Methods of quality control using single-nucleotide polymorphisms in pre-implantation genetic screening
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.
1 . A method for pre-implantation genetic screening of an embryo, the method comprising:
obtaining a genomic sample from an embryo pre-implantation, wherein a plurality of single nucleotide polymorphisms (SNPs) are distributed throughout the genomic sample;
performing FAST-SeqS on the genomic sample to produce sequencing reads;
identifying, using the sequencing reads, a set of SNPs from the plurality of SNPs in a region of the genomic sample covered by the sequencing reads;
determining, using the set of SNPs, a plurality of allele fractions for the set of SNPs in the region of the genomic sample covered by the sequencing reads, wherein each allele fraction of the plurality of allele fractions is a proportion of an allele at a particular locus within the region;
enumerating read counts from the sequencing reads;
determining a putative chromosome copy number of a chromosome of the genomic sample according to the read counts;
screening out the embryo from implantation when the putative chromosome copy number indicates diploidy and the plurality of allele fractions indicate aneuploidy or unexpected integral multiples of a haploid chromosome.
2 . The method of claim 1 , wherein an allele fraction in the plurality of allele fractions indicates a genomic locus in the region is homozygous or heterozygous.
3 . The method of claim 1 , wherein a putative chromosome copy number of 2 combined with an allele fractions inconsistent with diploidy indicates triploidy, haploidy, or isodisomic uniparental disomy.
4 . The method of claim 1 , wherein the embryo is a human embryo.
5 . The method of claim 1 , further comprising implanting the embryo when the chromosome copy number and the plurality of allele fractions indicate diploidy.
6 . The method of claim 1 , wherein screening out the pre-implantation embryo from implantation comprises screening out when the putative chromosome copy number is diploidy and the allele fractions deviate from an expected diploid allele fraction by more than a threshold amount.
7 . The method of claim 6 , wherein the threshold amount is 10%.
8 . The method of claim 6 , wherein the threshold amount is 20%.
9 . A method for confirming or refuting a putative chromosome copy number of a genomic sample of an embryo pre-implantation, the method comprising:
obtaining a genomic sample from an embryo pre-implantation, wherein a plurality of single nucleotide polymorphisms (SNPs) are distributed throughout the genomic sample;
performing FAST-SeqS on the genomic sample to produce sequencing reads;
obtaining a putative chromosome copy number for the genomic sample, the putative chromosome copy number calculated from counts of the sequencing reads;
identifying, using the sequencing reads, a set of SNPs from the plurality of SNPs in a region of interest of the genomic sample covered by the sequencing reads;
determining, using the set of SNPs, a plurality of allele fractions of the set of SNPs in the region of interest in the genomic sample, wherein each allele fraction of the plurality of allele fractions is a proportion of an allele of one SNP of the set of SNPs; and
confirming the putative chromosome copy number when the putative chromosome copy number is consistent with the plurality of allele fractions; or
refuting the putative chromosome copy number when the putative chromosome copy number is inconsistent with the plurality of allele fractions.
10 . The method of claim 9 , wherein determining the putative chromosome copy number comprises determining a diploid putative chromosome copy number.
11 . The method of claim 9 , wherein an allele fraction of the plurality of allele fractions indicates a locus of interest is homozygous or heterozygous.
12 . The method of claim 9 , wherein an allele fraction of 100% and a putative chromosome copy number of 1 for the region of interest indicates monosomy; wherein an allele fraction of 50% and a putative chromosome copy number of 2 for the region of interest indicates disomy; or wherein an allele fraction between 10% and 40% or between 60% and 90% and a putative chromosome copy number of 3 for the region of interest indicates trisomy.
13 . The method of claim 9 , 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.
14 . The method of claim 9 , wherein the putative chromosome copy number is determined to be a trisomy 21, trisomy 18, trisomy 13, or another aneuploidy condition.
15 . The method of claim 9 , wherein refuting the putative chromosome copy number comprises identifying an allele fraction that deviates from an expected allele fraction of the putative chromosome copy number by more than a threshold amount.
16 . The method of claim 15 , wherein the threshold amount is 10%.
17 . The method of claim 15 , wherein the threshold amount is 20%.
18 . The method of claim 9 , further comprising implanting the embryo when the chromosome copy number and the plurality of allele fractions indicate diploidy.
19 . The method of claim 9 , wherein the embryo is a human embryo.