Digital PCR provides sensitive and absolute calibration for high throughput sequencing

TL;DR

Digital PCR enables highly sensitive, accurate, and absolute quantification of sequencing libraries, significantly reducing sample input requirements and improving sequencing efficiency on next-generation platforms.

Contribution

The paper demonstrates the use of digital PCR for absolute quantitation of sequencing libraries, improving accuracy and reducing sample input needs compared to traditional methods.

Findings

Digital PCR provides sensitive and robust library quantification.

It reduces DNA input requirements by over 1000-fold.

Enables optimal DNA concentration setup without titration.

Abstract

Several of the next generation sequencers are limited in their sample preparation process by the need to make an absolute measurement of the number of template molecules in the library to be sequenced. As currently practiced, the practical effects of this requirement compromise sequencing performance, both by requiring large amounts of sample DNA and by requiring extra sequencing runs to be performed. We used digital PCR to quantitate sequencing libraries, and demonstrated its sensitivity and robustness by preparing and sequencing libraries from subnanogram amounts of bacterial and human DNA on the 454 and Solexa sequencing platforms. This assay allows absolute quantitation and eliminates uncertainties associated with the construction and application of standard curves. The digital PCR platform consumes subfemptogram amounts of the sequencing library and gives highly accurate results, allowing the optimal DNA concentration to be used in setting up sequencing runs without costly and time-consuming titration techniques. This approach also reduces the input sample requirement more than 1000-fold: from micrograms of DNA to less than a nanogram.