Methods of quality control using single-nucleotide polymorphisms in pre-implantation genetic screening

Abstract

The present invention provides methods for validating results of a pre-implantation genetic screen. Methods of the invention increase the efficacy of the common PGS assay FAST-SeqS by taking advantage of single-nucleotide polymorphisms (SNPs) generated from the assay to confirm copy number calls, detect errors, identify samples, and recognize and identify sources of contamination. Methods of the invention increase the reliability of a PGS result, thereby making embryo selection more precise and improving outcomes of in vitro fertilization.

What is claimed is: 
     
         1 . A method for validating a putative chromosome copy number in a genomic sample, the method comprising:
 obtaining sequencing reads from a genomic sample amplified by FAST-SeqS;   enumerating read counts from the sequencing reads;   calculating putative chromosome copy numbers of the genomic sample based on the read counts;   obtaining allele fractions for SNPs in a region covered by the sequencing reads; and   comparing the allele fractions to the putative chromosome copy numbers to validate the putative chromosome copy numbers.   
     
     
         2 . The method of  claim 1 , wherein the genomic sample is biopsied from an embryo. 
     
     
         3 . The method of  claim 1 , wherein the genomic sample comprises circulating cell-free fetal DNA, amniotic fluid, chorionic villus, fetal cells in maternal blood, trophoblasts, umbilical cord blood, tumor biopsy, or circulating tumor DNA. 
     
     
         4 . The method of  claim 1 , wherein an allele fraction that is inconsistent with the putative chromosome copy number invalidates the putative chromosome copy number. 
     
     
         5 . The method of  claim 1 , wherein a putative chromosome copy number of 1 indicates monosomy; wherein a putative chromosome copy number of 2 indicates disomy; and wherein a putative chromosome copy number of 3 indicates trisomy. 
     
     
         6 . The method of  claim 1 , wherein an allele fraction indicates a genomic locus is homozygous or heterozygous. 
     
     
         7 . The method of  claim 1 , wherein an allele fraction or set of allele fractions of 100% indicates monosomy; wherein an allele fraction or set of allele fractions of 50% indicates disomy; and wherein an allele fraction or set of allele fractions between 10% and 40% or between 60 and 90% indicates trisomy or tetrasomy. 
     
     
         8 . The method of  claim 1 , wherein a putative chromosome copy number of  2  combined with allele fractions inconsistent with diploidy indicates triploidy, haploidy, or isodisomic uniparental disomy. 
     
     
         9 . The method of  claim 1 , further comprising identifying allele fractions that deviate from an expected allele fraction by more than a threshold amount. 
     
     
         10 . The method of  claim 1 , further comprising diagnosing trisomy 21, trisomy 18, trisomy 13, or another aneuploidy condition. 
     
     
         11 . A method for validating a putative chromosome copy number in a genomic sample, the method comprising:
 obtaining putative chromosome copy numbers for a genomic sample, the copy numbers calculated from sequence read counts of FAST-SeqS-amplified DNA;   obtaining allele fractions of SNPs in the genomic sample, the SNPs sequenced from FAST-SeqS-amplified DNA;   comparing the allele fractions to the putative chromosome copy numbers; and   determining whether the putative chromosome copy numbers are consistent with the allele fractions.   
     
     
         12 . The method of  claim 11 , wherein the genomic sample is biopsied from an embryo. 
     
     
         13 . The method of  claim 11 , wherein the genomic sample comprises circulating cell-free fetal DNA, amniotic fluid, chorionic villus, fetal cells in maternal blood, trophoblasts, umbilical cord blood, tumor biopsy, or circulating tumor DNA. 
     
     
         14 . The method of  claim 11 , wherein an allele fraction or set of allele fractions that is inconsistent with the putative chromosome copy number invalidates the putative chromosome copy number. 
     
     
         15 . The method of  claim 11 , wherein a putative chromosome copy number of 1 indicates monosomy; wherein a putative chromosome copy number of 2 indicates disomy; and wherein a putative chromosome copy number of 3 indicates trisomy. 
     
     
         16 . The method of  claim 11 , wherein an allele fraction indicates a genomic locus is homozygous or heterozygous. 
     
     
         17 . The method of  claim 11 , wherein an allele fraction or set of allele fractions of 100% indicates monosomy; wherein an allele fraction or set of allele fractions of 50% indicates disomy; and wherein an allele fraction or set of allele fractions between 10% and 40% or between 60 and 90% indicates trisomy or tetrasomy. 
     
     
         18 . The method of  claim 11 , wherein a putative chromosome copy number of  2  combined with an allele fraction or allele fractions inconsistent with diploidy indicates triploidy, haploidy, or isodisomic uniparental disomy. 
     
     
         19 . The method of  claim 11 , further comprising identifying allele fractions that deviate from an expected allele fraction by more than a threshold amount. 
     
     
         20 . The method of  claim 11 , further comprising diagnosing trisomy 21, trisomy 18, trisomy 13, or another aneuploidy condition.