Abstract: Methods and systems are provided for massively parallel genetic analysis of single cells in emulsions or droplets. A biological sample is divided into subsamples of single cells or cell supbopulations, and a fusion complex is formed by molecular linkage and amplification techniques. Methods, apparatuses, and systems are provided for high-throughput, massively parallel analysis of the subsamples. These methods integrate molecular, algorithmic, and engineering approaches. They have broad and useful application in a number of biological and medical fields, including immunology, noninvasive prenatal diagnosis, and noninvasive cancer diagnosis.

Abstract: Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.