Targeted enrichment of long nucleotide sequences using microfluidic partitioning

An in vitro method for enriching for one or more target DNA molecule from a sample of mixed DNA molecules comprising the steps of:

• a) providing a liquid sample of mixed DNA molecules comprising one or more specific target DNA molecule and reagents for specific detection of at least one of said target DNA molecules,
• b) formation of a multiple of liquid droplets each comprising mixed DNA molecules from said liquid sample,
• c) specific detection of droplets containing at least one of said target DNA molecules, wherein each droplet contains less than 0.5 of said one of more target DNA molecule on average, and
• d) physically selecting droplets containing at least one of said target DNA molecules, wherein the frequency of the target DNA molecule compared to its frequency in the sample of mixed DNA molecules in step (a) is increased between 0.01×(total number of droplets containing DNA molecules)×(number of droplets with target DNA)−1 and 100×(total number of droplets containing DNA molecules)×(number of droplets with target DNA)−1,
• e) general amplification of the mixed DNA molecules in the selected droplets from step d), where the mixed DNA molecules are in a total amount of less than 300 fg, wherein the selected droplets are coalesced and general amplification reagents are added to said coalesced selected droplets to form a general amplification reaction mixture, and wherein water-in-oil droplets are formed from the reaction mixture.