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 system for measuring an amount of DNA from a first individual in a biological sample of a second individual, comprising:
 a sequencer for sequencing a plurality of DNA molecules to produce sequencing reads, wherein the DNA molecules comprise a mixture of amplicons derived from a first individual and amplicons derived from a second individual, wherein the amplicons derived from the first individual and the amplicons derived from the second individual are obtained from targeted multiplex amplification of 50-20,000 polymorphic loci performed on cell-free DNA isolated from the biological sample of the second individual or DNA derived therefrom, wherein at least 80% of the sequencing reads map to the polymorphic loci; and   a computer processer programmed to receive the sequencing reads, quantify the sequencing reads corresponding to each allele at the polymorphic loci, and measure the amount of DNA from the first individual in the biological sample of the second individual based on allele frequencies at a plurality of the polymorphic loci.   
     
     
         2 . The system of  claim 1 , wherein the sequencer performs high-throughput sequencing to produce the sequencing reads. 
     
     
         3 . The system of  claim 1 , wherein the biological sample is a blood, serum, plasma, or urine sample. 
     
     
         4 . The system of  claim 1 , wherein the DNA molecules each comprises a sequencing tag, wherein the sequencer uses the sequencing tag to perform high-throughput sequencing. 
     
     
         5 . The system of  claim 1 , wherein the DNA molecules each comprises a sample index for multiplex sequencing, wherein the computer processer is programmed to determine a sample origin of a sequencing read using the sample index. 
     
     
         6 . The system of  claim 1 , wherein the DNA molecules each comprises a molecular barcode, wherein the computer processer is programmed to identify sequencing reads that originate from the same original DNA molecule using the molecular barcode. 
     
     
         7 . The system of  claim 1 , wherein the first individual is a fetus. 
     
     
         8 . The system of  claim 1 , wherein the first individual is a transplant. 
     
     
         9 . The system of  claim 1 , wherein the polymorphic loci comprise SNP loci. 
     
     
         10 . The system of  claim 1 , wherein the polymorphic loci comprise indel loci. 
     
     
         11 . The system of  claim 1 , wherein the amplicons are obtained from targeted multiplex amplification of 50-5,000 polymorphic loci. 
     
     
         12 . The system of  claim 1 , wherein the amplicons are obtained from targeted multiplex amplification of 100-2,000 polymorphic loci. 
     
     
         13 . The system of  claim 1 , wherein the amplicons are obtained from targeted multiplex amplification of 200-1,000 polymorphic loci. 
     
     
         14 . The system of  claim 1 , wherein at least 90% of the sequencing reads map to 50-5,000 polymorphic loci. 
     
     
         15 . The system of  claim 1 , wherein at least 90% of the sequencing reads map to 100-2,000 polymorphic loci. 
     
     
         16 . The system of  claim 1 , wherein at least 90% of the sequencing reads map to 200-1,000 polymorphic loci. 
     
     
         17 . The system of  claim 1 , wherein at least 95% of the sequencing reads map to 50-5,000 polymorphic loci. 
     
     
         18 . The system of  claim 1 , wherein at least 95% of the sequencing reads map to 100-2,000 polymorphic loci. 
     
     
         19 . The system of  claim 1 , wherein at least 95% of the sequencing reads map to 200-1,000 polymorphic loci. 
     
     
         20 . The system of  claim 1 , wherein one or more of the polymorphic loci are located on one or more chromosomes expected to be disomic.