Fields of Biology
Cancer Research
Overview
Every cancer type presents a unique combination of genetic mutations. Identifying which critical mutations to exploit as diagnostic and therapeutic targets remains a challenging task in cancer research. The 454 Sequencing system generates millions of long, highly-accurate sequences from individual DNA molecules, providing the statistical power to identify rare somatic sequence variations and offering unprecedented power to dissect the molecular basis of cancer.
Applications
Somatic variation detection
Effectively detect the spectrum of genetic variations in specific cancer-associated regions or genes by shotgun sequencing PCR products, cDNA libraries, or DNA fragments captured with NimbleGen's Sequence Capture array. The GS FLX System is also an optimal tool for Ultra-Deep Sequencing of amplicons to find low-frequency mutations.
Transcriptome sequencing
Improve understanding of disease states through the detection of polymorphisms, identification of splice-variants, and discovery of novel transcripts in tumor cell lines or tissue samples . Re-sequencing of mRNA products with the GS FLX System ensures specific and sensitive detection, and relative quantification of low-abundance variants.
Epigenetic studies
Simultaneously analyze genetic and epigenetic parameters with the GS FLX system. Characterize alterations in methylation and acetylation patterns in tumor samples through bisulfite sequencing and ChIP sequencing of amplified or pulled-down target regions.
Tumor virus detection
Quickly and accurately identify potential cancer causing agents of tumors suspected to be of infectious origin with the GS FLX System by sequencing and subtracting cDNA libraries from infected and non-infected samples.
Small RNA
Identify novel small RNAs and characterize differential expression profiles in different cell lines or tumor samples by sequencing small RNA transcriptomes. 454 Sequencing system's highly accurate, long reads ensure that all classes of small RNAs are captured.
Publications
- Thomas et al. High-throughput oncogene mutation profiling in human cancer. Nature Genetics 39: 347-51. March 2007.
- Sugarbaker et al. Transcriptome sequencing of malignant pleural mesothelioma tumors. PNAS 105: 3521-3526. March 4, 2008.
- Korshunova et al. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Research 18: 19-29. January 2008.
- Feng et al. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 9: 1096-100. Febuary 22, 2008.
- Yeager et al. Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Human Genetics. ePub August 14 2008.