Methods for simultaneous amplification of target loci

A method for preparing a biological sample containing DNA from a first individual and a second individual, comprising:

• isolating cell-free DNA from the biological sample, wherein the isolated cell-free DNA comprises the DNA from the first individual and DNA from the second individual;
• amplifying the isolated cell-free DNA at a plurality of polymorphic loci on one or more chromosomes expected to be disomic, wherein the plurality of polymorphic loci comprises between 200 and 1,000 polymorphic loci, wherein the amplifying comprises amplifying the between 200 and 1,000 polymorphic loci from the cell-free DNA isolated from the biological sample using between 200 and 1,000 distinct primer pairs configure to target the between 200 and 1,000 polymorphic loci in a single reaction volume;
• and
• preparing the isolated cell-free DNA amplified at the polymorphic loci for sequencing.