System and method for cleaning noisy genetic data and determining chromosome copy number

A method for determining genetic data for DNA from a first individual in a blood sample of a second individual, the method comprising:

• performing targeted PCR to amplify a plurality of SNP loci on cell-free DNA extracted from the blood sample to generate amplified products, wherein the SNP loci are on a plurality of chromosomes;
• sequencing the amplified products by sequencing-by-synthesis, wherein the sequencing-by-synthesis comprises clonal amplification of the amplified products and sequencing of the clonally amplified DNA;
• and
• receiving an output resulting from the most likely genetic data for DNA from the first individual that has been determined based on allele frequencies at the plurality of SNP loci in the genetic data produced by the sequencing.

A method for preparing a preparation of amplified DNA derived from a biological sample of a second individual useful for determining genetic data for DNA from a first individual in the biological sample, the method comprising:

• extracting cell-free DNA from the biological sample;
• preparing a preparation of amplified DNA by amplifying a plurality of target loci on the cell-free DNA extracted from the biological sample to generate amplified DNA;
• sequencing the amplified DNA using sequencing-by-synthesis;
• and
• receiving an output resulting from the most likely genetic data for DNA from the first individual that has been determined based on allele frequencies at the plurality of target loci in the genetic data produced by the sequencing.

A method for preparing a preparation of amplified DNA derived from a biological sample of a second individual useful for determining genetic data for DNA from a first individual in the blood sample, the method comprising:

• extracting cell-free DNA from the biological sample;
• preparing a preparation of amplified DNA by performing targeted PCR to amplify a plurality of SNP loci on the cell-free DNA extracted from the blood sample to generate amplified DNA, wherein the SNP loci are on a plurality of chromosomes;
• sequencing the amplified DNA using sequencing-by-synthesis, wherein the sequencing-by-synthesis comprises clonal amplification of the amplified DNA and sequencing of the clonally amplified DNA;
• and
• receiving an output resulting from the most likely genetic data for DNA from the first individual that has been determined based on allele frequencies at the plurality of SNP loci in the genetic data produced by the sequencing.