC107, IDC113, IDC117, IDC143, IDC152, IDC159A, IDC159B, IDC180, IDC186, IDC192, IDC197, IDC198, IDC207, IDC209, IDC216, IDC218, IDC222, IDC229, IDC232, IDC274, IDC282, IDC290, IDC299, IDC307, IDC338, IDC344, IDC346, ILC006, ILC012, ILC083 and ILC248.

  Dataset EGAD50000001149

• Human CMV-specific CD8+ T cells

  In this study we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles and sample multiplexing. With this technique we identified novel paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we review the ability of dCODE dextramers to detect antigenspecific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.

  Dataset EGAD50000000894

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731

• 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

• RNA-Seq data from study: Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  The ChRCC study RNA-Seq dataset contains raw whole transcriptome sequencing data of 16 tumor and 6 adjacent normal samples from 7 UTSW patients, who have consented to depositing their genomic data to public repository. RNA-Seq was performed using 50bp single-end on a HiSeq2500 platform (Illumina, San Diego, CA, USA). 50M reads per sample on average. The raw data is in fastq format.

  Dataset EGAD50000000416

• Bulk RNA-seq of human muscle-invasive bladder cancer tissue samples before and after platinum-based chemotherapy (Chelushkin, van Dorp, et al., 2024)

  The current dataset represents bulk RNA-Seq gene expression profiling (with an exome library preparation kit) of muscle-invasive bladder cancer tissue samples obtained before and after platinum-based chemotherapy. 89 samples are pre-treatment transurethral resection of the bladder tumor (TUR-BT) tissue at diagnosis (baseline), 86 are post-treatment cystectomy tissue (resected tumor bulk), comprising 76 pairs of samples from the same patients. FASTQ files contain gene expression data.

  Dataset EGAD50000000446

• Targeted sequencing (paired) of HR genes in primary and metastatic patient-derived xenografts (PDXs) of colorectal cancer (CRC)

  The dataset includes DNA targeted paired-wise (2 FASTQ per sample) sequencing of a manually curated panel of 44 genes with a documented role in homologous recombination (HR), a pathway of DNA damage response. Sequencing was conducted in 69 tumors from patients with metastatic colorectal cancer after serial passaging in mice (patient-derived xenografts, PDXs). For each PDX model profiled for HR gene mutations, therapeutic annotation of response to FOLFIRI (a chemotherapeutic regimen consisting of the combination of 5-fluorouracil and irinotecan) is available.

  Dataset EGAD50000000107

• AVENIO Expanded ctDNA panel sequence alignments (BAMs)

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 100 plasma samples from patients with lung cancer undergoing treatment in the OSCILLATE trial. After 150 bp paired-end sequencing, reads were aligned to the human genome reference with the AVENIO Oncology Analysis Software. These files are the sorted non-deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD50000000138

• Exploiting evolutionary steering in cancer therapy

  This dataset contains 9 bam files of exome sequencing for an experiment of evolved resistance. Here a barcoded cell line (HCC827 - POT) has been treated under high concentrations of gefitinib (GEF) and trametinib (TRM) until resistance has evolved, as well as under control conditions (DMSO). The dataset contains exome sequencing of confluent cells for three replicates for each anti-cancer drug as well as two replicates of growth under DMSO conditions. The original barcoded cell line (POT) was also exome sequenced and is included in the cohort. Sequencing was performed on the Illumina NovaSeq platform.

  Dataset EGAD00001005782

• Whole Genome Sequencing of HCC

  The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Dataset EGAD00001003994

• Renal Cancer Exome Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Dataset EGAD00001000287

• snATAC-seq BAM files from 10x Multiome profiling of human fetal liver hematopoiesis

  This dataset provides snATAC-seq BAM files from a single-nucleus multiome study of 53 human fetal liver samples (5–18 post-conception weeks). Live CD45+CD235- cells were sorted from dissociated tissue, and isolated nuclei were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Raw sequencing data were processed and aligned to GRCh38-2020-A-2.0.0 using Cell Ranger ARC v2.0.2.

  Dataset EGAD50000002571

• 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

• Whole exome sequencing in familial Multiple Sclerosis

  The purpose of the study is to determine whether variants of genes are associated with greater risk of Multiple Sclerosis (MS). We used whole-exome sequencing in 138 individuals from 23 families including at least 2 members with MS. We compare patients with MS, patients with other autoimmune diseases (AID), and unaffected individuals.

  Study EGAS00001004204

• Oncogenic gene fusions in primary colon cancers

  This study represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. The project goal was to identify novel oncogenic gene fusions in these data. In addition, we studied the detected gene fusions at the molecular level and defined their effects on downstream pathways.

