Why DNA clusters?

[HICORE]

I am new to next gen sequencing and I am going through the sequencing technology of the Illumina IIe. It says dense clusters of DNA are generated in the channels of the flow cell.

Why are there clusters of DNA formed instead of having it spread evenly throughout the channel?

[krobison]

Each cluster (aka polony) is a clonal population seeded from a single DNA molecule and amplified by bridge PCR. Ideally the clusters themselves would be spread evenly throughput the channel, but at this time they are randomly distributed.

Versus single molecule systems (Helicos, PacBio, Life/VisiGen), clusters give a stronger signal & more tolerance for missed incorporation events but trade that for extra prep time & complexity as well as the possibility of biased amplification.

[HICORE]

Ahhh

I think I understand. So clusters form because bridge amplification increases the concentration of DNA molecules in that one particular area. The area around the original DNA template.

[simonandrews]

The clusters are the basis of all subsequent measurements. The idea is that you seed templates on the flowcell at a low concentration so that you get single copies attaching in an evenly spread manner. You then do the amplification step to generate a cluster of copies around each sequence so that you can see enough signal to make your measurements.

[kmcarr]

There is a nice outline of the process with pictures in the the sticky thread on this forum