A method to screen gene variations that are associated with familial cancers based on the next generation exome sequencing data

• Main Authors: Kai-Ming Chou, 周楷茗
• Other Authors: Ueng-Cheng Yang
• Format: Others
• Language: zh-TW
• Published: 2013
• Online Access: http://ndltd.ncl.edu.tw/handle/24640394375292814085

碩士 === 國立陽明大學 === 生物醫學資訊研究所 === 101 === In this study, I took advantage of exome sequencing technology to determine genetic variants that would cause hereditary cancers. The methods used in this study have three parts: preprocessing (mapping and quality assessment), filtering and consequence prediction. For preprocessing, we used Burrows-Wheeler Aligner (BWA) and Samtools to align reads and to pick up variants. A quality assessment was then undertaken on the basis of exome probe coverage. The results from preprocessing step and the candidate variants found in common population were marked as background. Such variants were unlikely to cause hereditary disease. Ensembl perl APIs were used to annotate consequences of each candidate variants. We also used PolyPhen, SIFT and Condel to predict the severity of each candidate variants. This method has been applied to investigate cases of rare hereditary disease discovered in Taiwan population. These candidate SNVs in other families that have the same hereditary cancer should be validated by experimental appraoches. My method could point out candidate variants which might cause hereditary cancer. In principle, this method could also be applied to other diseases using exome sequencing data.