Search Results - EGA European Genome-Phenome Archive

Single-cell expression of Hodgkin lymphoma

Single-cell gene expression was profiled for 22 Hodgkin lymphoma tumors and 5 reactive lymph nodes (2 replicates were performed for RLN-1). Library preparation was performed with the 10x Chromium platform (3' version 2 assay). Sequencing was performed on an Illumina NextSeq. The BAM files were generated from the raw sequencing data using Cell Ranger (v2.1.0) mkfastq and count commands.

Dataset EGAD00001005739

KRAS Mutations in Multiple Myeloma

Fastq files for 80 Multiple Myeloma Patients and 12 cell-lines

Dataset EGAD00001005743

Whole genome sequencing generated from metastatic gliosarcoma patient samples

This dataset contains whole genome sequencing data aligned to the b37 reference genome for 4 spatially and temporally distinct tumors from one patient with a matched normal blood sample.

Dataset EGAD00001005745

Somatic mutation and clonal evolution in the human pancreas - WGS (2019-12-17)

In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma. This dataset contains all the data available for this study on 2019-12-17.

Dataset EGAD00001005751

Phased melanoma whole genomes

We have sequenced whole genomes of 10 melanoma samples (1 cell line; A375 and 9 patient derived short term cultures). Libraries were prepared with 10X linked reads technology in order to obtain phase information and subsequently sequenced on Illumina NovaSeq6000.

Dataset EGAD00001005773

Targeted Sequencing of Tumor-Normal pairs from advanced Melanoma

Aligned BAM files from NextSeq500 tageted panel sequencing of 84 samples from matched tumour-normal pairs of 42 melanoma patients. The dataset consists of 30 non-responders and 12 responders to ICB.

Dataset EGAD00001005778

Chromatin run-on and transcriptome sequencing of fibrolamellar carcinoma

Fastq files of chromatin run-on (14 fibrolamellar carcinoma, 3 non-malignant liver; single-end) and transcriptome (23 fibrolamellar carcinoma, 2 non-malignant liver; paired-end) sequencing of fibrolamellar carcinoma

Dataset EGAD00001005797

JAK and STAT alterations in CD30 positive LPD

JAK and STAT alterations in CD30 positive LPD, panel sequencing, 12 cutaneous lymphoma patients, 40 samples

Dataset EGAD00001005801

sWGS of RCC patients

Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort)

Dataset EGAD00001005804

Mutation analysis of 10 genes in plasma DNA of RCC patients

Mutation analysis of 10 frequently mutated genes in renal cell carcinoma (BAP1, KDM5C, MET, MTOR, PBRM1, PIK3CA, PTEN, SETD2, TP53, VHL) in plasma DNA of RCC patients using a custom QIASeq panel (MonRec Cohort)

Dataset EGAD00001005806

Spatial whole exome sequencing of metastatic melanoma

We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

Dataset EGAD00001005819

Spatial RNA-sequencing of metastatic melanoma

We performed RNA sequencing of 48 different regions sub-sampled from a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. RNAseq was performed on samples with a minimum RNA integrity number (RIN) of 5.5 except for two cases (6A10 and 8A3) with RINs greater than 3. A minimum of 700ng of RNA were required for all samples undergoing RNAseq. Paired-end transcriptome reads were aligned using TopHat2, to the UCSC hg19 reference genome.

Dataset EGAD00001005820

Spatial targeted gene sequencing of metastatic melanoma

We performed deep targeted DNA sequencing for a panel of 265 cancer-related genes. This included subsampling 35 different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. Samples with cancer cell purity greater than 80% based on pathologic assessment were used for cancer gene panel DNA sequencing. Mean sequencing coverage was 861x and paired-end reads in FASTQ format were generated by the Illumina pipeline and aligned to the reference human genome hg19 build using the Burrows-Wheeler Alignment Tool (BWA, v0.7.5) with default settings. Aligned reads were further processed using GATK with best practices for removing duplicates, indel removal and recalibration.

Dataset EGAD00001005821

Genome and transcriptome sequence data from a breast ductal carcinoma patient

Genome and transcriptome sequence data from a breast ductal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005823

mtDNA-Roma

mtDNA variant positions vcf files for 86 human samples

Dataset EGAD00010001844

Genome and transcriptome sequence data from an uveal melanoma patient

Genome and transcriptome sequence data from an uveal melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005824

Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005825

Genome and transcriptome sequence data from a metastatic choroidal melanoma patient

Genome and transcriptome sequence data from a metastatic choroidal melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005828

Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient

Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005831

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