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 of detecting aneuploidy of one or more chromosomes of interest in a fetus, the method comprising:
 obtaining chromosome segments from a maternal blood sample comprising chromosome segments from the one or more chromosomes of interest and chromosome segments from one or more reference chromosomes;   ligating at least one adapter to the chromosome segments;   measuring the amounts of amplified chromosome segments; and   detecting aneuploidy of the one or more chromosomes of interest using the amounts of amplified chromosome segments from the one or more chromosomes of interest and the amounts of amplified chromosome segments from the one or more reference chromosomes.   
     
     
         2 . The method of  claim 1 , wherein a statistical difference is detected by computing a standard deviation and a mean value for the measured amounts for each of the one or more chromosomes of interest and for each of the one or more reference chromosomes, and comparing the mean value for each of the chromosomes of interest to the mean value of the reference chromosome in terms of the standard deviations. 
     
     
         3 . The method of  claim 1 , wherein the method further comprises comparing the measured amounts of chromosome segments for the one or more chromosomes of interest from the maternal blood sample with measured amounts of chromosome segments for the one or more chromosomes of interest from maternal blood samples that are disomic for the one or more chromosomes of interest. 
     
     
         4 . The method of  claim 1 , wherein the measuring is performed irrespective of allele value. 
     
     
         5 . The method of  claim 1 , wherein the measuring comprises measurement of alleles having 100% penetrance. 
     
     
         6 . The method of  claim 1 , wherein the measured amounts for different alleles are combined. 
     
     
         7 . The method of  claim 1 , further comprising:
 performing clonal amplification of the amplified chromosome segments to generate clonally amplified chromosome segments before measuring the amounts, wherein the measuring comprises measuring the amounts of the clonally amplified chromosome segments, and wherein the detecting is performed using the amounts of clonally amplified chromosome segments from the one or more chromosomes of interest and the amounts of clonally amplified chromosome segments from the one or more reference chromosomes.   
     
     
         8 . The method of  claim 7 , wherein the amounts of amplified chromosome segments are measured using next generation sequencing. 
     
     
         9 . The method of  claim 8 , wherein the next generation sequencing is performed using sequencing by synthesis. 
     
     
         10 . The method of  claim 1 , wherein the chromosome segments from the one or more chromosomes of interest map to chromosomes 13, 18, and/or 21, and the method is used to detect trisomy at chromosomes 13, 18, and/or 21. 
     
     
         11 . The method of  claim 1 , wherein the measuring comprises quantitative allele measurements. 
     
     
         12 . The method of  claim 1 , wherein the measured amounts of amplified chromosome segments from each chromosome are combined into a single measurement for each chromosome. 
     
     
         13 . The method of  claim 1 , wherein aneuploidy of the one or more chromosomes of interest is detected by comparing the amount of amplified chromosome segments from the one or more chromosomes of interest in the maternal blood sample to a threshold determined from normal samples. 
     
     
         14 . The method of  claim 1 , wherein a statistical difference is detected by computing a standard deviation and a mean value for the measurement for each of the one or more chromosomes of interest and for each of the one or more reference chromosomes, and comparing the mean value for each of the chromosomes of interest to the mean value of the reference chromosome in terms of the standard deviations.