ID
45776
Descrição
Principal Investigator: Paul Spellman, PhD, Oregon Health and Science University, Portland, OR, USA MeSH: von Hippel-Lindau Disease https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001107 Patients affected with von Hippel-Lindau disease are at risk of developing multiple independent clear cell renal carcinomas. This study performed whole genome sequencing on 40 tumors from 6 VHL patients to compare somatic variation patterns within and between patients. Although tumors from the same patient showed many differences, within-patient patterns were discernible. Single-nucleotide substitution type rates were significantly different between patients and showed biases in trinucleotide mutation context. We also observed biases in chromosome copy number aberrations. These results show that genetic background and/or environment can influence the types of mutations that occur.
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Versões (1)
- 20/06/2023 20/06/2023 - Chiara Middel
Titular dos direitos
Paul Spellman, PhD, Oregon Health and Science University, Portland, OR, USA
Transferido a
20 de junho de 2023
DOI
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Licença
Creative Commons BY 4.0
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dbGaP phs001107 Patient-Specific Factors Influence Somatic Variations in VHL Tumors
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and renal tumor case control status of the subject. All subjects are VHL patients.
- 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, sex, age, germline VHL mutation, known other kidney surgeries, self-reported smoking habits, estimated lifetime smoking exposure rank, BMI of the subject, number of tumors/cysts sequenced in this study, and whether or not an adjacent normal kidney sample was also sequenced .
- This sample attributes table contains sample IDs, manuscript patient IDs, sample type, sequencing WGS coverage, estimated tumor purity using method outlined in publication, shorthand sample ID used in publication text and figures, tumor location and measurements (n=4 variables; length, width, depth and Fuhrman grade) , name of the center which conducted sequencing, and analyte type.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and renal tumor case control status of the subject. All subjects are VHL patients.
- 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, sex, age, germline VHL mutation, known other kidney surgeries, self-reported smoking habits, estimated lifetime smoking exposure rank, BMI of the subject, number of tumors/cysts sequenced in this study, and whether or not an adjacent normal kidney sample was also sequenced .
- This sample attributes table contains sample IDs, manuscript patient IDs, sample type, sequencing WGS coverage, estimated tumor purity using method outlined in publication, shorthand sample ID used in publication text and figures, tumor location and measurements (n=4 variables; length, width, depth and Fuhrman grade) , name of the center which conducted sequencing, and analyte type.
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