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nCounter® and Pathway Biology

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1. What is pathway cell biology?

A pathway is the way a cell gets a job done. It organizes its activities along particular functions and those functions are called pathways.

2. Why is it important?

Pathways are important because when people study cells, they want to take those cells and make them do something that they want them to do, or they want to fix the cells; one of those two things.

3. What are the biggest problems?

One of the real difficulties in understanding pathways and cells is that you have to be able to make a lot of highly detailed, precise measurements over many pathways, time points, conditions, cell types. It takes a lot of data, a lot of samples to make sense out of how pathways are operating in cells.

4. How do scientists deal with these problems?

With this kind of complexity, there are two types of scientists. One group will take a very narrow, detailed look at a limited number of genes using some technology like qPCR. The danger, of course, is that when you're looking at a very narrow group of genes and trying to extrapolate that floor into a larger pathway, you can make a mistake, and that's happened.

The other group of scientists typically take a much broader view, say like Next-Gen Sequencing, where they will just look at all of the information. Now the problem there is that the numbers of samples that you can examine are relatively limited. With all that information, you just cannot look at hundreds of samples. So in one respect you're too narrow, trying to extrapolate forward. In the other case, you're too broad and trying to extrapolate to multiple numbers and samples. Either case is difficult.

5. How does nCounter® solve these problems?

nCounter Technology is ideally suited for pathway-based studies, in a single tube, you can simultaneously measure from 10 to up to 100 pathways. You measure these pathways with a digital accuracy, allowing you to look at small fold changes. Important if you're going to measure multiple samples, multiple types, and lastly, you don't need a big army to get a big science result with this technology since the majority of the work is completely automated.

6. What is the best example of this?

There's a lot of great examples in the literature. One especially favorite of mine was a work done by Aviv Regev at the Broad Institute, appeared in Nature Biotechnology in 2011. And the key aspect of that paper is that, she was able to determine the entire regulation pathway of mRNA, both synthesis and degradation in mammalian cells.