Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Analyzing SNP-CGH data. (A) The log2 R ratio compares the observed normalized intensity (Rsubject) of the subject sample to the expected intensity (Rexpected; gray dot) based on the observed allelic ratio, θsubject, through a linear interpolation (gray lines) of the canonical clusters AA, AB, and BB (shown as circles) in the GenoPlot. The normalized intensity value obtained from a single SNP is represented as a purple dot. The R and θ values for the subject are shown with thick black dotted lines. (B) The canonical clusters (shown as circles) are also used to convert θ values, that is, θsubject, to B allele frequency (allelic copy ratio). This is accomplished by a linear interpolation of the known allele frequencies assigned to each cluster (0.0, 0.5, and 1.0). The allele frequency for an observed θ value falling between two clusters is also calculated by linear interpolation with lines D1 and D2. In the example shown, a data point falling approximately a third of the distance from the AB to the BB cluster (e.g., θsubject ∼ 0.76) has an allele frequency of 0.5 + 0.33 * 0.5 = 0.67. These two transformed parameters, log2 R ratio and B allele frequency, are then plotted along the entire genome for all SNPs on the array.

Article Snippet: Our results demonstrate the utility of using Infinium SNP-CGH bead arrays for detection of chromosomal aberrations including both homozygous and hemizygous deletions, copy-neutral LOH, monoallelic duplications, and amplifications.

Techniques: Transformation Assay

Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Examples of aberrations using HL-60 on the 109K BeadChip. The human promyelocytic leukemia cell line (HL-60) contains several well-characterized chromosomal aberrations. (A) An example of several discrete monoallelic amplifications across an ∼4.5-Mb region on chromosome 8 (green bar). The monoallelic amplification is evidenced by an increase in the log R ratio and the large split in the allele frequency. Based on the allelic ratios of ∼0.1 and ∼0.9, the level of amplification is on the order of five-to 10-fold. (B) Two deletions found on chromosome 9 (red bars). The first, which is ∼21 Mb, is detected by a deflection in the log R ratio and the collapse of heterozygotes in the allele frequency. The second deletion (∼2.4 Mb) was also detected using the same parameters. (C) The entire length of chromosome 18 (∼76 Mb) is duplicated (black bar), inferring a total copy number of 3. Notice the increase of the log R ratio to ∼0.5 and the cluster split in AF. (D) SNP-CGH arrays can detect a copy-neutral LOH event such as recombination or gene conversion. A small region on chromosome

Article Snippet: Our results demonstrate the utility of using Infinium SNP-CGH bead arrays for detection of chromosomal aberrations including both homozygous and hemizygous deletions, copy-neutral LOH, monoallelic duplications, and amplifications.

Techniques: Amplification

Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Verification of a chromosomal deletion with BAC array-CGH and FISH. We performed a blinded study on samples collected from patients with developmental clinical phenotypes previously characterized by karyotype, FISH, and BAC array-CGH analysis. (A) Data from a chromosomal BAC microarray showing the mean values of signal to noise (T/R) ratio and error bars of data from two separate hybridizations. The profile shown here represents an enlarged section of a chromosomal microarray showing a loss of three clones in the DiGeorge syndrome I critical region (encircled in red). (B) List of BAC clones, their location, and the log2 R ratio, indicating a loss of copy number in this region (three clones denoted in red). One additional clone shows a potential amplification present in another position in the genome (denoted in green; plots not shown). (C) FISH analysis using the F5 clone (for the DiGeorge region) showing one signal in red while the control probe in green shows two signals, confirming a deletion in the DiGeorge critical region. FISH analysis using the RP11-165F18 clone (distal to F5) shows no deletion. (D) The same aberration, an ∼1.5-Mb deletion on chromosome 22q11.2, detected by SNP-CGH on the Human-1 (109K) array as seen by the deflection in the log R ratio and the loss of heterozygote data points in the AF. (E) The same deletion on chromosome 22q11.2 detected by SNP-CGH on the HumanHap300 (317K) array. Notice the higher density of SNPs in this region on the HumanHap300 BeadChip. This finding confirms the deletion known to be present in the critical region of the DiGeorge syndrome. (F) Another deletion detected on chromosome 22q11.21 that is difficult to discern with the Human-1, which was not detected with any other method. (G) The same deletion can clearly be visualized with the HumanHap300 BeadChip, especially by the deflection in the log R ratio. For all plots, the blue line indicates a 500-kb and a 100-kb moving median, for the Human-1 and HumanHap300 BeadChips, respectively.

Article Snippet: Our results demonstrate the utility of using Infinium SNP-CGH bead arrays for detection of chromosomal aberrations including both homozygous and hemizygous deletions, copy-neutral LOH, monoallelic duplications, and amplifications.

Techniques: Microarray, Clone Assay, Amplification

Journal:

Article Title: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping

doi: 10.1101/gr.5402306

Figure Lengend Snippet: Effect of gDNA quantity and fragmentation on SNP-CGH data. SNP-CGH data quality as a function of the quantity and fragmentation length of gDNA in the amplification reactions was tested using a multisample 10K BeadChip format. (A) Various lengths of fragmented DNA were used as starting input for the whole-genome amplification reaction (Fragments 1, 2, and 3). (B) The call rate is relatively insensitive to input amount across the entire range of 200 ng to 3 ng or fragment length. The call rates for input DNA ranging from 25 to 200 ng were all above 0.999, and the call rates for the 3–12.5 ng were all above 0.996. (C) Genomic DNA was titrated from the standard 1× input (200 ng in a one-quarter scale reaction) down to 1/64th input (3 ng in a one-quarter scale reaction) as well as Fragments 1, 2, and 3. As the levels of input DNA decreased, the variability in the log R ratio noticeably increased, whereas the allelic ratio was relatively insensitive to input amounts. (D) The R 2 correlation between samples remains high when similar amounts of gDNA are used for input regardless if it falls into either high or low levels; however, the R 2 decreases dramatically between inputs that differ substantially in amount. (E) An example genome profile from chromosome 1 showing both the log R ratio and AF from the sample using 200 ng of input DNA. (F) The same plot as in E but with 3 ng of input DNA. Notice the slight increase in log R ratio variability with the lower amount of DNA input.

Article Snippet: Our results demonstrate the utility of using Infinium SNP-CGH bead arrays for detection of chromosomal aberrations including both homozygous and hemizygous deletions, copy-neutral LOH, monoallelic duplications, and amplifications.

Techniques: Amplification, Whole Genome Amplification