Information:
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ID
45297
Description
Principal Investigator: James Brugarolas, MD, PhD, UT Southwestern Medical Center, Dallas, TX, USA MeSH: Carcinoma, Renal Cell,Urogenital Neoplasms,Urologic Diseases https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000491 Study to evaluate the molecular genetics of ccRCC through integrative analyses of tumors and tumorgrafts using multiple platforms in clinically annotated samples. Genome and exome data for patients giving consent to have the information available on a public, secure, database is being submitted.
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Keywords
Versions (2)
- 10/15/22 10/15/22 - Chiara Middel
- 10/17/22 10/17/22 - Dr. Christian Niklas
Copyright Holder
James Brugarolas, MD, PhD, UT Southwestern Medical Center, Dallas, TX, USA
Uploaded on
October 17, 2022
DOI
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License
Creative Commons BY 4.0
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dbGaP phs000491 Whole-Genome and Exome Sequencing in Clear-Cell Renal Cell Carcinoma
The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type and histological type. Tumor samples have further information relating to the stage, grade, location, and if tumor sample was primary or metastatic.
- StudyEvent: SEV1
- This data table contains subject IDs, consent group information and affection status.
- The data table contains mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases and sample use (SNP_Array, WES_SRA, WGS_SRA, and totRNA_Expression).
- The subject phenotype data table includes sociodemography variables (n=2; age and race), disease status (n=2; disease and onset age), tumor stage and grade (n=3), and presence or absence of somatic mutations (n=3; BAP1, PBRM1, VHL).
- The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type and histological type. Tumor samples have further information relating to the stage, grade, location, and if tumor sample was primary or metastatic.
- The data table contains a mapping of sample IDs to GEO accessions.
Similar models
The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type and histological type. Tumor samples have further information relating to the stage, grade, location, and if tumor sample was primary or metastatic.
- StudyEvent: SEV1
- This data table contains subject IDs, consent group information and affection status.
- The data table contains mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes a mapping of sample IDs to other sample ID aliases and sample use (SNP_Array, WES_SRA, WGS_SRA, and totRNA_Expression).
- The subject phenotype data table includes sociodemography variables (n=2; age and race), disease status (n=2; disease and onset age), tumor stage and grade (n=3), and presence or absence of somatic mutations (n=3; BAP1, PBRM1, VHL).
- The sample attributes data table includes sample type, body site where sample was extracted, sample analyte type and histological type. Tumor samples have further information relating to the stage, grade, location, and if tumor sample was primary or metastatic.
- The data table contains a mapping of sample IDs to GEO accessions.
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
SAMPID
Item
De-identified Sample ID
string
C4684638 (UMLS CUI [1,1])
C1299222 (UMLS CUI [1,2])
C1299222 (UMLS CUI [1,2])
BODY_SITE
Item
Body site where sample was collected
string
C1515974 (UMLS CUI [1,1])
C0200345 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,2])
ANALYTE_TYPE
Item
Analyte Type
string
C4744818 (UMLS CUI [1,1])
CL Item
Is not a tumor (N)
CL Item
Is Tumor (Y)
HISTOLOGICAL_TYPE
Item
Cell or tissue type or subtype of sample
string
C0449475 (UMLS CUI [1,1])
C2713035 (UMLS CUI [1,2])
C0449560 (UMLS CUI [1,3])
C2713035 (UMLS CUI [1,2])
C0449560 (UMLS CUI [1,3])
PRIMARY_METASTATIC_TUMOR
Item
Primary tumor, metastasis, or transformed cell line
string
C0677930 (UMLS CUI [1,1])
C0027627 (UMLS CUI [1,2])
C0007601 (UMLS CUI [1,3])
C0027627 (UMLS CUI [1,2])
C0007601 (UMLS CUI [1,3])
PRIMARY_TUMOR_LOCATION
Item
Primary tumor location
string
C0677930 (UMLS CUI [1,1])
TUMOR_STAGE
Item
Tumor stage of sample
string
C1300072 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,2])
TUMOR_GRADE
Item
Tumor grade of sample
string
C0919553 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,2])
TUMOR_TREATMENT
Item
Type of tumor treatment for sample
string
C0332307 (UMLS CUI [1,1])
C0003392 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,3])
C0003392 (UMLS CUI [1,2])
C2347026 (UMLS CUI [1,3])