ID

45372

Description

Principal Investigator: Levi Garraway, M.D. Ph. D, Dana Farber Cancer Institute, Boston, MA USA; Broad Institute, Cambridge, MA USA MeSH: Melanoma https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000452 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.

Link

dbGap-study=phs000452

Keywords

Versions (1)
  1. 11/4/22 11/4/22 - Chiara Middel
Copyright Holder

Levi Garraway, M.D. Ph. D, Dana Farber Cancer Institute, Boston, MA USA; Broad Institute, Cambridge, MA USA

Uploaded on

November 4, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000452 Melanoma Genome Sequencing Project

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and 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.
Description

Elig.phs000452.v3.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C0025202
UMLS CUI [1,2]
C0543467
UMLS CUI [1,3]
C1268672
UMLS CUI [1,4]
C0475358
UMLS CUI [1,5]
C0677930
UMLS CUI [1,6]
C0027627
UMLS CUI [1,7]
C0443303
UMLS CUI [1,8]
C0040284
UMLS CUI [2,1]
C0012854
UMLS CUI [2,2]
C0185115
UMLS CUI [2,3]
C0475358
UMLS CUI [2,4]
C0443303
UMLS CUI [2,5]
C0040284
UMLS CUI [3,1]
C0012854
UMLS CUI [3,2]
C0185115
UMLS CUI [3,3]
C0475358
UMLS CUI [3,4]
C0677930
UMLS CUI [3,5]
C0205117
UMLS CUI [3,6]
C0684084
UMLS CUI [4,1]
C0012854
UMLS CUI [4,2]
C0185115
UMLS CUI [4,3]
C0005767
UMLS CUI [5,1]
C0012854
UMLS CUI [5,2]
C1516048
UMLS CUI [5,3]
C0034378
UMLS CUI [5,4]
C3897601
UMLS CUI [5,5]
C0013856
UMLS CUI [6,1]
C0752046
UMLS CUI [6,2]
C1707455
UMLS CUI [6,3]
C0750484
UMLS CUI [6,4]
C0596130
UMLS CUI [6,5]
C0445247
UMLS CUI [6,6]
C0237401
UMLS CUI [6,7]
C1298908
UMLS CUI [6,8]
C5552996
UMLS CUI [7,1]
C5414521
UMLS CUI [7,2]
C0750484
UMLS CUI [7,3]
C1511518
UMLS CUI [7,4]
C0025202
UMLS CUI [7,5]
C0475358
UMLS CUI [8,1]
C5414521
UMLS CUI [8,2]
C0750484
UMLS CUI [8,3]
C1707513
UMLS CUI [8,4]
C0205307
UMLS CUI [8,5]
C2347026
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
Elig.phs000452.v3.p1.1
Item
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.
boolean
C0025202 (UMLS CUI [1,1])
C0543467 (UMLS CUI [1,2])
C1268672 (UMLS CUI [1,3])
C0475358 (UMLS CUI [1,4])
C0677930 (UMLS CUI [1,5])
C0027627 (UMLS CUI [1,6])
C0443303 (UMLS CUI [1,7])
C0040284 (UMLS CUI [1,8])
C0012854 (UMLS CUI [2,1])
C0185115 (UMLS CUI [2,2])
C0475358 (UMLS CUI [2,3])
C0443303 (UMLS CUI [2,4])
C0040284 (UMLS CUI [2,5])
C0012854 (UMLS CUI [3,1])
C0185115 (UMLS CUI [3,2])
C0475358 (UMLS CUI [3,3])
C0677930 (UMLS CUI [3,4])
C0205117 (UMLS CUI [3,5])
C0684084 (UMLS CUI [3,6])
C0012854 (UMLS CUI [4,1])
C0185115 (UMLS CUI [4,2])
C0005767 (UMLS CUI [4,3])
C0012854 (UMLS CUI [5,1])
C1516048 (UMLS CUI [5,2])
C0034378 (UMLS CUI [5,3])
C3897601 (UMLS CUI [5,4])
C0013856 (UMLS CUI [5,5])
C0752046 (UMLS CUI [6,1])
C1707455 (UMLS CUI [6,2])
C0750484 (UMLS CUI [6,3])
C0596130 (UMLS CUI [6,4])
C0445247 (UMLS CUI [6,5])
C0237401 (UMLS CUI [6,6])
C1298908 (UMLS CUI [6,7])
C5552996 (UMLS CUI [6,8])
C5414521 (UMLS CUI [7,1])
C0750484 (UMLS CUI [7,2])
C1511518 (UMLS CUI [7,3])
C0025202 (UMLS CUI [7,4])
C0475358 (UMLS CUI [7,5])
C5414521 (UMLS CUI [8,1])
C0750484 (UMLS CUI [8,2])
C1707513 (UMLS CUI [8,3])
C0205307 (UMLS CUI [8,4])
C2347026 (UMLS CUI [8,5])
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