  Study EGAS00001002197

• The_British_Autozygosity_Populations_BioResource

  This data set contains whole exome sequences of 500 individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.

  Study EGAS00001001565

• Identification of causal mutation in two patients with Sotos Syndrome Features

  We performed whole exome sequencing (WES) on genomic DNA derived from two patients with Sotos Syndrome Features. Sequencing (100 base pair paired-end) was performed on an Illumina Hiseq 2000 sequencer after enrichment of 62Mb of exonic and adjacent intronic sequences with TruSeq Exome Enrichment Kit (Illumina, San Diego, CA, USA).

  Study EGAS00001000993

• 2014_AML_WES_51 samples

  2014 AML WES study contains 51 paired WES samples which were collected from SNUH. The study was designed to examine the molecular abnormalities from leukemic patients at initial diagnosis in comparison with corresponding germ line control (saliva samples). The results of WXS were analyzed by Mutect for ranking cancer variants and creating mutational matrix.

  Study EGAS00001002819

• 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

• Lymphocyte_LCM_WGS

  Using whole genome sequencing of lymphocytes excised from human tissue using laser capture microscopy (LCM), we identify the mutations arising in these microenvironments. This work will contribute towards developing a catalogue of mutations present in tissue resident lymphocytes across a range of tissues, and will characterize the mutational signatures that result from each microenvironment.

  Study EGAS00001003384

• Single cell RNA sequencing of CD19 CAR T-cell infusion products

  We performed single cell RNA sequencing of remnants from CD19 CAR T-cell infusion products used for standard of care treatment for relapsed/refractory large B-cell lymphoma. Libraries were prepared using 10X 5’ GEX chemistry and sequenced on an Illumina HiSeq 4000 to obtain >50,000 reads per cell.

  Study EGAS00001004576

• Targeted_sequencing_of_candidate_genes_in_calcific_aortic_valve_stenosis

  The objective is to identify new disease genes involved in calcific aortic valve stenosis (CAVS) by screening newly identified candidate genes. The recruitment of patients with CAVS has been achieved by l’institut du thorax (Nantes, France). DNA from the selected patients has been analysed by targeted capture (Agilent SureSelect) and massively parallel sequencing (Illumina).

  Study EGAS00001000308

• 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

• 2017_prospective_v2 Whole Exome Sequencing

  2017 AML prospective study contains 10 paired WES samples which were collected from SNUH.The study was designed to examine the molecular abnormalities from leukemic patients at initial diagnosis in comparison with corresponding germ line control (saliva samples). The results of WXS were analyzed by Mutect for ranking cancer variants and creating mutational matrix.

  Study EGAS00001002628

• Studying the single cell characteristics of pancreatic cancer

  Pancreatic cancer is a dangerous malignancy in the pancreas. In this study we use single-cell RNA sequencing technique to help understand the transcriptome characteristics of pancreatic tumor cells. This study help understands the complex microenvironment of pancreatic tumors and will likely to benefit clinical research of pancreatic cancer treatments.

  Study EGAS00001003889

• Targeted sequencing of patients affected by familial or sporadic Alzheimer's disease

  The study aimed at identifying variants related to familial cases of Alzheimer's disease by comparing the mutational state of approximately 4000 genes associated to many known diseases ("clinical exome") in members of a family (n=7) of with members with dementia (n=2) and unaffected members (n=5)

  Study EGAS00001003856

• The genomic landscape of lung adenocarcinoma in East Asians

  We performed exome sequencing of 210 and transcriptome sequencing of 181 LUADs of Chinese patients. For more details, please see publication "Genomic landscape of lung adenocarcinoma in East Asians" by Chen J. et. al. in Nature Genetics 2020. https://www.nature.com/articles/s41588-019-0569-6.

  Study EGAS00001002941

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  In this study, we performed whole genome bisulfite sequencing (WGBS) to characterize the methylome of representative iBCP-ALL cases from the Interfant study discovery cohort, including 2 pools of B-cell progenitors from healthy donors, 2 MLL-AF4+, 2 MLL-AF9+ and 2 non-MLLs from iBCP-ALL patients.

  Study EGAS00001003650

• Transcriptomic signatures of CD4+ T cells from visceral leishmaniasis (VL) patients

  Bulk RNA-sequencing was performed on CD4+ T cells isolated from the blood of visceral leishmaniasis patients (n = 12) and endemic controls (EC; n = 12). CD4+ T cells were obtained by magnetic-activated cell sorting (MACS). Alterations in the transcripts of T helper (Th) cells during infection were identified.

  Study EGAS00001004152