Methods and compositions for determining ploidy

A method for amplifying and sequencing DNA, comprising:

• (i) extracting cell-free DNA from a biological sample of a human subject to obtain extracted DNA;
• (ii) performing target multiplex amplification by forming a reaction mixture comprising the extracted DNA or DNA derived therefrom and a pool of primers and subjecting the reaction mixture to amplification conditions to obtain a plurality of amplicons comprising one or more SNP or SNV loci, wherein the pool of primers comprise 200 to 10,000 target-specific primers that each specifically bind to a different primer binding sequence that is located within an effective distance of one or more SNP or SNV loci to obtain the plurality of amplicons comprising one or more SNP or SNV loci, wherein at least 90% of the primer binding sequences are located within a plurality of haploblocks that may exhibit genetic variation associated with cancer, wherein each haploblock comprises at least 2 of the primer binding sequences, and wherein each haploblock comprises two or more SNP or SNV loci having strong linkage disequilibrium;
• and
• (iii) sequencing the amplicons to obtain phased allelic data of the SNP or SNV loci.