ID
45421
Description
Principal Investigator: Winnie S. Liang, PhD, Translational Genomics Research Institute, Phoenix, AZ, USA MeSH: Chromosome Breakpoints,Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000646 In this study, we hypothesize that shallow long insert whole genome sequencing (LI-WGS) increases our power for detecting breakpoints compared to shallow short insert WGS. We performed a priori analyses to demonstrate the benefits of LI-WGS, developed a long insert library preparation protocol based off Illumina's protocol, and compared LI-WGS against short insert WGS on test samples. We then used long insert WGS to identify translocations and copy number changes in tumor and germline samples collected from cancer patients with different malignancies.
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Versions (1)
- 11/25/22 11/25/22 - Chiara Middel
Copyright Holder
Winnie S. Liang, PhD, Translational Genomics Research Institute, Phoenix, AZ, USA
Uploaded on
November 25, 2022
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License
Creative Commons BY 4.0
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dbGaP phs000646 Breakpoint Detection Using Long Insert Whole Genome Sequencing
This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, and primary tumor location.
- StudyEvent: SEV1
- This data table contains subject IDs, consent group, and research type.
- This data table contains 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 includes age at biopsy and sex.
- This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, and primary tumor location.
Similar models
This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, and primary tumor location.
- StudyEvent: SEV1
- This data table contains subject IDs, consent group, and research type.
- This data table contains 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 includes age at biopsy and sex.
- This sample attributes table includes body site where sample was extracted, analyte type, histological type, tumor status, and primary tumor location.
C1299222 (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 [2,1])
C0007601 (UMLS CUI [3,1])
C1515974 (UMLS CUI [1,2])