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Kimberly Troutman
Field Applications Scientist
1-25-11
Agilent Confidential
Agilent Microarray Platform
Overview
Applications
Gene expression
Agilent Genomics
DNA RNA
3) Deblock 2) Oxidation 80
60
Repeat n times Agilent
Full Length
(%)
40
HO O Ni
O
O P O O N2 20
RO
O Conventional
O P O O N1 Processes
RO 0
O 0 50 100 150 200
O P O
RO Oligo Length
(bp)
Evolution of Ink-Jet Oligo Array Technology
2000 2004
22K 44K
135mm 100mm
55 mm 30 mm
244K 976K
2006 2009
Overview
Applications
Gene expression
Comparative Genomic Hybridization Agenda
Technical overview
Array CGH
BACs, cDNA's, oligos
Understanding CGH: DNA Analytics CGH
Data Output
Heterozygous deletion (-1) Normal Amplification (>1)
Homozygous deletion (-2)
-4 -2 -1 0 +1 +2 +4
Probes
Cy5
Cy3
Red
Green
Chromosomal
Significant aberration
position
regions
Amp
Del
Exp
Notes
Ref AGW DNA Analytics module
Data shown in log2 ratio
Understanding CGH: Analysis of Cytogenetic
Sample
Genome view
Software settings
ADM-2 threshold 10
NA14117, 46,XY,del(5)(qter>p14:).ish del(5) (D5S23-) Min 3 probes
Understanding CGH: Analysis of Cytogenetic
Sample
NA14117
46,XY,del(5)(qter>p14:)
.ish del(5) (D5S23-)
Software settings
ADM-2 threshold 10
Min 3 probes
Choice of CGH Labeling Kits
Remark: parental
samples needed
to detect
heterodisomy
What is LOH: Loss of Heterozygosity
UPD in tumor cells is referred to as acquired UPD or copy neutral LOH (cnLOH)
Common in both hematologic and solid tumors
LOH of entire
chromosome LOH of
Normal cell
part of
arm
Interstitial
regions of
LOH
Enzymatic labeling CG CT CG CT AG CT
CG CT AG CT AG CT
Hybridization
Wash
CG CT
CG CT
CT
CT
CG CT
AG
AG
Scan
Human only
Non-FFPE
Non-cancer
Overview
Applications
Gene expression
Low Input Quick 4x44K v2 SurePrint G3 Additional
Amp New Higher Content
Smaller content throughput Exon
sample Lower price arrays
Lower price
Introducing
Low Input Quick Amp Labeling Kit (LIQA)
Agilent Confidential
Low Input 4x44K v2 SurePrint Additional
Quick Amp G3 Content
New
Smaller sample content Higher
Exon
arrays
Lower price throughput
Lower
price
Introducing
4x44K V2 Gene Expression Arrays
Product Overview: Introducing 4x44K v2 Arrays for
Human, Mouse, & Rat
With current content, based on updated transcriptome databases
Full coverage of human, mouse, and rat genomes
All standard controls included, plus probes for 12 ERCC controls
Providing consistent, high quality data
Wide dynamic range (~ 5 logs)
High reproducibility (< 15% CV between arrays or slides)
For confidence in gene expression results
Total unique
genes covered
19,596 27,958 21,503 34,017 17,366 26,930
Product Overview: 4x44K v2 Features & Benefits
Feature Benefit
Updated content for human, Comprehensive coverage based on current
mouse, and rat databases
Detect low expressors and high expressors
Same performance as v1 arrays
More accurately represent range of
Wide dynamic range
expression levels
High reproducibility, accuracy
Feel confident in the results
SurePrint G3
8x60K Gene Expression Arrays
Product Overview: Product Structure for SurePrint
G3 Gene Expression Arrays
8x60K prices are set according to whole-genome coverage
Price advantages for 8x60K can be reached via bundling with LIQA or
volume purchases
# Slides
Part Number Microarray
(# Arrays)
G4851A SurePrint G3 Human GE 8x60K Kit 3 (24)
G4852A SurePrint G3 Mouse GE 8x60K Kit 3 (24)
G4853A SurePrint G3 Rat GE 8x60K Kit 3 (24)
G4102A SurePrint G3 Custom GE 8x60K 1 (8)
G4862A SurePrint G3 Custom GE 4x180K 1 (4)
G4861A SurePrint G3 Custom GE 2x400K 1 (2)
G4860A SurePrint G3 Custom GE 1x1M 1 (1)
G4858A SurePrint G3 Unrestricted GE 8x60K 1 (8)
G4857A SurePrint G3 Unrestricted GE 4x180K 1 (4)
G4856A SurePrint G3 Unrestricted GE 2x400K 1 (2)
G4855A SurePrint G3 Unrestricted GE 1x1M 1 (1)
Agilent Confidential
Product Overview: SurePrint G3 Catalog Arrays
General
8x60K format: human, mouse, rat (more may follow)
10 ng for 8x60K & 8x15K formats and 25 ng for 4x formats
Content
Biological same as 4x44K v2
Human array will also include lincRNAs
Controls same as 4x44K v2, except
4x44K v2 arrays include 12 ERCC probes, while
8x60K arrays will include all 96 ERCC probes
Included on human and mouse catalog designs (no plans for rat)
Product Overview: SurePrint G3 Features & Benefits
Feature Benefit
Increased content More comprehensive coverage, ability to correlate
(human lincs, custom) lincRNA and mRNA expression
Higher throughput Easier lab processing
Run more samples to increase power of a gene
More affordable
expression study
More flexibility in designs: look at splicing events or
Higher density multiple species on an array (eg, human +
bacteria)
Updated content for human, mouse, Comprehensive coverage based on current
and rat databases
Detect low expressors and high expressors
Same performance as HD arrays
More accurately represent range of expression
Wide dynamic range
levels
High reproducibility, accuracy
Feel confident in the results
Preserve precious material
Compatible with LIQA
Work with smaller samples
Low RNA input (>10 ng)
Easy, simple assay
Single-tube chemistry
Decreased pipetting, fewer pipetting errors
Annotations updated regularly Annotations stay current with evolving databases
Low Input 4x44K 8x60K Additional
Quick Amp Redesign Higher Content
Smaller sample New throughput Exon
Lower price content Lower price arrays
Exon Arrays
There here!
Agilent Gene Expression Exon Arrays
Catalog and Custom Arrays
Genome Projects: H. sapiens, H. neanderthalensis, H. influenzae, M. musculus, R. norvegicus, P. troglodytes, M. mulatta, G. gallus, M. eugenii, F. silvestris,
C. lupus familiaris, D. melangaster, S. cerevisiae, S. pombe, N. crassa, A. thaliana, O. sativa, T. aestivum, Z. mays, P. trichocarpa, E. coli, SARS virus, S.
purpuratus, C. elegans, B. rerio, X. laevis, O. latipes, T. rubipres, S. lycopersicum, S. tuberosum, A. mellifera, V. vineifera, O. anatinus, A. pisum, etc.
Agilent Microarrays