Compositions, methods, and systems for non-invasive prenatal testing

A method comprising:

• performing a non-invasive prenatal testing (NIPT) digital assay with a sample, upon generating 200,000 counts per chromosome for a set of chromosomes comprising chromosome 13, chromosome 18, and chromosome 21, wherein performing said NIPT digital assay comprises:
• simultaneously distributing a) nucleic acid molecules of the sample, said nucleic acid molecules comprising target loci of said set of chromosomes, and b) materials for an amplification reaction across a plurality of droplets comprising at least 15 million droplets, wherein each of said plurality of droplets contains less than or equal to one nucleic acid molecule of said nucleic acid molecules;
• amplifying said nucleic acid molecules with said materials for the amplification reaction, within said plurality of droplets;
• and
• generating said counts per chromosome upon detecting signals from said plurality of droplets.