ID
45616
Description
Principal Investigator: Hanlee Ji, MD, Stanford University School of Medicine, Stanford, CA, USA MeSH: Stomach Neoplasms,Krukenberg Tumor https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001362 In this study, linked read sequencing was performed on two ovarian metastases and matched normal tissue, from a patient with primary diffuse gastric cancer. Linked read sequencing is a DNA preparation technology whereby high molecular weight molecules of DNA are uniquely barcoded prior to fragmentation and sequencing, thus retaining information about genomic contiguity. This study performed an extended analysis of linked read sequencing data to resolve the complex structures of structural variants in the cancer genomes. Complex structural rearrangements were identified in the genomic region surrounding the known oncogene FGFR2, and the association between FGFR2 and gastric cancer metastasis was demonstrated in an organoid model.
Link
Keywords
Versions (1)
- 2/26/23 2/26/23 - Simon Heim
Copyright Holder
Hanlee Ji, MD, Stanford University School of Medicine, Stanford, CA, USA
Uploaded on
February 26, 2023
DOI
To request one please log in.
License
Creative Commons BY 4.0
Model comments :
You can comment on the data model here. Via the speech bubbles at the itemgroups and items you can add comments to those specificially.
Itemgroup comments for :
Item comments for :
In order to download data models you must be logged in. Please log in or register for free.
dbGaP phs001362 Linked Read Sequencing of Gastric Cancer Metastases
This sample attributes table contains sample ID, body site where tumor sample was collected, analyte type, tumor status, histological type, and primary tumor or metastasis.
- StudyEvent: SEV1
- The subject consent file includes subject IDs, consent information, and affection status of the subject for gastric cancer.
- 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, sex, age of onset, and race.
- This sample attributes table contains sample ID, body site where tumor sample was collected, analyte type, tumor status, histological type, and primary tumor or metastasis.
Similar models
This sample attributes table contains sample ID, body site where tumor sample was collected, analyte type, tumor status, histological type, and primary tumor or metastasis.
- StudyEvent: SEV1
- The subject consent file includes subject IDs, consent information, and affection status of the subject for gastric cancer.
- 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, sex, age of onset, and race.
- This sample attributes table contains sample ID, body site where tumor sample was collected, analyte type, tumor status, histological type, and primary tumor or metastasis.
C1299222 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,2])
C0007634 (UMLS CUI [1,2])
C0332307 (UMLS CUI [1,3])
C2347026 (UMLS CUI [2,1])
C0007634 (UMLS CUI [2,2])
C0449560 (UMLS CUI [2,3])
C1292533 (UMLS CUI [3,1])
C0332307 (UMLS CUI [3,2])
C1292533 (UMLS CUI [4,1])
C0449560 (UMLS CUI [4,2])
C0027627 (UMLS CUI [1,2])