The Pipeline Of Cancer Gene Detection Based On Amplicon Sequencing

Objective: The application of high-throughput sequencing technology in cancer research and clinic has been paid more and more attention.A wide variety of sequencing technologies and tools are also emerging.At present,a large number of high-throughput sequencing data of cancer samples are emerging.Only by selecting the appropriate data analysis process can we make a correct understanding and judgment of the biological information and significance behind the sequencing data.Amplicon sequencing is a very important sequencing technique.The method has advantages of high efficiency,high targeting,high coverage,high flexibility and low cost.In order to study a large number of amplicon sequencing data,an appropriate data analysis process needs to be establishedMethods: Genomic standards are widely used in benchmarking tests with sequencing techniques.Five sequencing samples were prepared using a mixture of Chinese Quartet genomic standard,which was used to evaluate the advantages and disadvantages of the analysis process.The sensitivity,accuracy and f1-score of detection results were calculated mainly through the known high confidence SNV,and the gene mutation detection software was selected and the parameters of the gene mutation detection software were adjusted.Results: We used F7 and M8 of the Chinese Quartet genomic standard to mix according to the ratios of 1:1,1:3 and 1:9,and obtained five samples of F7,M8,1:1(F7 / M8),1:3(F7 / M8)and 1:9(F7 / M8).Using our data analysis process to detect high-confidence SNV,the accuracy of the results were 62.87%,61.06%,69.21%,62.29% and 65.17%,respectively,with an average value of 64.12%.The sensitivity was 84.40%,82.05%,75.16%,77.30% and 79.43%,respectively,with an average value of 79.67.Conclusion: Our data analysis process can be applied to the analysis of cancer amplicon sequencing data.We performed genetic mutation detection on 40 samples of thyroid cancer nodules,which can help us to understand and study thyroid cancer.