PRE-IMPLANTATION GENETIC SCREENING AND ANEUPLOIDY DETECTION
Provided herein are methods for determining ploidy of an embryo. The methods can include the steps of amplifying, using a primer pair that amplifies a plurality of human genomic loci, nucleic acid from a preimplantation embryo to generate a plurality of amplicons, sequencing the amplicons to generate a plurality of sequence reads, matching the sequence reads to the genomic loci and counting a number of matches, and determining chromosome count based on the number of matches. Also provided herein are systems for determining chromosome count comprising a processor coupled to a tangible memory subsystem storing instructions. When executed by the processor, the instructions cause the system to implement the methods provided.
1 . A method for determining ploidy of an embryo, the method comprising:
amplifying, using a primer pair that amplifies a plurality of human genomic loci, nucleic acid from a preimplantation embryo to generate a plurality of amplicons;
sequencing the amplicons to generate a plurality of sequence reads;
matching the sequence reads to the genomic loci and counting a number of matches; and
determining chromosome count based on the number of matches.
2 . The method of claim 1 , further comprising obtaining a sample of nucleic acid.
3 . The method of claim 2 , further comprising obtaining the sample by biopsy.
4 . The method of claim 3 , wherein the biopsy is a trophectoderm biopsy.
5 . The method of claim 2 , wherein the sample includes at least one cell from the preimplantation embryo.
6 . The method of claim 5 , wherein the sample contains from about 1 to about 8 cells.
7 . The method of claim 6 , wherein the sample contains from about 1 to about 5 cells.
8 . The method of claim 1 , wherein the primer pair is complimentary to sequences distributed on at least 4 human chromosomes.
9 . The method of claim 1 , wherein not all of the amplicons are identical.
10 . The method of claim 1 , wherein the amplicons include sequences on at least one chromosome of interest and sequences on one or more reference chromosomes.
11 . The method of claim 10 , wherein the at least one chromosome of interest is selected from the group consisting of chromosome 9, chromosome 13, chromosome 18, chromosome 21, X chromosome and Y chromosome.
12 . The method of claim 1 , wherein the determining chromosome count step comprises the generation and comparison of a z-score for a chromosome of interest.
13 . The method of claim 1 , further comprising determining a euploidy or aneuploidy state of the embryo based on the chromosome count.
14 . The method of claim 1 , further comprising attaching sequence adapters and bar codes to the amplicons simultaneously with amplification of the nucleic acid.
15 . The method of claim 1 , wherein the primer comprises a universal primer binding site.
16 . The method of claim 15 , further comprising a second round of amplification comprising adding sequencing adaptors to the amplicons using second primers that hybridize to the universal primer binding site.
17 . The method of claim 1 , further comprising fragmenting the nucleic acid.
18 . A system for determining chromosome count, the system comprising:
a processor coupled to a tangible memory subsystem storing instructions that when executed by the processor cause the system to:
obtain sequence reads from amplicons, wherein the amplicons are generated by amplifying, using a primer pair that amplifies a plurality of human genomic loci, nucleic acid from a preimplantation embryo;
match the sequence reads to the genomic loci;
count a number of matches at the genomic loci; and
determine chromosome count based on the number of matches.
19 . The system of claim 18 , wherein the nucleic acid was obtained from a sample.
20 . The system of claim 19 , wherein the sample was obtained by biopsy
21 . The system of claim 20 , wherein the biopsy is a trophectoderm biopsy.
22 . The system of claim 19 , wherein the sample contains from about 1 to about 5 cells from the preimplantation embryo.
23 . The system of claim 19 , wherein the primer pair is complimentary to sequences distributed on at least 4 human chromosomes.
24 . The system of claim 19 , wherein the amplicons include sequences on at least one chromosome of interest and sequences on one or more reference chromosomes.
25 . The system of claim 24 , wherein the at least one chromosome of interest is selected from the group consisting of chromosome 9, chromosome 13, chromosome 18, chromosome 21, X chromosome and Y chromosome.
26 . The system of claim 1 , wherein the instructions further cause the system to determine and report a euploidy or aneuploidy state of the embryo based on the chromosome count.