The RainDance RainDrop System transforms the performance of molecular assays by enabling digital answers across a number of important applications including low-frequency tumor allele detection, gene expression, copy number variation, and SNP measurement.
Low-frequency allele detection
The RainDance RainStorm droplet-based microfluidics method utilizes up to 10 million reactions to enable detection of rare mutations in a background of wild-type DNA at levels better than 1 in 250,000. The combination of superior sensitivity, unprecedented multiplexing, and flexibility in experiment design provide a powerful genomic analysis platform for new research in cancer including rare variant detection, absolute quantitation of biomarkers, tumor profiling, and the ability to monitor residual disease.
Copy number variation
Copy number variations (CNVs) are involved in a large number of complex human diseases including many cancers and genetic conditions. An important measurement challenge in translational research involves identification of small CNV changes with high confidence. Cell free DNA (cfDNA) in blood plasma, for example, promises a readily available source of genetic material for tumor or pre-natal diagnosis with minimally invasive sampling techniques.
Early efforts using dPCR have reported the ability to detect a 1.25-fold difference in copy number 4. Additionally, the binary nature of dPCR means that the precision is more independent of variation in assay amplification, making it easier to optimize and standardize between laboratories. The RainDrop System is the only dPCR platform that is able to provide the required level of precision to measure smaller CNV differences in more challenging samples like cfDNA in a cost effective manner.
Histogram (heat map) of droplet fluorescence intensities, for the 5-plex assay against a synthetic model. Standard techniques were used to compensate for spectral overlap of FAM and VIC signals. The six droplet populations correspond to the five individual assays plus the empty droplets.
Results of the SMA pilot study on 20 different patient samples from the Coriell cell repositories: 4 afflicted with SMA, 1 SMA carrier, and 15 negative controls. The measured genotypes of the different patients were consistent with their disease conditions (unafflicted, carrier, or afflicted). The patients afflicted with SMA each had zero copies of SMN1 (numbers SMA 1–4 in the figure), the carrier had just one copy, and the negative controls all had two or three copies (patients 1–15)
References
1. Weaver S, Dube S, Mir A, Qin J, Sun G, Ramakrishnan R, Jones RC, Livak KJ. Taking qPCR to a higher level: analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods 2010;50:271-276
2. Q. Zhong, S. Bhattacharya, S. Kotsopoulos, J. Olson, V. Taly, A.D. Griffiths, D.R. Link and J.W. Larson, Lab on a Chip, 2011, 11, 2167-2174.