Search Results - EGA European Genome-Phenome Archive

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 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

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Spatial whole exome sequencing of metastatic melanoma

Spatial targeted gene sequencing of metastatic melanoma

Genome and transcriptome sequence data from a breast ductal carcinoma patient

Genome and transcriptome sequence data from an uveal melanoma patient

Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

Genome and transcriptome sequence data from a colon cancer patient

Genome and transcriptome sequence data from a primary unknown- upper GI or pulmonary patient

Genome and transcriptome sequence data from a metastatic choroidal melanoma patient

Genome and transcriptome sequence data from an ovarian cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient