Methods for non-invasive prenatal ploidy calling

Abstract

The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

What is claimed is: 
     
         1 . A method for preparing a preparation of amplified DNA derived from a blood, serum, or plasma sample of a pregnant women, the method comprising:
 (a) extracting cell-free DNA from the blood, plasma or serum sample, wherein the extracted cell-free DNA comprises a mixture of maternal DNA and fetal DNA;   (b) preparing a preparation of amplified DNA by binding a plurality of oligonucleotide probes to the extracted cell-free DNA or DNA derived therefrom, at a plurality of target loci on at least one chromosome or chromosome segment of interest, and amplifying 200 or more target loci having bound oligonucleotide probe in the same reaction mixture to obtain amplicons;   (c) analyzing the preparation of amplified DNA obtained in (b) by sequencing to measure the amount of amplicons derived from the fetal DNA in the blood, serum, or plasma sample using the measured quantity of each allele at the target loci.   
     
     
         2 . The method of  claim 1 , wherein the at least one chromosome or chromosome segment of interest comprises chromosome 13, chromosome 18, chromosome 21, chromosome X, and/or chromosome Y. 
     
     
         3 . The method of  claim 1 , wherein the sequencing is high-throughput sequencing. 
     
     
         4 . The method of  claim 1 , wherein step (b) comprises amplifying 1,000 or more target loci having bound oligonucleotide probe in the same reaction mixture. 
     
     
         5 . The method of  claim 1 , wherein step (b) comprises amplifying 2,000 or more target loci having bound oligonucleotide probe in the same reaction mixture. 
     
     
         6 . The method of  claim 1 , wherein step (b) comprises amplifying 5,000 or more target loci having bound oligonucleotide probe in the same reaction mixture. 
     
     
         7 . The method of  claim 1 , wherein the target loci are polymorphic loci. 
     
     
         8 . The method of  claim 1 , wherein the target loci are SNP loci. 
     
     
         9 . The method of  claim 1 , wherein steps (c) further comprises determining the copy number of the at least one chromosome or chromosome segment of interest in the genome of the fetus using the amount of amplicons derived from the fetal DNA. 
     
     
         10 . The method of  claim 1 , wherein the method is performed without prior knowledge of fetal or maternal genotypes.