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

Abstract

Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

1 . A method for measuring an amount of DNA from a first individual in a biological sample of a second individual, comprising:
 isolating cell-free DNA from the biological sample which comprises DNA from the first individual and DNA from the second individual;   performing targeted amplification using target-specific primers to amplify at least 70 loci of interest on the isolated DNA;   performing sequencing-by-synthesis that comprises clonal amplification and measurement of sequences of the clonally amplified DNA, and determining the amount of the DNA from the first individual in the biological sample.   
     
     
         2 . The method of  claim 1 , wherein the loci of interest are SNP loci. 
     
     
         3 . The method of  claim 1 , wherein the loci of interest are on a plurality of chromosomes. 
     
     
         4 . The method of  claim 1 , wherein the clonally amplified DNA comprises clonally amplified DNA from the first individual and clonally amplified DNA from the second individual. 
     
     
         5 . The method of  claim 4 , wherein sequences of the clonally amplified DNA from the first individual are measured along with sequences of the clonally amplified DNA from the second individual. 
     
     
         6 . The method of  claim 1 , further comprising performing a universal amplification after the targeted amplification. 
     
     
         7 . The method of  claim 1 , wherein the biological sample is a blood sample.