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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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 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).
- 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 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).
- 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
SUBJID
Item
Subject ID
string
C2348585 (UMLS CUI [1,1])
SAMPID
Item
Sample ID
string
C1299222 (UMLS CUI [1,1])
SAMPLE_USE
Item
Sample Use. SNP_Array: SNP genotypes obtained using standard or custom microarrays; WES_SRA: Whole exome sequencing data available through SRA; WGS_SRA: Whole genome sequencing data available through SRA; totRNA_Expression: Expression data for total RNA sample (array data)
text
C1524063 (UMLS CUI [1,1])
C2347026 (UMLS CUI [1,2])
C0752046 (UMLS CUI [2,1])
C0017431 (UMLS CUI [2,2])
C3640076 (UMLS CUI [3,1])
C0035668 (UMLS CUI [4,1])
C0017262 (UMLS CUI [4,2])
C1511726 (UMLS CUI [4,3])
C2347026 (UMLS CUI [1,2])
C0752046 (UMLS CUI [2,1])
C0017431 (UMLS CUI [2,2])
C3640076 (UMLS CUI [3,1])
C0035668 (UMLS CUI [4,1])
C0017262 (UMLS CUI [4,2])
C1511726 (UMLS CUI [4,3])