Fig. 1. Agilent

1
Quantitative analysis to assess the performance
of the complete Agilent oligo aCGH microarray
system. Sunny Song, Peter Webb, Anniek De Witte,
Diane Ilsley and Jim Collins Agilent
Technologies, Santa Clara, CA 95051
ABSTRACT
Fig. 4 244K microarray platform performance
using a range of genomic DNA input masses. A)
Log Ratio Noise. The standard deviation of Log2
Ratio values is lt 0.25 across the range of input
masses tested. B) Reproducibility across
replicate probes. The CV values for intra-array
replicate probes are all less than lt 5 for the
different DNA input masses. C) Accuracy. The
average Log2 Ratio of chrX probes in Male/Female
hybridizations is greater than 0.9 across the DNA
input masses tested indicating a high level of
accuracy.
Fig. 5 The high resolution 244K microarray
provides enhanced precision that enables novel
aberration detection . CGH Analytics views of
Agilent 244K and 44K analyses of chromosome 3 (A,
B) and chromosome 16 (C, D) in the human colon
carcinoma cell line HT29. A) Left, Scatter plot
(chromosome view) produced from Human CGH
Microarray 244K analysis reveals multiple 3p arm
deletions in regions such as 3p12.1-12.3
(horizontal shift to left of zero line) and a
focal deletion in 3p14.2 (horizontal shift to
left of zero line, outlined by dotted blue box).
Right, Zoomed-in gene view which focuses on a 7
MB window within 3p14.2 containing the focal
deletion. It distinctly shows two different
deletion patterns (homozygous and heterozygous
deletion) both within the single tumor suppressor
FHIT gene. B) Parallel scatter plots (chromosome
and gene views, respectively) from CGH 44K
Microarray analysis of the same sample as in
panel A. C) Left, Scatter plot (chromosome view)
produced from 244K analysis reveals a focal
homozygous deletion in 16p13.2. Right,
Zoomed-in gene view which focuses on a 0.5 MB
window within 16p13.2 containing a homozygous
deletion. It readily detects multiple deletion
patterns within the ataxin-2 binding protein
A2BP1 gene (green dots).
Fig. 2. Probe coverage on the 244K microarray.
Typical probe coverage characteristics on the
Human Genome CGH 244K and 44K microarrays
illustrated using the UCSC hg18 Human Genome
Browser, Feb 2006 (NCBI build 36) of human
chromosome 17. At the top of each view, each
short vertical bar represents a single probe on
Agilent Human Genome CGH 244K (red) or 44K (blue)
microarray. Annotations below the probes
indicate the location mapping of UCSC known genes
(blue or black) and Sanger microRNAs (red). A)
Variable probe density. A 3.0 MB microarray
window of 17q24-25 shows comprehensive coverage
that is more dense in coding regions. B)
Coverage of long genes. A 3.0 MB window of
17q11-12 depicts evenly distributed probe
coverage across long (ACCN1) as well as short
(NLE1) genes. C) Coverage of miRNAs. A 1.0 MB
region of 17q11.2 illustrates microRNA
representation (hsa-mir-193, hsa-mir-365-2).
Further, it shows a 50KB microdeletion within
16q23.1 (green dots in red circle). This
microdeletion (heterozygous deletion) was
verified by multiple consecutive probes. D)
Parallel scatter plots from CGH 44K Microarray
analysis of the same sample as in panel C.
Fig. 3. Probe Performance on the 244K
microarray. A) Low noise and high specificity.
aCGH 244K microarray log2 ratios are shown for
male/female hybridizations. A representative
separation histogram showing the distribution of
red/green fluorescence ratios for the autosomal
probes (green) and X-chromosomal probes (blue),
plotted as fraction of probes on the ordinate
(female, XX) versus red/green fluorescence ratio
(binned by intervals) on the abscissa of the
X-chromosome (male, XY) on the Agilent Human
Genome CGH 244K microarray. B) Improved signal
intensity. Signal intensities of probes on the
244K microarray show a tighter distribution and
medians of log10 signal Intensities. 244K
microarray (red) and 44K microarray (blue) were
hybridized with male/female DNA. More probes on
the 244K microarray show higher signal
intensities while the distribution of these
intensities is tighter.
Fig. 1. Agilents Microarray Comparative Genomic
Hybridization (CGH) Whole Platform Solution.
Schematic depiction of the procedures used to
measure DNA copy-number changes by CGH microarray
hybridization. Genomic DNA samples isolated from
tumor cells and normal cells are labeled with two
different fluorophores (Cy5 and Cy3,
respectively) and hybridized together to a single
CGH microarray. For each DNA probe on the
microarray, the ratio of intensity of the
fluorescence measured for the two fluors is
determined by dual laser scanning and data are
analyzed using the CGH Analytics software. A red
color represents increased DNA copy number, green
represents decreased copy number (i.e.,
deletion), and yellow represents no change in DNA
copy number in tumor cell DNA compared with
normal cell DNA.

• CONCLUSIONS
• Agilents 244K CGH microarray platform allows
  researchers to identify DNA copy variations with
  high resolution on a genome-wide scale.
• High quality data can be obtained from low input
  masses of genomic DNA without the need for sample
  amplification or complexity reduction.
• This high density platform provides enhanced
  precision that enables novel aberration
  detection.