This invention provides ultra-sensitive methods and compositions for detecting patient-specific mutations from cell free nucleic acids (cfDNA) without sequencing. Methods of the invention make use of fluidic partitions for multiplex amplification of cfDNA and thereby create a library of uniformly amplified amplicons. The uniformly amplified amplicons can be split into any number of different detection reactions (while maintaining detection sensitivity) for single-plex detection of mutations present in cfDNA. These methods provide substantially improved signal to noise ratio and easier discrimination of low-abundance mutations.

This invention provides ultra-sensitive methods and compositions for detecting patient-specific mutations from cell free nucleic acids (cfDNA) without sequencing. Methods of the invention make use of fluidic partitions for multiplex amplification of cfDNA and thereby create a library of uniformly amplified amplicons. The uniformly amplified amplicons can be split into any number of different detection reactions (while maintaining detection sensitivity) for single-plex detection of mutations present in cfDNA. These methods provide substantially improved signal to noise ratio and easier discrimination of low-abundance mutations.

An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.

An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.

The disclosed embodiments concern methods for determining sequences of interest using targeted unique molecular index (TUMI) sequences that are uniquely associated with individual polynucleotide fragments in plants, such as those present in a transgenic event, a site-specific mutation or a wild type variant. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.

An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.

The disclosed embodiments concern methods for determining sequences of interest using targeted unique molecular index (TUMI) sequences that are uniquely associated with individual polynucleotide fragments in plants, such as those present in a transgenic event, a site-specific mutation or a wild type variant. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

The disclosed embodiments concern methods for determining sequences of interest using targeted unique molecular index (TUMI) sequences that are uniquely associated with individual polynucleotide fragments in plants, such as those present in a transgenic event, a site-specific mutation or a wild type variant. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.