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45778
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Principal Investigator: Elaine A Ostrander, PhD, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001105 We collected DNA from fresh frozen prostate tumor samples and matched peripheral blood from 10 subjects with aggressive, Gleason score ≥8 disease. Tumor and normal samples were sequenced on the Illumina HiSeq 2000 to mean depths of 95.3X and 48.3X, respectively.
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- 20-06-23 20-06-23 - Chiara Middel
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Elaine A Ostrander, PhD, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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20 juni 2023
DOI
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Creative Commons BY 4.0
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dbGaP phs001105 NHGRI-Mayo Clinic Whole Genome Sequencing of Aggressive Prostate Tumors
This subject phenotype table contains subject IDs, family history of prostate cancer, ages at diagnosis and at surgery, prostate specific antigen (PSA) at diagnosis, treatment prior to surgey, lymphadenectomy, pathology Gleason score, pathology primary and secondary Gleason grades, total number of lymph nodes examined, number of positive lymph nodes, and estimated tumor volume (cc).
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and affection status of the subject for prostate tumor.
- This data table contains a 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 sample aliases and sample use.
- This subject phenotype table contains subject IDs, family history of prostate cancer, ages at diagnosis and at surgery, prostate specific antigen (PSA) at diagnosis, treatment prior to surgey, lymphadenectomy, pathology Gleason score, pathology primary and secondary Gleason grades, total number of lymph nodes examined, number of positive lymph nodes, and estimated tumor volume (cc).
- This sample attributes table contains sample IDs, analyte type, body site where sample was collected, tumor status, primary metastatic tumor, primary tumor location, DNA isolation method, sequencing platform, chemistry version, and name of the center which conducted genotyping.
Similar models
This subject phenotype table contains subject IDs, family history of prostate cancer, ages at diagnosis and at surgery, prostate specific antigen (PSA) at diagnosis, treatment prior to surgey, lymphadenectomy, pathology Gleason score, pathology primary and secondary Gleason grades, total number of lymph nodes examined, number of positive lymph nodes, and estimated tumor volume (cc).
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and affection status of the subject for prostate tumor.
- This data table contains a 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 sample aliases and sample use.
- This subject phenotype table contains subject IDs, family history of prostate cancer, ages at diagnosis and at surgery, prostate specific antigen (PSA) at diagnosis, treatment prior to surgey, lymphadenectomy, pathology Gleason score, pathology primary and secondary Gleason grades, total number of lymph nodes examined, number of positive lymph nodes, and estimated tumor volume (cc).
- This sample attributes table contains sample IDs, analyte type, body site where sample was collected, tumor status, primary metastatic tumor, primary tumor location, DNA isolation method, sequencing platform, chemistry version, and name of the center which conducted genotyping.
Name
Type
Description | Question | Decode (Coded Value)
Datatype
Alias
SUBJECT_ID
Item
Subject ID
string
C2348585 (UMLS CUI [1,1])
Item
Family History of Prostate Cancer
text
C0241889 (UMLS CUI [1,1])
C0600139 (UMLS CUI [1,2])
C0600139 (UMLS CUI [1,2])
CL Item
family history of prostate cancer (Yes)
Age at diagnosis
Item
Age at Diagnosis
text
C1828181 (UMLS CUI [1,1])
PSA at Daignosis (or closest)
Item
Earliest prostate specific antigen (PSA)
float
C1279919 (UMLS CUI [1,1])
C0201544 (UMLS CUI [1,2])
C0201544 (UMLS CUI [1,2])
Item
Treatment Before Sample Collection
text
C0087111 (UMLS CUI [1,1])
C0332152 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
C0332152 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])
CL Item
No treatment prior to sample collection (No)
Age at Surgery
Item
Age at Surgery
text
C0001779 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
C0543467 (UMLS CUI [1,3])
C0011008 (UMLS CUI [1,2])
C0543467 (UMLS CUI [1,3])
CL Item
Lymphadenectomy was performed (Yes)
Path Gleason Score
Item
Path Gleason Score
text
C3203027 (UMLS CUI [1,1])
C1521733 (UMLS CUI [1,2])
C0243095 (UMLS CUI [1,3])
C1521733 (UMLS CUI [1,2])
C0243095 (UMLS CUI [1,3])
Path Primary Gleason Grade
Item
Path Primary Gleason Grade
text
C0205225 (UMLS CUI [1,1])
C3203027 (UMLS CUI [1,2])
C1521733 (UMLS CUI [1,3])
C0243095 (UMLS CUI [1,4])
C3203027 (UMLS CUI [1,2])
C1521733 (UMLS CUI [1,3])
C0243095 (UMLS CUI [1,4])
Path Secondary Gleason Grade
Item
Path Secondary Gleason Grade
text
C1273605 (UMLS CUI [1,1])
C1521733 (UMLS CUI [1,2])
C0243095 (UMLS CUI [1,3])
C1521733 (UMLS CUI [1,2])
C0243095 (UMLS CUI [1,3])
Total # L. Nodes Exam
Item
Total # L. Nodes Exam
text
C0439810 (UMLS CUI [1,1])
C0750480 (UMLS CUI [1,2])
C0332128 (UMLS CUI [1,3])
C0024204 (UMLS CUI [1,4])
C0750480 (UMLS CUI [1,2])
C0332128 (UMLS CUI [1,3])
C0024204 (UMLS CUI [1,4])
# Pos. L. Nodes
Item
# Pos. L. Nodes
text
C1446409 (UMLS CUI [1,1])
C0024204 (UMLS CUI [1,2])
C0750480 (UMLS CUI [1,3])
C0024204 (UMLS CUI [1,2])
C0750480 (UMLS CUI [1,3])
Est. Tumor vol(cc)
Item
Est. Tumor vol. (cc)
float
C0750572 (UMLS CUI [1,1])
C0475276 (UMLS CUI [1,2])
C0475276 (UMLS CUI [1,2])
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