CGH Analytics Platform
CGH Analytics Platform
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Agilent’s CGH analytics software offers a sophisticated set of analytical tools for assessing chromosomal variations, helping you place results into biological context. Once you have identified key areas, you can then analyze specific regions-of-interest for common gains and losses across cohorts. Use software specifically designed for genomic variation analysis to gain a more complete perspective of the entire chromosome, delineate aberration boundaries, and make statistically relevant variation calls. Agilent’s CGH Analytics software integrates with our GeneSpring Software Platform, enabling analysis, comparison, and visualization of data across multiple applications. Analyze CGH and Gene Expression data jointly, validating the relationship between transcriptional and genetic regulation, while improving your confidence when making close aberration calls.
Robust Data Interpretation: Identify differentially expressed genes or genetic variations with advanced statistical analysis hypothesis testing.
Figure 1. View of Chromosome 8 from CGH Analytics showing deletion in the p arm and amplification in the q arm and a small heterogeneous loss at q23.1.
Copy number changes representing a Chromosome 8p deletion and 8q amplification detected on microarrays using the standard aCGH Version 3 protocol with 3 µg of input gDNA were also detected when using the modified aCGH protocol for Low Input gDNA with 500 ng input with genomic DNA (gDNA) from a female colon carcinoma cell line and pooled normal female gDNA as reference sample (HT29/XX).
(A) 3 µg genomic DNA (gDNA) input (polarity = 1, HT29(Cy5)/XX(Cy3)). (B) 3 µg gDNA input with dye-swap (polarity = -1, XX(Cy5)/HT29(Cy3)). (C) 500 ng gDNA input (polarity = 1). (D) 500 ng gDNA input with dye-swap (polarity = -1). Log2 ratio values for all oligonucleotide probes on chromosome 8 of HT29 cell line gDNA are plotted as a function of their chromosomal position. Every point represents 1 probe. The thin blue line shows a 1 Mb moving average, while the thick blue lines and shaded areas show the aberration calls identified by the ADM-1 algorithm.
Figure 2. View of Chromosome 18 from CGH Analytics showing the single copy amplification of the p arm and deletion of the q arm.
A single copy amplification of the p arm and deletion of the q arm of Chromosome 18 were also observed on microarrays using both gDNA input levels from a female colon carcinoma cell line and pooled normal female gDNA as reference sample (HT29/XX).
(A) 3 µg gDNA input (polarity = 1, HT29(Cy5)/XX(Cy3)). (B) 3 µg gDNA input with dye-swap (polarity = -1, XX(Cy5)/HT29(Cy3)). (C) 500 ng gDNA input (polarity = 1). (D) 500 ng gDNA input with dye-swap (polarity = -1). Log2 ratio values for all oligonucleotide probes on chromosome 18 of HT29 cell line gDNA are plotted as a function of their chromosomal position. Every point represents 1 probe. The thin blue line shows a 1 Mb moving average, while the thick blue lines and shaded areas show the aberration calls identified by the ADM-1 algorithm.
Figure 3. Gene view of Chromosome 16 from CGH Analytics showing a homozygous deletion at the A2BP1 locus.
A previously identified aberration was detected on Chromosome 16 using both the modified aCGH protocol for Low Input gDNA and the aCGH Version 3 protocol. The “Gene View” window (~2.5 Mb) of Chromosome 16 from CGH Analytics shows this homozygous deletion at the A2BP1 locus from a female colon carcinoma cell line and pooled normal female gDNA as reference sample (HT29/XX).
(A) 3 µg input gDNA (polarity = 1, HT29(Cy5)/XX(Cy3)). (B) 3 µg input gDNA with dye-swap (polarity = -1, XX(Cy5)/HT29(Cy3)). (C) 500 ng input gDNA (polarity = 1). (D) 500 ng input gDNA with dye-swap (polarity = -1). Log2 ratio values for oligonucleotide probes on chromosome 16 of HT29 cell line gDNA are plotted as a function of their chromosomal position. Every point represents 1 probe with no moving average. The thick blue lines and shaded areas show the aberration calls identified by the ADM-1 algorithm.
Reference: An Optimized aCGH Protocol Allows Reduced Input of Genomic DNA.
Agilent Publication Number 5989-5048EN.
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CGH Analytics: provides an intuitive user interface for visually exploring, detecting and analyzing aberration patterns from multiple Comparative Genomic Hybridization (CGH) microarray profiles.
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For research use only and not for use in diagnostic procedures.