ID

45530

Description

Principal Investigator: Priscilla Brastianos, Broad Institute, Cambridge, MA, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000730 Brain metastases are the most frequently occurring intracranial tumors in adults. Median survival after the diagnosis of a brain metastasis is in the order of a few months. Despite its large burden of disease and devastating clinical sequelae, we continue to have a limited understanding of the molecular mechanisms driving brain metastasis. We subjected 86 trios consisting of primary tumor, brain metastasis, and matched normal tissue to whole exome sequencing (WES). To analyze the data, we developed novel computational tools to perform an integrative analysis of somatic single nucleotide variants (SSNVs) and somatic copy-number alterations (SCNAs). This analysis allowed us to estimate the clonal architecture of the primary and metastatic samples of each patient, and to reconstruct a phylogenetic tree relating all of the subclones.

Link

dbGaP study = phs000730

Keywords

Versions (1)
  1. 12/28/22 12/28/22 - Simon Heim
Copyright Holder

Priscilla Brastianos, Broad Institute, Cambridge, MA, USA

Uploaded on

December 28, 2022

DOI

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License

Creative Commons BY 4.0
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dbGaP phs000730 Genomics of Brain Metastases

English

The dataset includes variables that describe e.g. location of tumor sites (primary, metastases), treatments, age of diagnosis, survival time, and participants' gender.

4 forms  
pht005060
Description

pht005060

Alias
UMLS CUI [1,1]
C3846158
Unique Participant Identifier
Description

SUBJID

Data type

string

Alias
UMLS CUI [1,1]
C2348585
Participant's gender as Male or Female
Description

Gender

Data type

string

Alias
UMLS CUI [1,1]
C0079399
Primary site of patient tumor
Description

Primary Site

Data type

string

Alias
UMLS CUI [1,1]
C0205225
UMLS CUI [1,2]
C0475445
Histology of Primary Tumor
Description

Histology group

Data type

string

Alias
UMLS CUI [1,1]
C0449574
UMLS CUI [1,2]
C0677930
Age of Diagnosis of Primary Tumor
Description

Diagnosis Age

Data type

string

Measurement units
  • Years
Alias
UMLS CUI [1,1]
C0677930
UMLS CUI [1,2]
C1828181
Years
Anti-HER2 treatment prior to brain metastasis (if breast cancer)
Description

HER2-prior

Data type

text

Alias
UMLS CUI [1,1]
C4722434
UMLS CUI [1,2]
C0332152
UMLS CUI [1,3]
C0220650
UMLS CUI [1,4]
C0006142
Clinical HER2 status of primary (if breast cancer)
Description

HER2-primary

Data type

text

Alias
UMLS CUI [1,1]
C0205210
UMLS CUI [1,2]
C1512413
UMLS CUI [1,3]
C0677930
UMLS CUI [1,4]
C0006142
Clinical HER2 status of metastasis (if breast cancer)
Description

HER2-met

Data type

text

Alias
UMLS CUI [1,1]
C0205210
UMLS CUI [1,2]
C1512413
UMLS CUI [1,3]
C0027627
UMLS CUI [1,4]
C0006142
Triple-negative primary (if breast cancer)
Description

Triple-Neq

Data type

text

Alias
UMLS CUI [1,1]
C3539878
UMLS CUI [1,2]
C1306459
Brain Metastasis Progression-Free Survival (years): Time elapsed from time of primary diagnosis to diagnosis of sequenced brain metastasis
Description

BM-PFS

Data type

string

Measurement units
  • Years
Alias
UMLS CUI [1,1]
C0220650
UMLS CUI [1,2]
C0242792
UMLS CUI [1,3]
C0872291
UMLS CUI [1,4]
C1442880
UMLS CUI [1,5]
C0677930
UMLS CUI [1,6]
C0011900
UMLS CUI [1,7]
C0220650
Years
Radiation prior to diagnosis of brain metastasis
Description

Radiation-prior

Data type

text

Alias
UMLS CUI [1,1]
C0220650
UMLS CUI [1,2]
C0851346
UMLS CUI [1,3]
C0332152
UMLS CUI [1,4]
C0011900
Smoking history
Description

Smoking

Data type

text

Alias
UMLS CUI [1,1]
C1519384
Other brain metastases
Description

Other-Brain

Data type

text

Alias
UMLS CUI [1,1]
C0205394
UMLS CUI [1,2]
C0220650
Other metastatic sites
Description

Other-Sites

Data type

text

Alias
UMLS CUI [1,1]
C0205394
UMLS CUI [1,2]
C0027627
UMLS CUI [1,3]
C1515974
Number of systemic treatment regimens prior to brain metastasis
Description

Treatments

Data type

text

Alias
UMLS CUI [1,1]
C1514463
UMLS CUI [1,2]
C0220650
UMLS CUI [1,3]
C5237812
UMLS CUI [1,4]
C5392213
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Similar models

The dataset includes variables that describe e.g. location of tumor sites (primary, metastases), treatments, age of diagnosis, survival time, and participants' gender.

