16802 results for "sec+and+unspecified+malignant+neoplasm"

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• Genome-wide data Resande and Swedes

  Dac EGAC00001002627

• INSERM U944 Team Genome and Cancer

  Dac EGAC00001002976

• SCANDARE MACARON project

  Among gynecological cancers, high-grade serous ovarian cancer has the highest prevalence and more than 75% of patients have advanced stage at diagnosis with a 5-year survival of 40%. When the initial complete surgical removal is not possible (60% of patients), an interval surgery can be considered after three to four cycles of neoadjuvant chemotherapy to reduce the tumor mass. However, in approximately 50% of cases the tumor has little or no response to neoadjuvant chemotherapy. Therefore, identification of potential drug targets, biomarkers and/or pathways whose modulation can help in the prevention, interception, or curing of the disease is essential to address the unmet need. Therefore, MACARON project aims to address these issues through the identification of shared neoantigens arising out of somatic alterations and aberrant transcriptional programs in ovarian cancer DNA/RNA datasets.

  Dac EGAC50000000104

• Type 2 Diabetes Starr County GWAS and Exome Sequencing

  The T2D Seq GWAS Starr County Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs001166 T2D Seq GWAS Starr County Cohort. phs000143 CIDR T2D Hanis phs001099 T2D GENES Starr County

  Study phs001166

• Identification of Recurrent SMO and BRAF Mutations in Ameloblastomas

  RNA-seq data from two cases of ameloblastoma was analyzed for candidate gene fusions and point mutations. Recurrent point mutations identified in the RNA-seq data, as well as mutations identified with limited panel targeted deep sequencing, were validated as somatic. Expanding to a larger cohort of 28, one of two activating mutations was found in 80% of cases. No recurrent gene fusions events were identified.

  Study phs000739

• Type 2 Diabetes in African Americans, GWAS and Exome Sequencing

  The T2D Seq GWAS AA Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001167 T2D Seq GWAS AA Cohort. phs000140 CIDR T2D Bowdens phs001102 T2D GENES AA

  Study phs001167

• Mapping the Evolution of T Cell States During Response and Resistance to Adoptive Cellular Therapy

  We investigated single T cell transcriptional states that define donor lymphocyte infusion (DLI) response and resistance from cryopreserved bone marrow mononuclear cells from 15 patients with relapsed chronic myeloid leukemia (CML) after allogeneic hematopoietic stem cell transplant. By integrating bulk ATAC-seq data from sorted T cell populations from these bone marrow samples, we also defined gene regulatory networks that underlay these clusters.

  Study phs002877

• Evolving Cell States and Oncogenic Drivers during the Progression of IDH-Mutant Gliomas

  The study aims to understand the changes in cell states during the progression of IDH mutant gliomas. We generated scATAC-seq data from tumor samples of patients with IDH mutant gliomas, ranging from grade 2 to grade 4, including both IDH mutant oligodendroglioma and IDH mutant astrocytoma samples. Additionally, we have generated scRNA-seq data from patient-derived organoids that were treated with a DNMT1 inhibitor.

  Study phs003697

• HLA-A*3101 and Carbamazepine-Induced Hypersensitivity Reactions in Europeans

  Based on the prior knowledge of involvement of the human leukocyte antigen locus in Han Chinese patients with carbamazepine-induced Stevens-Johnson syndrome, we imputed the HLA types for each case and control subject from the array of SNPs in the Human610-Quad GWAS platform (NCBI Build 36.1). We then performed a genome-wide association test which included the imputed HLA alleles as markers.

  Study EGAS00000000036

• Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  This study aims to evaluate the efficacy of the combination of olaparib, durvalumab, and fulvestrant for the treatment of patients with ER-positive, HER2-negative, locally advanced or metastatic breast cancer with BRCA gene alterations or alterations of genes involved in HRR or MSI status, in terms of the progression-free survival rate (PFSR) at 24 weeks.

  Study EGAS50000001166

• The genomic landscape of large and small tumors in early-onset prostate cancer patients

  This study characterizes the genomic landscape of prostate cancer (PCA) cells in patients below or at the age of 50 years. Tumors of such early onset patients already show a broad spectrum of sizes. To test if the size differences are indicative of special cancer subgroups, we sequenced the genome of the tumor cells and matched control samples from blood.

  Study EGAS00001000383

• Epigenetic analysis of clear cell renal cell carcinoma using ChIP-seq

  To investigate the epigenetic landscape of clear cell renal cell carcinoma (ccRCC), we performed ChIP-seq data for the CTCF, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, and HIF1A marks in the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as the 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 narrowPeak formats. Data were processed using the nf-core chipseq pipeline.

