Deciding whether to analyze the genome, exome, transciptome or genes

An important consideration for the application of next-generation sequencing (NGS) in cancer or clinical research is whether to interrogate the whole genome, whole transcriptome, whole exome (the 1% of the genome that encodes for all proteins), or targeted genes (see figure 1). While whole genome, transcriptome, and whole exome analyses are comprehensive, these approaches generally provide significantly more data than are required for many cancer and clinical research activities.

Targeted sequencing studies restrict analyses to specific exons, genes, sets of genes, or genomic regions associated with the disease. Focusing on a region of interest, and then analyzing the potentially clinically relevant genes, makes targeted sequencing a practical application in cancer research. Targeted next-generation sequencing can uncover rare variants occurring at low allelic frequency, verify germline and somatic variants across a large number of archived samples, and discover similar shared mutations in genes that drive disease.

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Figure 1. Next-generation sequencing (NGS) can provide a global genetic survey of the human genome and transcriptome, or it can be restricted to specific regions.

Next-generation sequencing can make targeted genetic analysis for cancer research more efficient

Figure 2. Sanger sequencing interrogates single genes per sample, requiring large-scale availability of sample input, time and cost. In contrast, our most popular and cited panel, the Ion Ampliseq™ Cancer Hotspot Panel v2, interrogates mutation hotspots in 50 genes in a single tube using just 10 ng of DNA.

Cancer researchers utilizing next-generation sequencing have already contributed to an explosion of genetic information that has helped elucidate the effects of mutations in many cancer genes at a functional level. While Sanger sequencing has traditionally been the gold standard in cancer research, it has limitations in throughput, speed, and resolution, and does not easily scale to projects with very large numbers of genes or samples (see figure 2). In contrast, the sequencing of tens or even hundreds, of genes in parallel using targeted next-generation sequencing may provide a more comprehensive picture of the cancer being studied.

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Ion AmpliSeq™ technology can make targeted next-generation sequencing more powerful

The ability to efficiently and evenly amplify just the genomic regions of interest and minimize the amount of input DNA used are critical factors, especially in cancer research applications. Ion AmpliSeq™ technology transforms targeted sequencing applications by enabling cancer researchers to rapidly amplify thousands of targets using just 10 ng of DNA. This technology, coupled with the Ion PGM™ System and easy-to-use Ion Reporter™ Software, enables researchers to go from precious FFPE samples to variants in a single day.

“With gene panel sequencing on Ion PGM™ System, we use Ion AmpliSeq™ Colon and Lung Cancer Panel, and are able to detect the changes in tens of genes at once, not just the particular mutations that you happen to be looking for in a few hotspot regions.”

Ian Cree, MD, PhD
Professor of Pathology
The University of Warwick Coventry, United Kingdom
Life Technologies OncoNetwork Consortia Member

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