Introduction to Genomic Technologies for Cancer Research

The Tumor Progression Pathway—Genomic technologies are helping researchers achieve a deeper understanding of the tumor progression pathway. Much of the research thus far has focused on the study of basic tumor biology and the identification of variants in germline DNA that influence cancer risk and susceptibility. However, there has been a shift over the past few years to more translational study designs, linking genetic information with phenotypes to understand the clinical significance. Source: https://www.illumina.com/

Genomic technologies have emerged as an extremely useful tools in cancer research. International projects such as the International Cancer Genome Consortium and The Cancer Genome Atlas, tasked with mapping the biological science of dozens of tumor types, would not have been possible without these tools. Next-generation sequencing (NGS) and high-density microarrays are used to study cancer biology. Both provide the cancer research community with a growing body of information that may lead to more effective medicine, better patient treatment options, and more accurate prognoses.

NGS is suited to the study of cancer biology.

  • Paired tumor-normal (T/N) whole-genome sequencing (WGS) or T/N whole-exome sequencing (WES) have emerged as ideal methods for the discovery of somatic mutations.
  • NGS-based RNA sequencing (RNA-Seq) has revolutionized gene expression studies by enabling researchers to measure relative expression changes across the whole genome in a single experiment and to identify novel transcripts.
  • RNA-Seq has emerged as a leading method for identifying gene fusions, a critical class of somatic driver mutations in tumor cells.
  • Chromatin immunoprecipitation sequencing (ChIP-Seq), bisulfite sequencing, or methylation-targeting microarrays, can be used to investigate the role of epigenetic factors in the biology of tumorigenesis.

The adoption of these genomic approaches in cancer research has led to a deeper understanding of tumor biology and is establishing the foundation necessary to support the long-term goals of personalized medicine. Researchers are also using NGS and microarray-based genotyping of germline DNA to identify inherited variations that influence cancer susceptibility. While NGS is an excellent tool for assessing the germline status of known cancer predisposition genes and identifying novel loci, microarrays are ideal for large-scale population studies, where large sample numbers are required to identify weakly predisposing genes. This primer describes the broad portfolio of genomic technologies offered by Illumina that are directly applicable to cancer research.

Terms to remember:

next-generation sequencing – refers to large-scale DNA sequencing technology that allows for querying the entire genome (whole genome), the exons within all known genes (whole exome), or only exons of selected genes (target panel)

exome sequencing – is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome)

RNA-seq – is a particular technology-based sequencing technique which uses next generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome

chromatin immunoprecipitation (ChIP) – is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest

Source:

Illumina. https://www.illumina.com/content/dam/illumina-marketing/documents/products/appspotlights/app_spotlight_cancer.pdf

https://www.sciencedirect.com/topics/medicine-and-dentistry/next-generation-sequencing

https://en.wikipedia.org/wiki/Exome_sequencing

Chu Y, Corey DR (August 2012). “RNA sequencing: platform selection, experimental design, and data interpretation”Nucleic Acid Therapeutics22 (4): 271–4. doi:10.1089/nat.2012.0367PMC 3426205PMID 22830413

Wang Z, Gerstein M, Snyder M (January 2009). “RNA-Seq: a revolutionary tool for transcriptomics”Nature Reviews. Genetics10 (1): 57–63. doi:10.1038/nrg2484PMC 2949280PMID 19015660

Thermofisher. Chromatin Immunoprecipitation Sequencing.


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