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

Subject ID, affection status, gender, age at biopsy and diagnosis, cancer stage of tumor, tumor characteristics, tumor treatment of participants with melanoma and involved in the "Melanoma Genome Sequencing Project" project.

5 forms  
pht002591
Description

pht002591

De-identified subject ID
Description

SUBJECT_ID

Data type

string

Alias
UMLS CUI [1,1]
C2348585
UMLS CUI [1,2]
C4684638
Gender of patient [Male, Female, Unknown]
Description

Gender

Data type

string

Alias
UMLS CUI [1,1]
C0079399
Participant's age at diagnosis [Unknown]
Description

Age at Diagnosis

Data type

text

Measurement units
  • years
Alias
UMLS CUI [1,1]
C1828181
years
Participant's age at time of biopsy used for current study [Unknown, Not reported]
Description

Age at Biopsy

Data type

text

Measurement units
  • years
Alias
UMLS CUI [1,1]
C0001779
UMLS CUI [1,2]
C0011008
UMLS CUI [1,3]
C0005558
years
Primary diagnosis of patient
Description

Primary Disease

Data type

string

Alias
UMLS CUI [1,1]
C0332137
Indicates whether patient was diagnosed for a primary melanoma prior to recurrence or metastasis [Yes, No, Unknown]
Description

Melanoma Primary Diagnosed

Data type

string

Alias
UMLS CUI [1,1]
C0011900
UMLS CUI [1,2]
C0025202
UMLS CUI [1,3]
C0332152
UMLS CUI [1,4]
C0027627
UMLS CUI [1,5]
C0521158
Body site of patient's primary melanoma [Skin, Acral, Occult, Mucosa, Other]
Description

Localization of Primary Melanoma

Data type

string

Alias
UMLS CUI [1,1]
C0449695
UMLS CUI [1,2]
C0025202
Body site, detailed, of patient's primary melanoma
Description

Sub-localization of Primary Melanoma

Data type

string

Alias
UMLS CUI [1,1]
C1522508
UMLS CUI [1,2]
C0449695
UMLS CUI [1,3]
C0025202
Indicates extent or severity of patient's disease at the time of diagnosis of their primary melanoma
Description

Tumor Stage at Time of Primary

Data type

string

Alias
UMLS CUI [1,1]
C0449279
UMLS CUI [1,2]
C0521117
UMLS CUI [1,3]
C2316983
UMLS CUI [1,4]
C0677930
UMLS CUI [1,5]
C0025202
Description of how deeply the primary melanoma invaded skin tissue by time of diagnosis, suggestive of prognosis
Description

Breslow's Depth of Primary Melanoma

Data type

float

Measurement units
  • mm
Alias
UMLS CUI [1,1]
C0678257
UMLS CUI [1,2]
C1275362
UMLS CUI [1,3]
C2316983
UMLS CUI [1,4]
C1705535
UMLS CUI [1,5]
C1287404
mm
Cancer stage of patient's primary melanoma as defined by the American Joint Committee on Cancer staging system
Description

AJCC Cancer Stage: Primary

Data type

string

Alias
UMLS CUI [1,1]
C0027646
UMLS CUI [1,2]
C0677930
UMLS CUI [1,3]
C0025202
UMLS CUI [1,4]
C1515946
UMLS CUI [1,5]
C0449394
Cancer stage of patient lymph nodes as the time of primary melanoma as defined by the American Joint Committee on Cancer staging system
Description

AJCC Cancer Stage: Regional Nodes at Time of Primary

Data type

string

Alias
UMLS CUI [1,1]
C0027646
UMLS CUI [1,2]
C0024204
UMLS CUI [1,3]
C0677930
UMLS CUI [1,4]
C0025202
UMLS CUI [1,5]
C1515946
UMLS CUI [1,6]
C0449394
Indicates whether patient received systemic therapy for their cancer, pre and post biopsy are indicated when known
Description

Systemic Therapy

Data type

string

Alias
UMLS CUI [1,1]
C1515119
UMLS CUI [1,2]
C0332152
UMLS CUI [1,3]
C0005558
UMLS CUI [2,1]
C1515119
UMLS CUI [2,2]
C0231290
UMLS CUI [2,3]
C0005558
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Similar models

Subject ID, affection status, gender, age at biopsy and diagnosis, cancer stage of tumor, tumor characteristics, tumor treatment of participants with melanoma and involved in the "Melanoma Genome Sequencing Project" project.

