Whole genome sequencing of primary and metastatic Melanoma cases in an Australian cohort.

Study

Study ID	Alternative Stable ID	Type
EGAS00001001552		Other

Study Description

Melanoma is the fourth most common cancer in Australia and the leading cause of cancer death in young adults. The Australian Melanoma Genome Project (AMGP) is analysing whole genomes from melanomas. We include the results of whole genome sequencing (WGS) for a number of datasets that include cutaneous, acral and mucosal melanoma subtypes.

Study Datasets 9 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Samples
EGAD00001003353	BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70 BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70	56
EGAD00001003357	Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients. Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients.	106
EGAD00001003388	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM. Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM.	366
EGAD00001004409	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 134 samples: matched tumour-normal pairs from 67 mucosal melanoma cases Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 134 samples: matched tumour-normal pairs from 67 mucosal melanoma cases	134
EGAD00001004474	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 28 samples: matched tumour-normal pairs from 14 melanocytic nevi cases Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 28 samples: matched tumour-normal pairs from 14 melanocytic nevi cases	28
EGAD00001005454	Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 103 cases of melanoma Uveal subtype Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 103 cases of melanoma Uveal subtype	206
EGAD00001005500	Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 88 cases of melanoma Acral subtype. 64 cases also have RNASeq sequencing from the tumour sample. Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 88 cases of melanoma Acral subtype. 64 cases also have RNASeq sequencing from the tumour sample.	237
EGAD00001005501	Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma	41
EGAD00001005738	79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy. 79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy.	79

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