Methods for simultaneous amplification of target loci

A method for amplifying and sequencing DNA, comprising:

• extracting cell-free DNA from a blood sample or a portion thereof collected from a subject who is not a pregnant woman;
• amplifying extracted cell-free DNA or DNA derived therefrom one or more times to generate amplification products, wherein one of the amplification steps comprises targeted amplification of a plurality of single nucleotide polymorphism or variant loci in a single reaction volume, wherein the plurality of single nucleotide polymorphism or variant loci comprises 25-2,000 loci associated with cancer, wherein the method does not comprise splitting the extracted cell-free DNA or DNA derived therefrom into parallel reactions and pooling of amplification products from parallel reactions;
• tagging the amplification products with one or more universal tail adaptors to generate tagged products, and amplifying the tagged products using adaptor-specific primers to generate final amplification products, wherein the final amplification products comprise at least one barcode and at least one sequencing tag, wherein tagging the amplification products comprises appending the one or more universal tail adaptors to the amplification products;
• and
• performing massively parallel sequencing on the final amplification products to sequence the plurality of single nucleotide polymorphism or variant loci, wherein the final amplification products derived from multiple samples are combined and sequenced together.