UC San Diego

Genome sequencing of single cells has a variety of applications, including characterizing difficult-to- culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and simultaneously amplified via multiple displacement amplification for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated nanoliter-scale reactors, thus increasing the template concentration by reducing the reaction volume. MIDAS is first applied to single E. coli cells, facilitating the de novo assembly of near-complete microbial genomes to unprecedented levels. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1-2 Mb resolution, resolutions not possible with standard whole genome amplification. MIDAS will further the characterization of genomic diversity in many heterogeneous cell populations