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- Study Description
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Important Links and Information
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- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
Melanoma is the most prevalent cause of skin cancer morbidity and mortality. In order to characterize the full range of somatic mutations that may drive the growth of melanoma, we are sequencing tumor and normal DNA from a set of roughly 150 melanomas. For the majority of samples (approximately 90% of the cases) mutations in protein coding genes will be assessed in the exonic DNA of tumor-normal pairs using hybrid capture and paired-end DNA sequencing. Additionally, in a few DNA samples (approximately 10% of the cases) the entire genomes will be analyzed to assess the possible contribution of complex structural rearrangements contributing to oncogenesis. The sequencing data are supplemented by copy number profiling on the same tumors using high-density SNP arrays. Integration of these approaches will enable the unbiased and comprehensive characterization of both known and novel recurrent DNA alterations that arise in melanoma.
- Study Design:
- Case Set
- Study Type:
- Case Set
- Total number of consented subjects: 432
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data (Public ftp)
- Study Inclusion/Exclusion Criteria
Primary tumor tissue samples, metastatic tumor tissue samples and metastatic short-term culture obtained from patients undergoing surgery for melanoma were selected based on high density of tumor tissue. DNA was extracted from tumor tissue or short-term culture and from either adjacent normal skin tissue (in the case of the primary tumor tissue samples) or blood for use as a normal DNA comparator. DNA was assessed for high quality and integrity on Affymetrix SNP 6.0 arrays and by agarose gel electrophoresis. SNP comparison was used to confirm that a sequenced tumor-normal pair could be attributed to the same individual and that no significant contamination by foreign DNA was present. Gross copy number analysis based on the SNP array data confirmed aberrant copy number in the case of the melanoma samples and diploid, unremarkable copy number profiles in the case of the normal samples.
- Molecular Data
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Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074 Whole Genome Sequencing Illumina HiSeq 2000 N/A N/A Whole Exome Sequencing Illumina HiSeq 2000 N/A N/A Custom Target Sequencing Illumina HiSeq 2000 N/A N/A Whole Exome Sequencing Agilent SureSelect Human All Exon v.2 Kit N/A N/A RNA Sequencing Illumina TruSeq RNA Access Library Prep V1.0 N/A N/A - Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
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- Primary Phenotype: Melanoma
- Links to Related Resources
- Authorized Data Access Requests
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See research articles citing use of the data from this study
- Study Attribution
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Principal Investigator
- Levi Garraway, M.D. Ph. D. Dana Farber Cancer Institute, Boston, MA USA; Broad Institute, Cambridge, MA USA.
- Eric Lander, Ph. D. Broad Institute, Cambridge, MA USA.
- Stacey Gabriel, Ph. D. Broad Institute, Cambridge, MA USA.
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Co-Investigator
- Lynda Chin, M.D. M. D. Anderson Cancer Center, Houston, TX USA.
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Funding Source
- U54 HG003067. National Human Genome Research Institute (NHGRI), National Health Institute, Bethesda, MD, USA.
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Principal Investigator