4 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
pht005060
C3846158 (UMLS CUI [1,1])
SUBJID
Item
Unique Participant Identifier
string
C2348585 (UMLS CUI [1,1])
Gender
Item
Participant's gender as Male or Female
string
C0079399 (UMLS CUI [1,1])
Primary Site
Item
Primary site of patient tumor
string
C0205225 (UMLS CUI [1,1])
C0475445 (UMLS CUI [1,2])
Histology group
Item
Histology of Primary Tumor
string
C0449574 (UMLS CUI [1,1])
C0677930 (UMLS CUI [1,2])
Diagnosis Age
Item
Age of Diagnosis of Primary Tumor
string
C0677930 (UMLS CUI [1,1])
C1828181 (UMLS CUI [1,2])
Item
Anti-HER2 treatment prior to brain metastasis (if breast cancer)
text
C4722434 (UMLS CUI [1,1])
C0332152 (UMLS CUI [1,2])
C0220650 (UMLS CUI [1,3])
C0006142 (UMLS CUI [1,4])
HER2-prior
Code List
Anti-HER2 treatment prior to brain metastasis (if breast cancer)
CL Item
Untreated (0)
CL Item
Treated (1)
CL Item
Not Reported (Not Reported)
Item
Clinical HER2 status of primary (if breast cancer)
text
C0205210 (UMLS CUI [1,1])
C1512413 (UMLS CUI [1,2])
C0677930 (UMLS CUI [1,3])
C0006142 (UMLS CUI [1,4])
HER2-primary
Code List
Clinical HER2 status of primary (if breast cancer)
CL Item
Untreated (0)
CL Item
Treated (1)
CL Item
Not Reported (Not Reported)
Item
Clinical HER2 status of metastasis (if breast cancer)
text
C0205210 (UMLS CUI [1,1])
C1512413 (UMLS CUI [1,2])
C0027627 (UMLS CUI [1,3])
C0006142 (UMLS CUI [1,4])
HER2-met
Code List
Clinical HER2 status of metastasis (if breast cancer)
CL Item
Untreated (0)
CL Item
Treated (1)
CL Item
Not Available (NA)
Item
Triple-negative primary (if breast cancer)
text
C3539878 (UMLS CUI [1,1])
C1306459 (UMLS CUI [1,2])
Triple-Neq
Code List
Triple-negative primary (if breast cancer)
CL Item
No (0)
CL Item
Yes (1)
CL Item
Not Reported (Not Reported)
BM-PFS
Item
Brain Metastasis Progression-Free Survival (years): Time elapsed from time of primary diagnosis to diagnosis of sequenced brain metastasis
string
C0220650 (UMLS CUI [1,1])
C0242792 (UMLS CUI [1,2])
C0872291 (UMLS CUI [1,3])
C1442880 (UMLS CUI [1,4])
C0677930 (UMLS CUI [1,5])
C0011900 (UMLS CUI [1,6])
C0220650 (UMLS CUI [1,7])
Item
Radiation prior to diagnosis of brain metastasis
text
C0220650 (UMLS CUI [1,1])
C0851346 (UMLS CUI [1,2])
C0332152 (UMLS CUI [1,3])
C0011900 (UMLS CUI [1,4])
Radiation-prior
Code List
Radiation prior to diagnosis of brain metastasis
CL Item
Untreated (0)
CL Item
Treated (1)
Item
Smoking history
text
C1519384 (UMLS CUI [1,1])
Smoking
Code List
Smoking history
CL Item
No (0)
CL Item
Yes (1)
Item
Other brain metastases
text
C0205394 (UMLS CUI [1,1])
C0220650 (UMLS CUI [1,2])
Other-Brain
Code List
Other brain metastases
CL Item
No (0)
CL Item
Yes (1)
Item
Other metastatic sites
text
C0205394 (UMLS CUI [1,1])
C0027627 (UMLS CUI [1,2])
C1515974 (UMLS CUI [1,3])
Other-Sites
Code List
Other metastatic sites
CL Item
No (0)
CL Item
Yes (1)
Treatments
Item
Number of systemic treatment regimens prior to brain metastasis
text
C1514463 (UMLS CUI [1,1])
C0220650 (UMLS CUI [1,2])
C5237812 (UMLS CUI [1,3])
C5392213 (UMLS CUI [1,4])
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