Search Results - EGA European Genome-Phenome Archive

Whole genome sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study".

Whole genome sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are libraries from 41 patients. Specifically: 15 transformed follicular lymphoma (TFL), 6 early progressers (PFL), and 20 non-early progressers (NPFL). For TFL and PFL patients, trios consisting of diagnostic (T1), transformed/progressed (T2) and a matching normal are available (n = 63 libaries in total). For NPFL patients, a tumor-normal pair are available (n = 40 libraries).

Dataset EGAD00001002897

Oliocapture sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study".

Oliocapture sequencing libraries from the study "Histological Transformation and Progression in Follicular Lymphoma: a Clonal Evolution Study". These are sequencing libraries from the extension cohort of 277 patients. Specifically, there are 402 tumor libraries and 82 normal libraries.

Dataset EGAD00001002898

BLUEPRINT September 2016, ATAC-seq Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38

ATAC-seq data for 4 sample(s) Multiple Myeloma for plasma cell from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002920

BLUEPRINT September 2016, ATAC-seq Mantle Cell Lymphoma from venous blood, on Genome GRCh38

ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002918

BLUEPRINT September 2016, ChIPmentation Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38

ChIPmentation data for 2 sample(s) Activated B-Cell-Like Diffuse Large B-Cell Lymphoma from lymph node, on Genome GRCh38. 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002944

BLUEPRINT September 2016, ChIPmentation Burkitt Lymphoma from lymph node, on Genome GRCh38

ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002939

Melanoma C32 ENU Resistance to Single Agent Therapy

This study involves mutagenizing C32, a melanoma cell line, with ENU to identify those mutations which engender resistance to a targeted treatment.

Dataset EGAD00001003239

Identification of drug resistance genes in melanoma by mRNA gene expression

We aim to sequence the mRNA transcriptome of 22 human melanoma cell lines in biological triplicate in order to define the gene expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset EGAD00001003244

Identification of drug resistance genes in melanoma by small RNAs expression analysis

We aim to sequence the small RNAs of 22 human melanoma cell lines in biological triplicate in order to define the microRNAs expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset EGAD00001003245

Genetic Basis of Hepatosplenic T Cell Lymphoma (HSTL)

Whole exome sequencing of hepatosplenic T cell lymphoma (HSTL) tumors, paired normals, and cell lines, including (1) 68 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL tumor samples, (2) 20 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL paired normal samples, and (3) 2 exome capture, paired-end Illumina Hiseq sequencing, BAM files from HSTL cell lines.

Dataset EGAD00001003246

Clonal expansion of mutated cell population in bladder urothelium

1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

Dataset EGAD00001003250

Identification of drug resistance genes in melanoma by Exome Sequencing

The cell lines in this study are a combination of internally sequenced (cosmic) and externally sequenced cell lines known to be “double-wild-type” (lacking BRAF and NRAS somatic mutations). These sequences were realigned in this data set for consistency.

Dataset EGAD00001003260

Whole-genome sequencing (WGS) data of Gastric adenocarcinoma and adjacent normal tissues

High-coverage WGS sequencing of DNA samples from 90pairs GCs was performed on the Illumina HiSeq X Ten System.

Dataset EGAD00001003269

WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded.

Dataset EGAD00001003271

Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients.

Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients. The sequencing was performed by Illumina HiSeq 4000. Background and aims: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) could reflect nearly the entire mutation spectrum in given tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC).Methods: Thirty-two multi-regional HCC samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS). ITH extent was measured by the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Matched cfDNAs were also analyzed by WES and TDS. Profiling efficiencies of single tumor specimen and cfDNA were compared and the one better depicted mutational landscape was selected to screen therapeutic targets.Results: We found variable extents of ITH in HCCs and observed branched and parallel evolution patterns. ITH level decreased at higher sequencing depth of TDS than that measured by WES (28.1% vs 34.9%, P < 0.01) but it remained unchanged upon additional samples analyzed. TDS of single tumor specimen detected an average of 70% the total mutations in HCC. Although more mutations were detected in cfDNA under TDS than WES, an average of 47.2% total HCC mutations uncovered by cfDNA suggested tissue outperform cfDNA and the latter may serve as alternative in profiling HCC genome. Consequently, TDS of single tumor tissue in 66 patients and cfDNAs in four unresectable HCCs identified 38.6% (26/66 and 1/4) patients bearing therapeutic targets.Conclusions: TDS of single tumor specimen could largely circumvent ITH to uncover mutations indicative of target therapy in HCC.

Dataset EGAD00001003278

RNA data for medulloblastoma samples (ICGC)

RNA sequencing data for 170 medulloblastoma tumor samples

Dataset EGAD00001003279

Genomics of enteropathy-associated T cell lymphoma (EATL)

Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

Dataset EGAD00001003284

Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - dcc_release_24_dataset

WGS sequencing for cases from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 24

Dataset EGAD00001003292

RNA-Seq and WXS from 6 glioblastoma patients

Dataset EGAD00001003293

Whole-genome and transcriptome sequencing of NUT midline carcinoma

In this study, we sequenced three NUT midline carcinoma genomes and their transcriptomes (NMC1, NMC2 and Ty-82), and two paired normal blood samples (for NMC1 and NMC2). Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X machines. Transcriptome (mRNA) sequencing was performed in HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

Dataset EGAD00001003117

Whole-genome sequencing (WGS) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

We used WGS (Complete Genomics) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

Dataset EGAD00001003120

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