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht002591
SUBJECT_ID
Item
De-identified subject ID
string
C2348585 (UMLS CUI [1,1])
C4684638 (UMLS CUI [1,2])
Gender
Item
Gender of patient [Male, Female, Unknown]
string
C0079399 (UMLS CUI [1,1])
Age at Diagnosis
Item
Participant's age at diagnosis [Unknown]
text
C1828181 (UMLS CUI [1,1])
Age at Biopsy
Item
Participant's age at time of biopsy used for current study [Unknown, Not reported]
text
C0001779 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
C0005558 (UMLS CUI [1,3])
Primary Disease
Item
Primary diagnosis of patient
string
C0332137 (UMLS CUI [1,1])
Melanoma Primary Diagnosed
Item
Indicates whether patient was diagnosed for a primary melanoma prior to recurrence or metastasis [Yes, No, Unknown]
string
C0011900 (UMLS CUI [1,1])
C0025202 (UMLS CUI [1,2])
C0332152 (UMLS CUI [1,3])
C0027627 (UMLS CUI [1,4])
C0521158 (UMLS CUI [1,5])
Item
Body site of patient's primary melanoma [Skin, Acral, Occult, Mucosa, Other]
string
C0449695 (UMLS CUI [1,1])
C0025202 (UMLS CUI [1,2])
Localization of Primary Melanoma
Code List
Body site of patient's primary melanoma [Skin, Acral, Occult, Mucosa, Other]
CL Item
N/A (N/A)
CL Item
Unknown (Unknown)
Sub-localization of Primary Melanoma
Item
Body site, detailed, of patient's primary melanoma
string
C1522508 (UMLS CUI [1,1])
C0449695 (UMLS CUI [1,2])
C0025202 (UMLS CUI [1,3])
Tumor Stage at Time of Primary
Item
Indicates extent or severity of patient's disease at the time of diagnosis of their primary melanoma
string
C0449279 (UMLS CUI [1,1])
C0521117 (UMLS CUI [1,2])
C2316983 (UMLS CUI [1,3])
C0677930 (UMLS CUI [1,4])
C0025202 (UMLS CUI [1,5])
Breslow's Depth of Primary Melanoma
Item
Description of how deeply the primary melanoma invaded skin tissue by time of diagnosis, suggestive of prognosis
float
C0678257 (UMLS CUI [1,1])
C1275362 (UMLS CUI [1,2])
C2316983 (UMLS CUI [1,3])
C1705535 (UMLS CUI [1,4])
C1287404 (UMLS CUI [1,5])
AJCC Cancer Stage: Primary
Item
Cancer stage of patient's primary melanoma as defined by the American Joint Committee on Cancer staging system
string
C0027646 (UMLS CUI [1,1])
C0677930 (UMLS CUI [1,2])
C0025202 (UMLS CUI [1,3])
C1515946 (UMLS CUI [1,4])
C0449394 (UMLS CUI [1,5])
AJCC Cancer Stage: Regional Nodes at Time of Primary
Item
Cancer stage of patient lymph nodes as the time of primary melanoma as defined by the American Joint Committee on Cancer staging system
string
C0027646 (UMLS CUI [1,1])
C0024204 (UMLS CUI [1,2])
C0677930 (UMLS CUI [1,3])
C0025202 (UMLS CUI [1,4])
C1515946 (UMLS CUI [1,5])
C0449394 (UMLS CUI [1,6])
Systemic Therapy
Item
Indicates whether patient received systemic therapy for their cancer, pre and post biopsy are indicated when known
string
C1515119 (UMLS CUI [1,1])
C0332152 (UMLS CUI [1,2])
C0005558 (UMLS CUI [1,3])
C1515119 (UMLS CUI [2,1])
C0231290 (UMLS CUI [2,2])
C0005558 (UMLS CUI [2,3])
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