15020 results for "cancer studies using rna-seq"

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• Reference epigenome Islet-derived-MSC03 input ChIP-Seq data generated from KEP study

  Islet-derived-MSC03 input ChIP-Seq paired end data

  Dataset EGAD00001007428

• Reference epigenome Islet-derived-MSC04 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived-MSC04 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007429

• Reference epigenome Islet-derived-MSC04 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived-MSC04 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007432

• Reference epigenome Islet-derived-iPSC01 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007436

• Reference epigenome Islet-derived-iPSC01 h3k27me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007437

• Reference epigenome Islet-derived-iPSC01 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007438

• Reference epigenome Islet-derived-iPSC01 h3k4me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007440

• Reference epigenome Islet-derived-iPSC01 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007441

• Reference epigenome Islet-derived-iPSC01 input ChIP-Seq data generated from KEP study

  Islet-derived-iPSC01 input ChIP-Seq paired end data

  Dataset EGAD00001007442

• Reference epigenome Islet-derived-iPSC02 h3k27ac ChIP-Seq data generated from KEP study

  Islet-derived-iPSC02 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007443

• Reference epigenome Islet-derived-iPSC02 h3k9me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC02 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007448

• ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq

  ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq

  Dataset EGAD00001006185

• Reference epigenome Islet-derived-MSC01 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived-MSC01 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007404

• Reference epigenome Islet-derived-MSC02 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived-MSC02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007412

• Reference epigenome Islet-derived-iPSC02 h3k36me3 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC02 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007445

• Reference epigenome Islet-derived-iPSC02 h3k4me1 ChIP-Seq data generated from KEP study

  Islet-derived-iPSC02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007446

• The evolutionary steps from primary to metastatic prostate cancer are largely uncharted, and the ability to use DNA present in body fluids as correlates of aggregate metastatic status is under-examined. We reconstructed phylogenies in ten prostate cancer patients with fatal disease using deep targeted sequencing of the prostate, adjacent and distant organs, as well as plasma, serum, and cerebrospinal fluid at various time points. A total of 163 samples are studied.

  The evolutionary steps from primary tumor to metastasis in prostate cancer are largely uncharted, and the ability to use serum, plasma, and cerebrospinal fluid as a correlate of aggregate metastatic tumor genomic status has not been tested. We used deep targeted sequencing to reconstruct tumor evolution in ten prostate cancer patients with fatal disease encompassing examination of the prostate and adjacent and distant organs, as well as plasma, serum, and cerebrospinal fluid at various time points. We show that there is substantial evolution from a common ancestor within the prostate that results in branching to multiple lineages which form an intermixed multi-clonal primary tumor mass. After the occurrence of key driver aberrations, one of these lineages will metastasize to multiple sites in a sequential fashion. These metastatic sites are then susceptible to being populated by cells from other intra-prostatic lineages or from other metastases. Genomic representation of metastases in body fluids is not uniform. Cerebrospinal fluid analysis can detect lineages not detected in circulating DNA, suggesting possible clinical utility.

  Study EGAS00001003848

• Detection of cancers three years prior to diagnosis using plasma cell-free DNA

  A major goal of early cancer detection is to identify subclinical disease when the tumor burden is low, so that treatments are more effective. But how early can cancers be detected prior to clinical signs or symptoms? This question can be answered only through the evaluation of participants whose clinical course has not been altered by the study itself. We here describe such an evaluation, performed on prospectively collected plasma samples from the Atherosclerosis Risk in Communities (ARIC) study, including 26 participants diagnosed with cancer and 26 matched controls. At the index time point, eight of these 52 participants scored positively with a multicancer early detection (MCED) blood test. All eight of these participants were diagnosed with cancer within 4 months after blood collection. In six of these 8 participants, we were able to assess an earlier plasma sample collected 3.1 to 3.5 years prior to clinical diagnosis. In four of these six participants, the same mutations detected by the MCED test could be identified, but at 8.6 to 79-fold lower levels. These results demonstrate that it is possible to detect circulating tumor DNA (ctDNA) more than three years prior to clinical diagnosis, and provide benchmark sensitivities required for the success of ctDNA-based tests for this purpose.

  Study EGAS00001008068

• Million Veteran Program (MVP) Summary Results from Non-Sensitive Omics Studies

  MVP is an ongoing prospective cohort study and mega‐biobank in the Department of Veterans Affairs Healthcare System designed to study genetic influences on health and disease among veterans. This is the accession to hold publicly available results. Results from sensitive phenotypes or MVP population subsets can be found at accession phs001672 and will require an application for access.

  Study phs002453

• Gliomas, glioneuronal and neuronal tumors

  The dataset represents a total of 85 DNA samples from 22 male and 20 female pediatric patients affected with gliomas, glioneuronal, and neuronal tumors. The samples were subject to whole genome sequencing, WGS, [71 samples, (representing 18 male and 17 female individuals)] and whole exome sequencing, WES, [14 samples, (representing 4 males and 3 female individuals)]. One tumor tissue sample and one peripheral blood sample were analyzed from each of 84 patients, whereas two tumor tissue samples and one peripheral blood sample were analyzed from one patient. The WGS samples were sequenced 2x150 bp paired-end on an Illumina HiSeqX v2.5 instrument, and the WES samples were sequenced 2x100 bp paired-end on an Illumina HiSeq 2500 instrument. The FASTQ files generated were aligned to the human reference genome sequence GRCh38/hg38 using bwa-mem, with the ALT-aware option turned on. Sorting of reads and marking of PCR duplicates was performed with GATK. Base quality score recalibration and joint realignment of reads around insertions and deletions (indels) were conducted using GATK tools. The dataset consists of 85 files in the CRAM format (lossless compression) with a total file size of ~13,3 TB. Additional genomic and molecular data (FASTQ, BAM, IDAT, and VCF files) and limited clinical data can be requested by ethically approved projects conducting research in the field of pediatric cancer.

  Dataset EGAD50000000300

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001888

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001890

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001896

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001897

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by targeted sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by a targeted panel for somatic mutation and sCNA analysis (7 samples), subject to cell availability. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them.

  Dataset EGAD50000001898