16488 results for "sec+and+unspecified+malignant+neoplasm"

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• Host pathogen interaction long read transcriptome

  Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

  Study EGAS00001006779

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities WGS

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006865

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities RNA-Seq

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006866

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities DNA-Methylation

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically uniquely defined by alterations in the SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be further classified in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT-MYC and ATRT-SHH subgroups. Whereas ATRT-MYC universally displayed high sensitivity to multi-targeted tyrosine kinase inhibitors, ATRT-SHH showed a more heterogeneous response with a subset showing high sensitivity to Notch inhibitors, which corresponded to high expression of Notch receptors. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing a representative pre-clinical model which enables the development of subgroup-specific therapies.

  Study EGAS00001006881

• WTCCC case-control study for Hypertension

  WTCCC genome-wide case-control association study for Hypertension (HT) using the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000009

• Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC)

  Genomics of Colorectal Cancer Metastases - Massively Parallel Sequencing of Matched Primary and Metastatic tumours to Identify a Metastatic Signature of Somatic Mutations (MOSAIC)

  Dataset EGAD00001000080

• LITS

  Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers.

  Dataset EGAD00010001400

• Mutational consequences of precancerous liver disease

  Clonally expanded liver adult stem cell clones of healthy liver and cirrhotic liver (due to alcohol abuse, NASH and PSC), as well as biopsies of liver cancers were subjected to whole genome sequencing to determine the mutational impact of precancerous liver disease

  Dataset EGAD00001004105

• RFMix

  This dataset contains the per-chromosome RFMix input and output files for the local ancestry inference of 59 Aboriginal Australian genomes as reported in Malaspinas et al., 2016. Local ancestry was inferred assuming four mixing ancestral populations represented by: Europeans (27 individuals), Asians (29 individuals), Papuans (13 individuals) and Native Australians (7 individuals from the WCD region).

  Dataset EGAD00010001575

• Human TRIM24-MET fusion HGG RNA-seq

  Human RNA-seq data for TRIM24-MET fusion tumor primary samples and patient/PDOX-derived cell lines. Cells were treated with 0.1% DMSO or EC90 of MET inhibitors (capmatinib, cabozantinib, crizotinib) for 4 hours. BAM files containing aligned (and unaligned) reads to hg19 are provided.

  Dataset EGAD50000000194

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are WGS data generated from differentiated neural stem cells (NSCs) of NXPG-32 patient (XPG patient with neurodegeneration) and a matched healthy control CTRL-33.

  Dataset EGAD50000000232

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from XP patients and controls as well as rescued patient hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000230

• Oxidative DNA damage and ubiquitin proteasome system dysfunction underpins neurodegeneration in young adults with a DNA repair disorder

  Deposited here are time series bulk RNA-seq data generated from isogenic wild-type (WT), XPA and XPG gene knockouts hiPSC cells during cortical neuronal differentiation.

  Dataset EGAD50000000228

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• Cord blood progenitor CITE-seq dataset

  Sequencing results of single-cell transcriptome and antibody libraries from two biological experiments of cord blood progenitor cells. Four samples from different time points were processed using 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Gene expression and antibody-derived libraries were sequenced separately.

  Dataset EGAD50000000405

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Dataset EGAD50000000395

• Whole genome sequencing of preneoplasia lung adenocarcinoma

  Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

  Dataset EGAD50000000396

• Antibody Repertoires in CVID

  The data consist of the DNA sequences of antibody gene rearrangements from peripheral blood human B cells of subjects with Common Variable Immune Deficiency (CVID) and healthy controls subjects.

  Study phs000934

• ADCC Pilot RNAseq Study on Posterior Cingulate Astrocytes in Alzheimer's Disease

  In this study, RNA sequencing was performed on astrocytes microdissected from the posterior cingulate cortex of Alzheimer's disease subjects and healthy elderly controls.

  Study phs000745

• Immuno-nephrology Data Access Committee Amsterdam UMC

  In this experiment we investigated kidney immunology in two autoimmune kidney diseases (ANCA-associated glomerulonephritis and Lupus Nephritis). Single cell transcriptome analysis of CD45+ immune cells from freshly retrieved kidney biopsies of 5 AGN patiënts, 1 disease-control with lupus nephritis (class II), and 1 "healthy" nephrectomy control was performed using 10X Genomics technology.

  Dac EGAC50000000024

• TCRseq

  T cell receptor sequencing of tumor samples. Briefly, DNAse I treated tumor RNA samples were subjected to library preparation using AmpliSeq Immune Repertoire Panel (Illumina) and sequenced using NextSeq500.

  Study EGAS50000000258

• Transcriptional Reference Map of Human Natural Killler Cells

  Here we performed single-cell RNA sequencing of both bulk NK and sorted NK subsets to establish a transcriptional reference map of human natural killer cells.

  Study EGAS50000000014

• Exome - Uveal Melanomas

  Whole exome sequencing on 11 uveal melanoma samples and corresponding germline samples. Libraries were prepared using the SureSelectXT2 Clinical Research Exome V2 kit (Agilent, 5190-9500 and G9621B). Paired-end libraries (2 x 100 bp) were sequenced on HiSeq 2000/2500 or NovaSeq 6000 instruments (Illumina).

  Dataset EGAD50000000767

• CITE-seq data of six CK-AML patient samples

  We performed cellular indexing of transcriptomes and epitopes (CITE-seq) of six primary leukemia samples from CK-AML patients. The dataset contains BAM files for each individual sample (D1922 and R0836) or for the hashed pool (HIAML47-HIAML85, P9D-P9R)

  Dataset EGAD50000000633

• Pregnancy-associated melanoma

  The aim of this project is to assess differences in intratumoral immune composition in pregnant melanoma patients versus non pregnant melanoma controls. Samples (N=25) were obtained from a local patient database. From archived FFPE we isolated RNA and performed NGS and bio-informatica data-analysis.

  Dataset EGAD50000000706