ID
45828
Description
Principal Investigator: Brock A. Peters, PhD, Complete Genomics, Inc. Mountain View, CA, USA MeSH: Breast Neoplasms,Neoplasm Metastasis,Carcinoma, Lobular https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001028 Circulating tumor cells (CTCs) are considered to be informative non-invasive biopsy for the early detection, diagnosis or therapy guidance of cancer. CTCs also contain most of the heterogeneity found across multiple metastatic sites. In this study, we combine recently improved CTC isolation methods, resulting in almost pure CTCs, with advanced whole genome sequencing (WGS) based on Long Fragment Read (LFR) technology to demonstrate, for the first time, the research and clinical utility of an accurate, comprehensive, phased, and quantitative genomic analysis of CTCs. In particular, genomes of 34 CTCs, collected at two different time points from a patient whose metastatic breast cancer ultimately became resistant to standard treatments, were analyzed as 3072 barcoded sub-genomic compartments of long DNA. An average read coverage of 23X per cell enabled the high-resolution detection of somatic variants, cancer copy number variations (CNVs) and structural variants, including 133 CNVs shorter than 1Mb and an early chromothripsis-like event.
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Versions (1)
- 7/29/23 7/29/23 - Simon Heim
Copyright Holder
Brock A. Peters, PhD, Complete Genomics, Inc. Mountain View, CA, USA
Uploaded on
July 29, 2023
DOI
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License
Creative Commons BY 4.0
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dbGaP phs001028 Complete Genomics Deep Whole-Genome Sequencing of Circulating Tumor Cells
This sample attributes table contains de-identified sample ID, body site where sample was collected, analyte type, tumor status, histological type and names of the center which conducted genotyping and sequencing.
- StudyEvent: SEV1
- The subject consent file includes subject IDs, consent information and case control status for circulating tumor cells.
- This subject sample mapping 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 de-identified subject ID, sex and age of the subject.
- This sample attributes table contains de-identified sample ID, body site where sample was collected, analyte type, tumor status, histological type and names of the center which conducted genotyping and sequencing.
Similar models
This sample attributes table contains de-identified sample ID, body site where sample was collected, analyte type, tumor status, histological type and names of the center which conducted genotyping and sequencing.
- StudyEvent: SEV1
- The subject consent file includes subject IDs, consent information and case control status for circulating tumor cells.
- This subject sample mapping 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 de-identified subject ID, sex and age of the subject.
- This sample attributes table contains de-identified sample ID, body site where sample was collected, analyte type, tumor status, histological type and names of the center which conducted genotyping and sequencing.
C1299222 (UMLS CUI [1,2])
C1518422 (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])
C5575037 (UMLS CUI [1,2])
C1285573 (UMLS CUI [1,3])
C5575037 (UMLS CUI [1,2])
C3640076 (UMLS CUI [1,3])
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