Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome sequencing of acral melanomas

ABSTRACT: We conducted whole genome sequencing of 5 acral melanoma genomes and their matched DNA from blood.

PROVIDER: EGAS00001000486 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Genome wide analysis of acral melanoma (Affymetrix)

Project description:Genotyping of a matched normal, primary and metastatic acral melanoma DNA from blood and one matched Primary and one metastatic acral melanoma was genotyped on Affmetrix SNP6

2011-12-13 | E-GEOD-28910 | biostudies-arrayexpress

Genome wide analysis of acral melanoma (Illumina)

Project description:Assessment of mutation on expression levels Transcriptomic profile of a matched primary and metastatic acral melanoma One Primary and one metastatic acral melanoma transcript expression were assayed (no matched normal)

2011-12-13 | E-GEOD-28909 | biostudies-arrayexpress

Genome wide analysis of acral melanoma (Affymetrix)

Project description:Genotyping of a matched normal, primary and metastatic acral melanoma

2011-12-13 | GSE28910 | GEO

Genome wide analysis of acral melanoma (Illumina)

Project description:Assessment of mutation on expression levels Transcriptomic profile of a matched primary and metastatic acral melanoma

2011-12-13 | GSE28909 | GEO

Genome wide analysis of acral melanoma

Project description:This SuperSeries is composed of the following subset Series: GSE28909: Genome wide analysis of acral melanoma (Illumina) GSE28910: Genome wide analysis of acral melanoma (Affymetrix) Refer to individual Series

2011-12-13 | E-GEOD-28913 | biostudies-arrayexpress

Whole genome sequencing of matched primary and metastatic acral melanomas.

Project description: Not available

| S-EPMC3266028 | biostudies-literature

Acral Melanoma

Project description:Acral Melanoma

| PRJNA682608 | ENA

Acral melanoma whole genomes - samples

Project description:Acral melanoma study whole genomes

| EGAD00001000060 | EGA

Whole genome sequencing of matched primary and metastatic acral melanomas

Project description:Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here we used whole genome sequencing to characterise somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational rates in this acral melanoma sample pair was more comparable to the rate reported in cancer genomes not associated with mutagenic exposure than in the genome of a melanoma cell line or the transcriptome of melanoma short-term cultures. Despite the perception that acral skin is sun-protected, the dominant mutational signature in these samples is compatible with damage due to ultraviolet light exposure. A nonsense mutation in ERCC5 discovered in both the primary and metastatic tumours, could also have contributed to the mutational signature through accumulation of unrepaired dipyrimidine lesions. However, evidence of transcription-coupled repair was suggested by the lower mutational rate in the transcribed regions and expressed genes. The primary and the metastasis are highly similar at the level of global gene copy number alterations, loss of heterozygosity and single nucleotide variation (SNV). Furthermore, the majority of the SNVs in the primary tumour were propagated in the metastasis and one non-synonymous coding SNV and one splice site mutation appeared to arise de novo in the metastatic lesion.

| EGAS00001000169 | EGA

Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

Project description:We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

| EGAS00001000472 | EGA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data