Search Results - EGA European Genome-Phenome Archive

CNS Embryonal tumors

The dataset represents a total of 58 DNA samples from 16 male and 12 female pediatric patients affected with embryonal central nervous system tumors. The samples were subject to whole genome sequencing, WGS, [48 samples, (representing 12 male and 11 female individuals)] and whole exome sequencing, WES, [10 samples, (representing 4 male and 1 female individuals)]. One tumor tissue sample and one peripheral blood sample were analyzed from each of 26 patients, whereas two tumor tissue samples and one peripheral blood sample were analyzed from two patients. 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 58 files in the CRAM format (lossless compression) with a total file size of ~8,8 TB. All CRAM files but one, are derived from one sequence run and one sample. P4551_227N_P4552_112N is a CRAM file where 2 sequence runs (P4551_227N and P4552_112N) from peripheral blood samples from the same individual, P019, were aligned into one single CRAM file. 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 EGAD50000000298

WGS dataset for Genomic rearrangements in Pediatric Cancer

Dataset EGAD00001008272

Somatic mutations, clonal architecture and genomic evolution in multiple myeloma

Multiple myeloma is an incurable plasma cell malignancy whose molecular pathogenesis is incompletely understood. We used whole exome sequencing, copy number profiling and cytogenetic to analyses 84 samples from 67 patients with myeloma. In addition to known myeloma genes, we identify new candidate genes, including truncations of SP140, ROBO1 and FAT3 and clustered missense mutations in EGR1. We find oncogenic mutations in cancer genes not previously implicated in myeloma, including SF3B1, PI3KCA and PTEN. We define diverse processes contributing to the mutational repertoire, including kataegis and somatic hypermutation. Most cases have at least one cluster of subclonal variants, including subclonal driver mutations, implying on-going tumor evolution. Serial samples revealed diverse patterns of clonal evolution, including linear evolution, differential clonal response and branching evolution. Our findings reveal the myeloma genome to be heterogeneous across patients and, within individual patients, to exhibit diversity in clonal admixture and dynamics in response to therapy.

Dataset EGAD00001000339

12213 results for "cancer rna-seq"

in 56.82 milliseconds.

CNS Embryonal tumors

WGS dataset for Genomic rearrangements in Pediatric Cancer

Somatic mutations, clonal architecture and genomic evolution in multiple myeloma

Genome and transcriptome sequence data from a metastatic large cell neuroendocrine tumour of the lung patient

Genome and transcriptome sequence data from a serous carcinoma of fallopian tube patient

Genome and transcriptome sequence data from a metastatic adult granulosa cell tumour patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma presumably of ovarian origin patient

Genome and transcriptome sequence data from a metastatic uterine leiomyosarcoma patient

Genome and transcriptome sequence data from a squamous cell carcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectum patient

Genome and transcriptome sequence data from a metastatic ductal carcinoma of the breast patient

Genome and transcriptome sequence data from a metastatic clear cell sarcoma patient

Genome and transcriptome sequence data from a metastatic uveal melanoma patient

Genome and transcriptome sequence data from a metastatic renal cell carcinoma patient

Genome and transcriptome sequence data from an anaplastic myxopapillary ependymoma patient

Genome and transcriptome sequence data from a metastatic gastric adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic colon adenocarcinoma patient

Genome and transcriptome sequence data from a squamous cell carcinoma of ge junction patient

Genome and transcriptome sequence data from a metastatic spindle cell sarcoma patient

Genome and transcriptome sequence data from an advanced adenocarcinoma of lung patient

Genome and transcriptome sequence data from a non-small cell lung carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient