Ion Ampliseq™ Chemistry is like your favorite Swiss Army Knife. It is highly flexible and can be used across a multitude of applications. So what are the key applications for this targeted sequencing? Let’s find out today.
If you’ve had the chance to watch our “What is Ion AmpliSeq Chemistry and how does it work?” video, then you will already know that Ion AmpliSeq Chemistry enables researchers to zoom-in on specific genomic regions of interest and investigate the presence of specific SNPs, indels and gene fusions faster, with less cost and with far less DNA input — as little as 10ng of DNA — compared to other genetic analysis approaches. So what are the key applications the research community is using for this targeted sequencing technology?
Let’s take a look at our lab book
First off, Ion AmpliSeq Technology can be used to sequence both DNA and RNA (well actually the RNA is first converted to cDNA but hopefully you get the gist). Ion AmpliSeq RNA sequencing is commonly used to answer gene expression questions such as “which genes are differentially expressed in my abnormal or diseased research sample compared to my control?” In fact, the ability to highly multiplex the enrichment process with Ion AmpliSeq chemistry means that a single PCR reaction can be used to generate greater than 20,000 different amplicons. That means that something like the Ion AmpliSeq Transcriptome Human Gene Expression Kit can be used to measure the expression levels of over 20,000 RefSeq genes in a single assay… and using as little as 10ng of input total RNA! Quite remarkable.
The other major application of Ion AmpliSeq RNA sequencing is the detection of gene fusions, an important focus in cancer research. While many chromosomal translocations have been identified, the breakpoints are often highly variable. This makes using an Ion AmpliSeq targeted sequencing approach using a panel such as the RNA Lung Fusion Research Panel ideal for this type of work.
Okay, now onto DNA analysis… Ion AmpliSeq genomic DNA sequencing is largely being used to understand genetic variation – detecting SNPs, indels, and even gene copy number changes at specific base positions or across whole genes in the genome. This mapping of genetic variation using Ion AmpliSeq Technology is a research application that is being applied to the understanding of genetic disorders, such as inherited syndromes, studying trait inheritance, furthering our understanding of evolution and even being used to identify and detect important genetic markers to assist with breeding programs for livestock and crops.
As a result of its flexibility, Ion AmpliSeq Technology enables researchers to zoom-in on specific hotspot mutation sites using a panel such as the Ion AmpliSeq Cancer Hotsport Panel v2 for rapid analysis of research samples across a wide range of common driver mutations. Alternatively, if the goal is the discovery of new mutations, gene level sequencing with a panel such as the Ion AmpliSeq Comprehensive Cancer Panel provides an all-inclusive approach. And, lastly, we can’t forget its use in the field of human identification. Ion AmpliSeq Technology’s ability to work with mixed or highly degraded samples or trace DNA quantities is ideal for forensic applications to help generate more investigation leads or crack that tough case.
What’s unique about Ion AmpliSeq is the ability for users to design their own panels targeting almost any genome. A free design tool, Ion AmpliSeq Designer, can be used to create primer pools targeting a defined region of interest within a reference sequence. You can go to ampliseq.com to get started on your designs today! It’s really easy, and remember, IT’S FREE
Well there you have it. What, on the surface, is a straight forward technology that is enabling researchers in very different application areas to answer extremely challenging underlying questions. Whether one of the predesigned and Ready-To-Use Ion AmpliSeq Panels fits your needs or you need to consider the custom panel route, Ion AmpliSeq Technology has the ability to help answer your targeted sequencing questions.
I hope this video was helpful on the Ion AmpliSeq Technology, and I am sure you’ll have more questions.
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