Methods, systems, and compositions for counting nucleic acid molecules

A method for nucleic acid molecule analysis, comprising:

• a) providing a plurality of molecular inversion probes (MIPs) and a sample of nucleic acid molecules;
• b) hybridizing MIPs of the plurality of MIPs to the nucleic acid molecules to generate hybridized MIPs;
• c) in a reaction mixture, circularizing hybridized MIPs to form a plurality of circularized nucleic acid probes;
• d) forming a plurality of complexes comprising a plurality of primers hybridized to a plurality of circularized nucleic acid probes from the reaction mixture following d), wherein the plurality of primers is bound to a solid support, wherein the solid support comprises a polymeric coating polymerized from surface-modifying monomers comprising one or more monomers selected from the group consisting of dopamine, tannic acid, caffeic acid, pyrogallol, gallic acid, epigallocatechin gallate, and epicatechin gallate monomers, and wherein the primers are bound to the polymeric coating;
• e) extending the plurality of primers in the plurality of complexes in an amplification reaction to form a plurality of amplification products immobilized to the solid support;
• f) in a presence of at least one detergent, hybridizing a set of labeled probes to the plurality of amplification products to generate a plurality of amplification products comprising hybridized labeled probes;
• and
• g) using imaging to count the plurality of amplification products comprising hybridized labeled probes.