CytoSure™ Interpret Software — Tips and Tricks

Friday 19 August 2011
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Analysis of CytoSure arrays that contain SNP data

A new analysis interface, with accompanying reporting and database functionality, has been added to enable analysis of CytoSure arrays that contain SNP data (e.g., CytoSure ISCA UPD array). The following article explains the use of these new features.

Note: This functionality is only available with CytoSure Interpret Software version 3.3.2 onwards. Request the latest version atproducts@ogt.co.uk.

Genotyping data contained on CytoSure arrays can now be analysed using the new UPD analysis interface, located in theIdeogram View in the CNVs/SNPs tab (or by clicking Tools ->SNP/UPD Data).

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                Figure 1: Ideogram view with SNP data.

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In addition to displaying the locations of gains and losses in the data, each chromosome ideogram will also display SNP locations and colour-code them according to genotype, with heterozygotes coloured black and homozygotes coloured red. There are two views of the distribution of homozygous and heterozygous SNPs available, and these can be toggled by clicking on the area covered by the SNP data:

View 1: Each SNP is represented by a circle.

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Figure 2: Circle SNP representation.

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View 2: Each contiguous stretch of homozygosity/heterozygosity is represented by a rectangle covering the region between the first and last SNP in the stretch. Stretches containing more than 10 probes are filled in.

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Figure 3: Rectangle SNP representation.

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The dials above the ideograms display the percentage of homozygous SNPs for the chromosome.

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Figure 4: Percent homozygosity dials.

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Ideograms of chromosomes with a homozygosity level above a user-definable threshold will be displayed with a red background.

Analysis options

It is possible to modify this threshold and other analysis settings by clicking on the Options... button which is displayed at the bottom of the screen when the mouse hovers over the ideogram view.

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Figure 5: Location of the Options... button.

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Clicking on the Options... button will display the UPD Optionsdialog box. The dialog box contains two tabs: Genotype Callingand SNP Probe Filters. The Genotype Calling tab contains the following:

  • Homozygosity Threshold slider — Ideograms of chromosomes whose percentage homozygosity exceeds this threshold will be given a red background.
  • Limits for Genotype Assignment — This graph displays the distribution of the log2 signal intensity ratio for all pairs of SNPs on the array. Two thresholds can be modified in order to determine the genotype of each SNP:
    • Lower Bound — SNPs whose absolute log2 signal intensity ratio falls below this value will be called asheterozygousUpper Bound — SNPs whose absolute log2 signal intensity ratio falls above this value will be called as homozygous.
    • SNPs whose absolute log2 signal intensity ratio fallsbetween these two thresholds will not be included in the analysis and will be visualised as an empty black circle in the ideogram view.

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Figure 6: UPD Options dialog box with Genotype Calling tab displayed.

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The SNP Probe Filters tab contains the following:

  • Apply SNP Probe Filters check box — Determines whether the proceeding probe filters will be applied if selected.
  • Exclude Non-Uniform Outliers check box — If selected, SNPs with 1 or more non-uniform probes will be excluded from the analysis.
  • Exclude SNPs within aberrant regions? check box — If selected, SNPs within regions covered by gains or losses already identified in the CNV data will be excluded from the analysis.
  • Exclude SNPs Based on... graphs — SNPs whose Signal Intensity or Reproducibility values fall within the grey area are excluded from the analysis.

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          Figure 7: UPD Options dialog box with SNP Probe

                             Filters tab displayed.

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Chromosome overview

More detailed information relating to an individual chromosome is available by clicking on its ideogram. This information includes:

  • Larger, horizontal ideogram.
  • Log2 signal intensity ratio (allele A probe signal / allele B probe signal) distribution plot for SNPs in the chromosome compared to the whole genome.
  • Table of largest (most SNPs) regions of loss of heterozygosity (LOH) in the chromosome.
  • Graph of percent homozygosity against number of SNPs in each chromosome, with the selected chromosome highlighted in red.

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Figure 8: Chromosome overview including signal ratio distribution graph and table of largest regions of loss of heterozygosity.

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Reporting

HTML and PDF reports generated from data containing genotyping information will include a table of the percentage of homozygous SNPs for each chromosome.

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Figure 9: Percent homozygosity table included in a PDF report.

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Database functionality

If sample information is submitted to the database, the table of homozygosity will be available by clicking on the icon in the UPDcolumn of the Submissions table of the Database Managementtab. If the percentage homozygosity of any of the autosomes of a particular sample exceeds the current threshold, the icon will be displayed in red; otherwise, it will be displayed in blue.

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Figure 10: Percent homozygosity table dialog box in Database Management tab.

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Request the latest version of CytoSure Interpret Software

CytoSure™ products are for research use only; not for use in diagnostic procedures.