THE APPLICATION OF NEXT-GEN SEQUENCING IN CANCER RESEAERCH


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Yingrui Li1, Wangting Chen1, Ruiqing Li1
1BGI, Shenzhen, China

Background

The revolutionary progress of next generation sequencing technology has enabled us to get an all-round view of complex diseases including cancer at DNA, RNA and also epigenetic levels. Exome is the collection of all exons within a genome, therefore sequencing the exomes is informative and at the same time cost-effective. Additionally, exome sequencing is more suitable for research of a large sample size.

Method

Exomes of 10 clear cell renal cell carcinomas (ccRCCs) were captured and sequenced by next generation sequencing technology. Comparison of sequences between those cancer exomes and their non-disease controls were made and various forms of differences were detected.

Results

somatic Single Nucleotide Variants (SNV) were investigated by two methods, Short Oligonucleotide Analysis Package (SOAP) and frequency difference based algorithm. 67 de novo somatic indels were detected by SoapSV. Tissue Differentiation Methylation Regions (tDMR) profile was constructed. Difference between tumour and normal tissue at transcription level was revealed by alternative splicing detection and differentially expression detection and miRNA comparison was performed. Pathway and network analysis were done for the detected variants.

Conclusion

The downstream analysis of tumour and normal tissue sequencing data provides us a panoramic view of the features of cancer at whole-genome level. The knowledge of cancer genomics will lead to characterization and biological study of tentative disease-causing variants and finally benefit cancer prevention and treatment.