Mutational Profiling of a Long--term Surviving Stage Ⅲ Colorectal cancer Patient Using High Throughput Next--Generation Sequencing

目录

声明

ACKNOWLEDGEMENTS

ABSTRACT

摘要

TABLE OF CoNTENTS

LIST OF FIGURES

LIST OF TABLES

LIST OF ABBREVIAIATIONS

CHAPTER 1

1． Introduction

1．1 Risk factors of colorectal cancer

1．2 Colorectal cancer Diagnosis and Staging

1．3 Tumor staging

1．4 Colorectal cancer Symptoms

1．5 Management of colorectal cancer

1．6 Next-Generation Sequencing Technology

1．7 NGS Applications in Cancer Research

1．8 Dissertation outline

CHAPTER 2

2．1 Study Samples

2．2 DNA extraction and library preparation

2．3 Whole genome sequencing

2．4 Bioinformatics analysis

2．4．1 Mapping

2．4．2 Marking of reads duplicates

2．4．3 Local realignment and base quality score recalibration

2．4．4 Germline variants detection

2．4．5 Somatic variants detection

2．4．6 AnnotatiOIlS

2．4．7 Copy number alternation and structural variation analysis

2．4．8 Evaluation of somatic mutational signatures

2．5 Mutation significance Analysis

2．6 Gene Ontology Enrichment analysis

2．TCGA analysis

CHAPTER 3

3．1 Tumor purity and coverage statistics

3．2 Germline mutations

3．3 Somatic mutations

3．4 Mutational signatures in the patient

3．5 Structural variation and copy number alternation analysis

3．6 Gene Ontology enrichment

3．7 Comparison of patient data with TCGA

3．8 Discussion

CHAPTER 4

4．1 Conclusions

4．2 Future perspectives

References

Publications