Devices, processes, and systems for determination of nucleic acid sequence, expression, copy number, or methylation changes using combined nuclease, ligase, polymerase, and sequencing reactions

A system for identifying a plurality of nucleic acid molecules in a sample, said system comprising:

• (i) an inlet port and
• (ii) a cartridge defining a space containing:
• multiple primary reaction chambers fluidically coupled to said inlet port to receive material from said inlet port and produce primary reaction chamber products from the material and
• a product capture housing enclosing a solid support with a plurality of separate columns of a plurality of product capture subdivisions configured in separate rows and columns, with each separate product capture subdivision comprising an array of a plurality of individual hydrophilic micro-pores or micro-wells, wherein each of said individual hydrophilic micro-pores or micro-wells is separated by hydrophobic surfaces where primary reaction products are further reacted to create array products which are detected in the micro-pores or micro-wells, wherein one or more of the columns of separate product capture subdivisions receive material which has passed through one of said multiple primary reaction chambers.