Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays  Nathan R. Treff, Ph.D., Jing Su, M.Sc., Xin Tao, M.Sc., Brynn Levy, Ph.D., Richard T. Scott, M.D.  Fertility and Sterility  Volume 94, Issue 6, Pages 2017-2021 (November 2010) DOI: 10.1016/j.fertnstert.2010.01.052 Copyright © 2010 American Society for Reproductive Medicine Terms and Conditions

Figure 1 Graphic representation of copy number changes observed in various aneuploid cell lines using Copy Number Analysis Tool 4.0.1. Left. Results from microarray analysis performed on “genomic DNA” extracted from cultured cell lines. Right. Results from whole genome amplified DNA from single cells derived from the same cell line as shown in the left panel. Each graph indicates the copy number assignments (0, 1, 2, 3, or 4) on the y-axis and the chromosome number on the x-axis. Gains (copy number state >2) and losses (copy number state <2) are seen as bars above and below the copy number state of 2, respectively. The likely karyotype is indicated for each sample and is consistent with the designated karyotype assigned by the Coriell Cell Repository using standard cytogenetic analysis. Fertility and Sterility 2010 94, 2017-2021DOI: (10.1016/j.fertnstert.2010.01.052) Copyright © 2010 American Society for Reproductive Medicine Terms and Conditions

Figure 2 Loss of heterozygosity (LOH) probability plots for (A) a single cell derived from a female cell line with monosomy 21, and (B) a single cell derived from a male cell line with trisomy 13. Each upper graph indicates the single nucleotide polymorphism (SNP) copy number assignments (0, 1, 2, 3, or 4) on the y-axis. Each lower graph indicates the SNP LOH probability (0–1) on the y-axis. The chromosome number is indicated for both graphs on the x-axis. Arrows indicate chromosomes with unique LOH probability distributions. In the monosomy 21 cell line, there is only one copy of each SNP present on chromosome 21. This is reflected by a shift in the LOH probability of the SNPs toward 1 on the graph (i.e., a complete LOH). In the trisomy 13 cell line, the number of alleles is increased for all SNPs along chromosome 13 due to the extra copy. This is reflected in a greater frequency and distribution of all probes between 0 and 1 in the graph. Because this cell line is male, the LOH due to the single X chromosome is also evident by a shift in the LOH probability of the SNPs toward 1. Fertility and Sterility 2010 94, 2017-2021DOI: (10.1016/j.fertnstert.2010.01.052) Copyright © 2010 American Society for Reproductive Medicine Terms and Conditions

Figure 3 Examples of copy number results from four blastomeres within each of two embryos, embryo A (A) and embryo B (B). Results indicate meiotic aneuploidy of chromosomes 8, 11, and 14 in embryo A, and chromosome 22 in embryo B, as well as mitotic aneuploidy of chromosomes 1, 4, and 14 in embryo B. Shifts in the loss of heterozygosity (LOH) probability of aneuploidy chromosomes (arrows) in a blastomere from embryo A are also shown in C, illustrating the utility of this quality control analysis for verification of copy number assignments. Fertility and Sterility 2010 94, 2017-2021DOI: (10.1016/j.fertnstert.2010.01.052) Copyright © 2010 American Society for Reproductive Medicine Terms and Conditions