Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA

Abstract

Uniform amplification of low-input DNA is important for applications across biology, including single-cell genomics, forensic science, and microbial and viral sequencing. However, the requisite biochemical amplification methods are prone to bias, skewing sequence proportions and obscuring signals relating to copy number. Digital droplet multiple displacement amplification enables uniform amplification but requires expert knowledge of microfluidics to generate monodisperse emulsions. In addition, existing microfluidic methods are tedious and labor intensive for preparing many samples. Here, we introduce rapid-emulsification multiple displacement amplification, a method to generate monodisperse droplets with a hand-held syringe and hierarchical droplet splitter. Although conventional microfluidic devices require >10 min to emulsify a sample, our system requires tens of seconds and yields data of equivalent quality. We demonstrate the approach by using it to accurately measure copy number variation (CNV) in single cancer cells.