15147 results for "cancer studies using rna-seq"

in 26.34 milliseconds.

• German early-onset prostate cancer cohort of the Pan-Prostate Cancer Genome (PPCG) project

  Prostate cancer is the most frequent malignant tumor in males and the second most frequent cause of cancer-related death. Currently, in Germany, more than 60,000 prostate cancers are diagnosed every year. Although most of these patients are treated in a curative attempt, more than 10,000 German men die from prostate cancer annually. Owing to the demographic changes of our society, a further doubling of prostate cancer incidences during the next 20 years is expected. Prostate cancer is generally considered a tumor of elderly men. However, a fraction of prostate cancers are diagnosed at the age of 55 years or less. For several reasons, these “early onset prostate cancers” may represent a key entity for the understanding of prostate cancer biology. First, it is likely that early onset prostate cancers represent a distinct molecular subgroup of prostate cancer (PCa), potentially characterized by relatively small numbers of genetic changes, some of which may be particularly strong driver mutations for PCa development. Second, a fraction of prostate cancers in young individuals could represent classical prostate cancers that are detected at a very early stage and might therefore have accumulated molecular changes/mutations occurring that are most instrumental for prostate cancer early detection. Third, PCa with hereditary backgrounds are likely to accumulate in the age group below 55 years. A comparison with other sample sets (e.g. from other ICGC consortia), a systematic genomic analysis of young men with PCa could therefore lead to the detection of mechanisms for hereditary PCa. Fourth, a better understanding of these tumors is particularly relevant as finding optimal treatment regimens is most critical in young cancer patients. We are analyzing the entire genomic DNA sequences of at least 200 PCas (and matched non-tumorous DNA) of young men (≤ 55y), to at least 30 fold coverage, and integrate single-nucleotide variants and genomic structural variations with differential methylation, mRNA and miRNA expression data.Tissues were collected at the University Medical Center Hamburg-Eppendorf. Sequencing was performed at DKFZ and NCT (Heidelberg), EMBL (Heidelberg), and MPIMG (Berlin). Data management and bioinformatic data analyses is being conducted at DKFZ.

  Study EGAS00001003373

• Lung_Rearrangement_Study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from cancer samples and subjected to 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000005

• CLL_Cancer_Whole_Genome_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000014

• Burden_of_Disease_in_Sarcoma

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from cancer samples and subjected to 50 bp, paired end sequencing on the llumina HiSeq 2000. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000087

• Primary_Lung_Cancer_whole_genome_study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000354

• Somatic_mutation_and_clonal_evolution_in_the_human_bladder_WGS

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-genome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer.

  Study EGAS00001002658

• Cancer_Exome_Resequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000206

• Somatic_mutation_and_clonal_evolution_in_the_human_bladder_WES

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The data in this study will be generated by whole-exome sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer.

  Study EGAS00001002842

• Lung_Plasma_rearrangement_screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from lung cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000289

• Osteosarcoma_whole_genome_rearrangement_screen

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000330

• PLCRC_study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Colorectal cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000612

• Targeted sequencing of paired tumour/blood of 78 Ta stage bladder cancer patients

  In continuation of our whole-exome and targeted sequencing study on non-muscle-invasive bladder cancer, we carried out this targeted paired tumour/blood sequencing study including 78 Ta stage bladder cancer patients. Agilent’s SureDesign tool was used to design a 1.133 Mb SureSelect custom capture for all coding exons of the 140 selected candidate genes.

  Study EGAS00001005766

• Sequencing of cancer autopsies and ctDNA

  Tumor heterogeneity is a major obstacle for precision oncology strategies. To characterize inter-lesion heterogeneity in pre-treated cancers, we performed genetic and transcriptomic profiling of synchronous lesions from ten rapid autopsies comprising six cases of breast cancer, three of cholangiocarcinoma and one lung cancer case. For nine patients, we studied mutation representation in circulating cell-free DNA (cfDNA).

  Study EGAS00001005109

• Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer

  Circulating tumor DNA (ctDNA) sequencing provides a minimally-invasive method for tumor molecular stratification. We compared the commercial Guardant360 ctDNA test to an academic sequencing approach for profiling of metastatic prostate cancer. Plasma cell-free DNA (cfDNA) from 24 patients was sequenced with a validated, prostate cancer specific targeted research panel, and sent for simultaneous Guardant360 analysis.

  Study EGAS00001003352

• Global Architecture of anti-Tumor B-Cell Immunity against Gastric Cancer

  Recent successes in tumor immunotherapies have warranted the importance of tumor immunity. Compared to the T-cell immunity, B-cell immune system in cancer is largely elusive. Here we immunogenetically profiled tumor-infiltrating B-cell and T-cell repertoires for exome- characterized diffuse-type gastric carcinoma (DGC), which is remarkable for its B-cell infiltrations, unraveling previously un-defined architectures of B-cell immunity and its interplays with T-cell immunity in cancer. We also performed transcriptome analysis to enumerate the proportions of tumor-infiltrating immune cells in the gastric cancer environment .

  Study JGAS000141

• Global Architecture of anti-Tumor B-Cell Immunity against Gastric Cancer

  Recent successes in tumor immunotherapies have warranted the importance of tumor immunity. Compared to the T-cell immunity, B-cell immune system in cancer is largely elusive. Here we immunogenetically profiled tumor-infiltrating B-cell and T-cell repertoires for exome- characterized diffuse-type gastric carcinoma (DGC), which is remarkable for its B-cell infiltrations, unraveling previously un-defined architectures of B-cell immunity and its interplays with T-cell immunity in cancer. We also performed transcriptome analysis to enumerate the proportions of tumor-infiltrating immune cells in the gastric cancer environment .

  Study JGAS000103

• Identification_of_drug_resistance_genes_in_cancer_cell_lines_by_insertional_mutagenesis

  Our aim is to identify genes involved in resistance to anti-cancer therapies. In order to do this we have taken advantage of a lentiviral vector (LV)-based insertional mutagen to mutagenize cancer cell lines. LV-transduced cell lines were then treated with anti-cancer therapies and the emergence of resistant clones scored. DNA from pools of resistant clones was collected, subjected to custom capture by baits designed against the LV sequence, and then sequenced to identify the LV-genomic junction. We hope that the identification of recurrently targeted genes in resistant cell population will allow us to identify genes that mediate drug resistance.

  Study EGAS00001001035

• Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer

  DNA mismatch repair defects (MMRd) and tumor hypermutation are rare and under-characterized in metastatic prostate cancer. Furthermore, since hypermutated MMRd prostate cancers can respond to immune checkpoint inhibitors, there is an urgent need for practical detection tools. We analyzed cell-free DNA targeted sequencing data from 434 metastatic prostate cancer patients with circulating tumor DNA (ctDNA) purity above 2%. Samples with somatic hypermutation were subjected to 150x whole exome sequencing. These data allowed us to interrogate the salient genomic properties of this rare prostate cancer subtype and correlate findings with patient clinical outcomes.

  Study EGAS00001003899

• Triple Negative Breast Cancer sequencing

  Triple Negative Breast Cancer sequencing

  Dataset EGAD00001000063

• Expression profiles and genetic makeup of metastases of a cancer of unknown primary.

  Study EGAS00001004059