Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/34655
Title: LONG SPAN DNA PAIRED-END TAGS (DNA-PET) FOR UNRAVELING GENOMIC REARRANGEMENTS IN CANCER GENOMES
Authors: YAO FEI
Keywords: long span, DNA-PET, sequencing, structural variations, breast cancer, gastric cancer
Issue Date: 20-Dec-2011
Source: YAO FEI (2011-12-20). LONG SPAN DNA PAIRED-END TAGS (DNA-PET) FOR UNRAVELING GENOMIC REARRANGEMENTS IN CANCER GENOMES. ScholarBank@NUS Repository.
Abstract: All cancers are the result of changes that have occurred in the DNA sequence of the genomes of the cancer cells. Now, we are moving to the new era in which it is possible to get the complete DNA sequence of large number of cancer genomes with the help of the next generation sequencing technologies. In this study, by comparing the characteristics of the large insert libraries (10-20 kb) with short insert (1 kb) libraries, we show that large inserts are superior to short inserts in providing higher physical genome coverage and therefore achieve greater sensitivity for the identification of the different types of SVs, including copy number neutral and complex events. Applying the 10 kb DNA-PET technology to 15 cancer genomes, including both primary tumors and cancer cell lines, we show some important genomic characteristics in breast and gastric cancer genomes.
URI: http://scholarbank.nus.edu.sg/handle/10635/34655
Appears in Collections:Ph.D Theses (Open)

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Appendix Table 1. MCF7_SV.xls236 kBMicrosoft Excel

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Appendix Table 2. HCT116_SVs.xls135.5 kBMicrosoft Excel

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Appendix Table 3.K562_SVs.xls347.5 kBMicrosoft Excel

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Appendix Table 4. dPET clusters of 17 genomes.xls7.56 MBMicrosoft Excel

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Appendix Table 5. Amplified region in breast cancer genomes.xls190.5 kBMicrosoft Excel

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Appendix Table 6. Deleted region in breast cancer genomes.xls42.5 kBMicrosoft Excel

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Appendix Table 7. Amplified region in gastric cancer.xls79.5 kBMicrosoft Excel

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Appendix Table 8. Deleted region in gastric cancer.xls41 kBMicrosoft Excel

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Appendix Table 9. SVs obsered in 16-17 genomes.xls1.3 MBMicrosoft Excel

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Appendix Table 10. SVs sheared by 2-15 genomes.xls5.01 MBMicrosoft Excel

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Appendix Table 11. SVs unique to single genomes.xls2.91 MBMicrosoft Excel

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Appendix TablE 12. Potential recurrent events.xls26 kBMicrosoft Excel

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Appendix Table 13 . Sequence feature of confirmed breakpoints.xls139 kBMicrosoft Excel

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Appendix Table 14. Complex regions in cancer genomes.xls633 kBMicrosoft Excel

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HCT116 reconstruction.zip966.63 kBUnknown

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K562 reconstruction.zip1.33 MBUnknown

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MCF-7 reconstruction.zip1.36 MBUnknown

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YAOFei.pdf6.7 MBAdobe PDF

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