Schematic Representation of Two Genomic Regions That Involve CNVs Associated with SLE [65,66]

<div><p>(A) The region of Chromosome 1 containing the <i>FCGR3</i> gene cluster is highly variable and contains segmental duplications with a high sequence identity. Several CNVs have been reported that span this region. The genomic organization of the cluster is highly complex and not well solved in the current assembly of the genome sequence. The Affymetrix 500K and Illumina HumanHap 550 arrays do not cover this region well (red dotted lines).</p><p>(B) The region of Chromosome 6p21, containing the <i>C4A</i> and <i>C4B</i> genes, is embedded in a region of complex genomic organization [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b067" target="_blank">67</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b069" target="_blank">69</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b070" target="_blank">70</a>]. The region has been shown to contain segmental duplications and CNVs. The Affymetrix 500K and Illumina HumanHap 550 genotyping platforms do not cover this region, either (red dotted lines).</p></div

Types of Genomic Structural Changes Affecting Segments of DNA, Leading to Deletions, Duplications, Inversions, and CNV Changes (Biallelic, Multillelic, and Complex)

<p>The only segment that is constant is “A.” Segment “B” varies in orientation in the inversion. Segments “C” and “D” show different types of variation.</p

Expected and Observed Size Distribution of CNV Changes Identified to Date

<p>Blue bars represent the frequencies of the currently identified CNVs in the size ranges depicted in the <i>x</i>-axis. A plausible scenario of variation in CNV size frequency is depicted as red vertical bars. An under-detection of variable fragments of small size (<50 kb) can be observed, which is likely due to technological limitations in the high-throughput assays used so far to identify CNVs, largely based on array CGH (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-g002" target="_blank">Figure 2</a>). Observed and expected CNVs that are >50 kb coincide, due to the powerful array methods, which cover the medium-to-large-size CNVs well. Dark blue bars represent the small-sized CNVs, which are more of a challenge to detect.</p

CNV Characterization Strategies

<div><p>(A) Scales of resolution at the nucleotide level and maximum number of loci interrogated by the different methods (only the most widely used approaches are shown).</p><p>(B) Diagram of different approaches in CNV analysis, either at the genome-wide scale or at individual/multiplex loci. Arrows indicate the deeper analysis that is needed after initial detection by one methodology or another.</p><p>DASH, dynamic allele-specific hybridization [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b080" target="_blank">80</a>]; PRT, paralogue ratio test [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b081" target="_blank">81</a>]; MAQ, multiple amplicon quantification [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030190#pgen-0030190-b082" target="_blank">82</a>]; qPCR, quantitative PCR.</p></div

Approaches Used for the Identification of CNVs and Other Types of Structural Changes in the Human Genome

<p>Myriad methods and technologies have been employed to identify structural variants in the human genome. They are based on completely different experimental procedures and provide very different levels of resolution. The majority of findings (>80%) are attributable to a restricted number of high-throughput experiments with a limited resolution.</p

Abstract overview of the chromosomal regions that were included and excluded from our analysis

<p><b>Copyright information:</b></p><p>Taken from "On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees"</p><p>http://genomebiology.com/2007/8/10/R230</p><p>Genome Biology 2007;8(10):R230-R230.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2246304.</p><p></p> A colinear and an inverted chromosome are presented. The inversion in the rearranged chromosome is highlighted in red. For every chromosome, regions considered in this paper are labeled in black. Regions excluded from the main analysis (telomeres, centromeres and breakpoints (BKP)) are within boxes and labeled in red

Oligonucleotide Arrays <i>vs.</i> Metaphase-Comparative Genomic Hybridisation and BAC Arrays for Single-Cell Analysis: First Applications to Preimplantation Genetic Diagnosis for Robertsonian Translocation Carriers

<div><p>Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.</p></div

Examples of a) totally coincident profiles and b) highly similar profiles, obtained with oligonucleotide aCGH and BAC aCGH.

<p>Oligonucleotide aCGH profiles are shown at the top of the figure and BAC-aCGH profiles are shown below.</p

Cytogenetic results obtained from human single blastomeres analyzed by BAC aCGH and oligonucleotide aCGH.

<p>BL: Blastomere; SC: Sexual chromosomes, A: Aneuploidies; S: Segmental imbalances.</p><p>Cells 19-34: PGDs for six different couples with either male factor or repeated implantation failures.</p><p>Cytogenetic results obtained from human single blastomeres analyzed by BAC aCGH and oligonucleotide aCGH.</p

Examples of a) oligonucleotide aCGH profiles and b) their corresponding mCGH profiles.

<p>The first profile from a) and b) correspond to one blastomere with totally coincident profiles between techniques, and the second profile from a) and b) correspond to one blastomere with highly similar cytogenetic results.</p