  Dataset EGAD50000001886

• Investigation of chromatin accessibility in clear cell renal cell carcinoma using ATAC-seq

  To identify regions of open and accessible chromatin in clear cell renal cell carcinoma (ccRCC), we performed ATAC-seq on the 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 processed narrowPeak fomats. Data were processed using the nf-core atacseq pipeline.

  Dataset EGAD50000001885

• cfMeDIP-seq for 18 patients with pleural mesothelioma

  The dataset contains cfMeDIP-sequencing data (bam files) for 18 plasma samples from pleural mesothelioma patients. The libraries were prepared according to the published protocol (Shen, S. Y., Burgener, J. M., Bratman, S. V. & De Carvalho, D. D. Preparation of cfMeDIP- seq libraries for methylome profiling of plasma cell-free DNA. Nat. Protoc. 14, 2749–2780 (2019)). Whole genome sequencing (WGS) was performed for pre-made libraries on NovaSeq X Plus with a 150 paired-end strategy. Low-quality reads and adapters were removed with Trim Galore version 0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). The trimmed reads were aligned to hg38 with Bowtie2 version 2.3.4.3. SAMTools version 1.9 was used to convert the SAM alignment files to BAM files, sort and index reads, and remove duplicates.

  Dataset EGAD50000002126

• High-depth whole genome sequencing of paired ductal carcinoma in-situ (DCIS) and germline control samples from 51 individuals.

  Deposited here are whole-genome sequencing data for 51 paired breast cancer DCIS and matched-normal samples taken from the same individual. Average sequence depth is 110x for DCIS samples and 39x for matched-normals. Matched-normals are from blood (n=14) or adjacent normal breast (n=37). Sequencing was performed on Illumina HIseqX (n=70) or Illumina Novoseq (n=32). They are a part of a broader project that uses high-depth WGS to investigate the somatic mutation genomic landscape of DCIS in order to uncover biological insights into breast cancer progression as well as possible methods to stratify DCIS patients for individualised therapy or disease monitoring.

  Dataset EGAD50000002071

• Bulk RNAseq FASTQ files of three PDAC organoid lines treated with LGK974 or DMSO for 24h

  This dataset contains raw FASTQ files from bulk RNA sequencing of three patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid lines (P28, P40, P47). Each organoid line was treated with either the WNT secretion inhibitor LGK974 or DMSO for 24 hours, with three biological replicates per treatment condition. RNA was extracted using the Qiagen QiaSymphony SP system, and libraries were prepared with the Illumina Truseq stranded polyA kit. Sequencing was performed on an Illumina NextSeq2000 platform using single-end 50bp reads. Quality control was conducted with FastQC, and reads were trimmed with TrimGalore as appropriate. Data are controlled-access and intended for transcriptomic analysis of WNT pathway perturbation in PDAC organoid models.

  Dataset EGAD50000002219

• Survival and safety of laser interstitial thermal therapy and adjuvant pembrolizumab in recurrent high-grade astrocytoma: a Phase 1/randomized Phase 2b trial

  This dataset is the immune profiling of the trial patients. Cryopreserved PBMCs obtained from the patients at different time points were processed to single-cell transcriptomic or TCR libraries using 10x next GEM single Cell 5' v2 kit. We also performed whole exome sequencing (WES) of the tumor to identify the mutation burden. The WES data was generated by sequencing company Novogene. There are total of 69 of single cell libraires, 69 of single cell TCR libraries, and 13 of tumor WES data being generated from 18 trial patients recruited at University of Florida.

  Dataset EGAD50000001639

• Whole-genome sequencing data of human hematopoietic stem and progenitor cells in post-transplant clonal hematopoiesis

  This dataset contains BAM files of whole-genome sequencing data of single human HSPCs after colony expansion, for three individuals who harbor a DNMT3A mutant clonal hematopoiesis clone in their blood system after hematopoietic cell transplantation. 29 samples are present in this dataset; 10 samples for LTHIT005, 10 samples for LTHIT131, and 9 samples for LTHIT069. In the sample name, samples are annotated for being DNMT3A wildtype (wt) or mutant (mut), except for LTHIT069 (wt samples: F13, H4, K2, L16, N12, mut samples: C8, E10, L9, N5). Whole-genome sequencing was performed after standard Illumina WGS library preparation and sequenced on a Novaseq 6000 using 150 bp paired-end sequencing. The sequencing depth is 15x genome coverage, or 50Gbases per sample.

