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.

What is claimed is: 
     
         1 . A method for determining genetic data for DNA from cancer cells, comprising:
 obtaining cell-free DNA from a blood sample, wherein the cell-free DNA comprises DNA from cancer cells comprising one or more chromosome segments;   ligating at least one adapter to the chromosome segments, wherein the at least one adapter comprises a universal amplification sequence;   performing targeted amplification using a universal primer that binds to the universal amplification sequence, and target-specific primers, to generate amplified nucleic acid molecules; and   determining genetic data for the cell-free DNA from cancer cells by performing next-generation sequencing.   
     
     
         2 . The method of  claim 1 , wherein the method further comprises detecting a point mutation, insertion or deletion. 
     
     
         3 . The method of  claim 1 , wherein the next-generation sequencing is performed using sequencing-by-synthesis. 
     
     
         4 . The method of  claim 1 , wherein the targeted amplification is targeted PCR. 
     
     
         5 . The method of  claim 1 , wherein the targeted amplification amplifies SNP loci.