Data generated using microdroplet PCR technology as an enrichment method is well suited to performing sequence-based association studies, according to a recent study.
The study, entitled 'Microdroplet-based PCR Enrichment for Large-Scale Targeted Sequencing', was conducted by researchers at the Scripps Translational Science Institute, the University of California, San Diego School of Medicine and Raindance Technologies.
It evaluated microdroplet PCR's advantages in performing sequence enrichment for targeted sequencing over the gold-standard traditional PCR approach.
These benefits translated into a much higher efficiency of sequencing and a much more cost-effective way to do population studies.
It is believed that this new technology will be used to study the basic underpinnings of diseases and to understand their root causes.
For instance, scientists are now using it to understand the causes of anorexia nervosa.
The technology can also be used to comprehend a disease's response to a therapy or to determine a drug's side effects.
It can even be employed to study the healthy ageing process.
To efficiently perform population-based sequencing studies using next-generation sequencing platforms, it is important to be able to simultaneously examine large numbers of targeted sequences.
The results indicate that even when simultaneously amplifying 3,976 targeted sequences, microdroplet PCR generates a high ratio of target sequence to background sequence.
The study concluded that data quality is independent of the number of amplicons.
A path to scale to 20,000 amplicons while maintaining high performance was also demonstrated.
The microdroplet PCR process is said to have proved extremely efficient, with more than 99.6 per cent of all amplicons being successful and with highly reproducible amplification of targeted sequences between samples.
The data also showed that equivalently accurate SNP calling can be performed using microdroplet PCR whether the DNA is unamplified or whole-genome amplified from nanogram quantities.
The allelic bias error rate of approximately 0.1 per cent resulted in few known variants to be incorrectly called, further attesting to the robustness of the process.
Compared to other types of sequence enrichment, the researchers were able to generate greater uniform coverage of targeted sequences.
The problems typically encountered with standard PCR, such as difficult primer design and high allelic bias, were not observed with the microdroplet-based PCR workflow.
This study confirmed that the RDT 1000 microdroplet-based platform from Raindance Technologies is able to detect higher numbers of variants in the targeted sequences than either solution-based hybridisation or molecular inversion probes.