  Dataset EGAD50000001347

• RNA sequencing data from 10 patient derived colorectal cancer organoids

  This dataset comprises RNA-sequencing data from ten colorectal cancer (CRC) organoids, derived from histologically verified primary tumor tissues of patients undergoing surgical resection. Paired-end sequencing produced 20 FASTQ.gz files. The organoids were cultured in Geltrex-based droplets using PDO culture medium and harvested for RNA extraction. Total RNA was isolated and subjected to full-length mRNA sequencing, producing high-quality RNA-seq data. The dataset includes transcriptomic profiles of seven microsatellite stable (MSS) and three microsatellite instable (MSI) tumors, providing a valuable resource for the analysis of non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline. This dataset aids in uncovering potential immunotherapy targets in CRC, particularly in hard-to-treat low-TMB MSS cases.

  Dataset EGAD50000000962

• ovarian cancer sample RNA-seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to bulk RNA-sequencing on 17 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy. - Group C1, Epithelial Ovarian Cancer(EOC) patients with estrogen responsiveness : 6 samples - Group C2, Epithelial Ovarian Cancer(EOC) patients with estrogen non-responsiveness : 10 samples - non-classified 1-sample

  Dataset EGAD50000000613

• Cell-Free DNA Genomic Profiling and its Clinical Implementation in Advanced Prostate Cancer

  Sixty-eight patients with advanced prostate cancer in castration-resistant or castration-sensitive settings undergoing treatment at the University Hospital Basel or the St. Claraspital Basel (Switzerland) were selected for targeted parallel sequencing analysis on liquid biopsy (plasma cfDNA) and matched formalin-fixed, paraffin-embedded (FFPE) tumor tissue samples. The liquid biopsy sequencing (plasma cfDNA) was performed using a custom-designed targeted AmpliSeq HD Prostate Cancer cfDNA panel on all 68 patients. The sequencing on 42 matched FFPE tumor biopsy samples was performed using a custom-designed or an alternative commercial panel (ThermoFisher). Raw data underwent automated processing on the Ion Torrent Server v5.16.1 (ThermoFIsher) and were aligned to a hg19 reference genome using the Torrent Alignment Software (ThermoFihser).

  Dataset EGAD50000000348

• Table of gene-level RNA counts from newborn screening dried blood spot samples

  Table of gene-level RNA counts from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). Rows correspond to genes and columns to samples, where there is an additional column (BS13sub), corresponding to sample BS13, which was downsampled to 1/4 of its original depth.

  Dataset EGAD00010001707

• 3q-capture DNA sequencing of primary AMLs with 3q26 rearrangements

  This dataset contains DNA sequencing of the chromosome 3q region in 28 primary AML cases with 3q26 rearrangements (3q26-rearranged AML). Genomic DNA was fragmented using the Covaris shearing device (Covaris), and sample libraries were assembled following the TruSeq DNA Sample Preparation Guide (Illumina). After ligation of adapters and an amplification step, target sequences of chromosomal regions 3q21.1-q26.2 were captured using custom in-solution oligonucleotide baits (Nimblegen SeqCap EZ Choice XL). The design of target sequences was based on the human genome assembly hg19: chr3q21.1:126036241-130672290 - chr3q26.2:157712147-175694147. Amplified captured sample libraries were paired-end sequenced (2x100 bp) on the HiSeq 2500 platform (Illumina) and aligned against the hg19 reference genome using the Burrows-Wheeler Aligner (BWA).

  Dataset EGAD00001006820

• Modeling glioblastoma invasion using human brain organoids and single-cell transcriptomics

  We performed scRNA-seq of patient-derived glioblastoma cells alone or after co-culture with human iPSC-derived cerebral organoid cells. Transcriptional changes implicated in the invasion process that are coherent across patient samples indicate that GBM cells reactively upregulate genes required for their dispersion. Potential interactions between GBM and organoid cells identified by an in silico receptor-ligand pairing screen suggest functional therapeutic targets.

  Study EGAS00001003852

• The Causes of Clonal Blood Cell Disorders Study - SCOR_Custom (2018-04-19)

  We took a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We grew these up into colonies, then whole genome sequenced each colony. Somatic mutations act as a unique barcode for each clone. We have designed a panel for targeted resequencing of the mutations that we find. We are now looking for these mutations in the peripheral blood, to see the dynamics of how HSCs contribute to the peripheral blood in health. This dataset contains all the data available for this study on 2018-04-19.

  Dataset EGAD00001004087