Analysis of nucleic acids

A method of haplotype analysis, the method comprising:

• partitioning an aqueous phase containing nucleic acid into a plurality of discrete volumes;
• amplifying in the volumes at least one allele sequence from each of a first polymorphic locus and a second polymorphic locus contained in a target region of the nucleic acid;
• collecting allele-specific amplification data for each of the loci from individual volumes;
• correlating allele-specific amplification data for the first locus with allele-specific amplification data for the second locus from the same volumes, wherein correlating includes determining a number of volumes exhibiting co-amplification of a particular allele sequence from both loci;
• and
• selecting a haplotype of the target region for the first and second loci based on the step of correlating.

A method of haplotype analysis, the method comprising:

• partitioning an aqueous phase including nucleic acid into a plurality of discrete volumes, wherein partitioning includes forming an emulsion, and wherein forming an emulsion includes passing the aqueous phase through an orifice such that monodisperse droplets of the aqueous phase are generated;
• amplifying in the volumes an allele sequence from each of a first polymorphic locus and a second polymorphic locus in the nucleic acid;
• collecting allele-specific amplification data for each allele sequence from individual droplets of the emulsion;
• and
• selecting a haplotype of the nucleic acid based at least in part on whether the amplification data indicates a negative or a positive correlation for amplification of the allele sequences in the same volumes.