ID
45702
Description
Principal Investigator: Todd Fehniger, MD, PhD, Washington University School of Medicine, St Louis, MO, USA MeSH: Lymphoma, Follicular https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001229 We performed exome sequencing of tumor (lymph node) and normal (skin) frozen tissue pairs from 24 patients in a discovery cohort with untreated follicular lymphoma (FL), relapsed FL, or transformed FL/iNHL (indolent non-Hodgkin lymphoma). From 24 patients, 28 tumor samples were exome sequenced including 1 patient with both untreated and relapse samples and 3 patients with samples derived from both bulk lymph node and following flow-sorting to purify light chain-restricted CD19+ lymphoma cells. We developed a custom capture assay (NimbleGen) that targets 7.05 MB corresponding to the exons and splice sites of 1716 genes (WUSM-LP). The custom capture genes included somatic nucleotide variants (SNVs) identified in our exome discovery cohort (898 genes) or SNVs previously published to be recurrently mutated in B cell NHL (818 genes). This custom capture reagent was used to sequence additional FFPE samples (and corresponding normal tissue, when available) from patients with follicular lymphoma. This approach was used to identify recurrently mutated genes in pathways in FL.
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Versions (1)
- 14/05/2023 14/05/2023 - Chiara Middel
Détendeur de droits
Todd Fehniger, MD, PhD, Washington University School of Medicine, St Louis, MO, USA
Téléchargé le
14 mai 2023
DOI
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Licence
Creative Commons BY 4.0
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dbGaP phs001229 Sequencing Follicular Lymphoma
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and affection status of the subject for lymphoma.
- 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 use.
- This subject phenotype table contains subject ID, gender, non-hodgkin lymphoma type, age at diagnosis, grade of biopsy sequenced, lymphoma stage, nodal sites, LDH, hemoglobin, ECOG performance status score, prognostic index score, and sequencing cohort.
- This sample attributes table contains sample ID, sample name, histological type, analyte type, body site where sample was collected, tumor status, tissue type, and capture type.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and affection status of the subject for lymphoma.
- 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 use.
- This subject phenotype table contains subject ID, gender, non-hodgkin lymphoma type, age at diagnosis, grade of biopsy sequenced, lymphoma stage, nodal sites, LDH, hemoglobin, ECOG performance status score, prognostic index score, and sequencing cohort.
- This sample attributes table contains sample ID, sample name, histological type, analyte type, body site where sample was collected, tumor status, tissue type, and capture type.
C0680251 (UMLS CUI [1,2])
C0021430 (UMLS CUI [1,2])
C1524063 (UMLS CUI [1,3])
C0370003 (UMLS CUI [1,4])
C1512693 (UMLS CUI [2,1])
C0470187 (UMLS CUI [2,2])
C0184921 (UMLS CUI [2,3])
C0200345 (UMLS CUI [3,1])
C1518371 (UMLS CUI [3,2])
C0870078 (UMLS CUI [3,3])
C1521733 (UMLS CUI [4,1])
C1704362 (UMLS CUI [4,2])
C4039816 (UMLS CUI [4,3])
C0024204 (UMLS CUI [4,4])
C0750484 (UMLS CUI [4,5])
C0011900 (UMLS CUI [4,6])
C0006826 (UMLS CUI [4,7])
C0007634 (UMLS CUI [4,8])
C0456205 (UMLS CUI [4,9])
C1524063 (UMLS CUI [5,1])
C4039816 (UMLS CUI [5,2])
C0205409 (UMLS CUI [5,3])
C0887950 (UMLS CUI [5,4])
C0012854 (UMLS CUI [5,5])
C1698493 (UMLS CUI [6,1])
C4288191 (UMLS CUI [6,2])
C0803951 (UMLS CUI [6,3])
C3846158 (UMLS CUI [6,4])
C1524062 (UMLS CUI [7,1])
C1328887 (UMLS CUI [7,2])
C1269815 (UMLS CUI [7,3])
C0024301 (UMLS CUI [7,4])
C1512693 (UMLS CUI [8,1])
C0470187 (UMLS CUI [8,2])
C4039816 (UMLS CUI [8,3])
C0184921 (UMLS CUI [8,4])
C0205210 (UMLS CUI [8,5])
C1533716 (UMLS CUI [8,6])
C0205265 (UMLS CUI [8,7])
C0087111 (UMLS CUI [8,8])
C1522577 (UMLS CUI [8,9])
C1704362 (UMLS CUI [9,1])
C4039816 (UMLS CUI [9,2])
C0750484 (UMLS CUI [9,3])
C0011900 (UMLS CUI [9,4])
C1708936 (UMLS CUI [9,5])
C0205145 (UMLS CUI [9,6])
C0006826 (UMLS CUI [9,7])