Genomics Technologies Features and Considerations

Platform Comparison


Gene Expression.

 
Affymetrix
Agilent
Illumina
NimbleGen
Amount of total RNA requested for UHNMAC service 100 ng 2 µg 100 ng 10 µg
Amplification involved in labeling the amount of RNA listed above Yes Yes Yes No
Amplification method available? Minimum amount of total RNA required Yes, 500 pg No (as little as 50 ng total RNA can be used, although less reliable) No Yes, 100 ng*
Protocol for partially degraded samples Yes No Yes No
One- or two-colour One Both One (streptavidin-Cy3 staining) Both
Probe size 25-mer 60-mer 50-mer 60-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms) Human
Mouse
Yeast
Rat
Arabidopsis
Drosophila
C. elegans
Zebrafish
& others

Affymetrix is the only platform to offer catalogue Grape, Soybean & Citrus arrays

Human
Mouse
Yeast
Rat
Arabidopsis
Drosophila
C. elegans
Zebrafish
& others

Agilent is the only platform to offer catalogue Brassica, Salmon & Tobacco arrays

Human
Mouse
Yeast
Human
Mouse
Yeast
Rat
Arabidopsis
Drosophila
C. elegans
Zebrafish
& others

Prokaryotic designs covering over 200 organisms

Number of probes Millions of features (i.e. >5.3 million on Human Exon 1.0ST array 15K, 44K, 2x105K, 244K formats available up to 48K (Human whole genome array) 385K, HD2 (2.1 million) 4x72K 12x135K
Software for analysis Expression Console GeneSpring BeadStudio ArrayStar

* NimbleGen suggests using MessageAmp II aRNA Amplification kit (Ambion)
 

ChIP-on-Chip.

 
Affymetrix
Agilent
NimbleGen
Amount of DNA requested for UHNMAC service 9 µg 4 µg PCR amplified 2.5 µg (385K array) 6.5 µg (HD2 array)
Probe size 25-mer 60-mer 50-75-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms) Human
Mouse
Yeast
Arabidopsis
Drosophila
C. elegans
Promoter-specific Chromosome 21/22 ENCODE
Human
Mouse
Yeast
Arabidopsis
Drosophila
C. elegans
CpG Promoter-specific ENCODE
Human
Mouse
Rat
Drosophila
C. elegans
Array formats >6 million features possible 2x244K Custom arrays (15K, 105K, 244K) HD2, 385K
 

DNA Methylation

 
Agilent
Illumina
NimbleGen
Amount of DNA requested for UHNMAC service 2 µg PCR amplified or genomic 1 µg genomic DNA 1 µg PCR amplified or genomic
Probe size 60-mer 50-mer 50-75-mer
Species for which catalogue arrays are available (Custom printing is available on all platforms) Human
Mouse
Human Human
Mouse
Rat
Arabidopsis
Dog
Chicken
Array formats 2x244K Custom arrays (15K, 105K, 244K) Human CGI 8.1K, 12K 385K, HD2
 

miRNA Profiling.

 
Affymetrix
Agilent
Illumina
Amount of RNA requested for UHNMAC service please inquire 100 ng total RNA 100-200 ng total RNA (DASL assay*)
One- or two-colour One One One
Probe size 25-mer 60-mer 50-mer
Species for which arrays are available Human
Mouse
Rat
Canine
Monkey
*all species represented on one array*
Human
Mouse
Rat

Custom printing available

Human
Mouse

Custom printing available

Sanger miRNA database version number used (as of March 9, 2009) ver.11 Human:ver.12
Mouse: ver.12
Rat: ver.10.1
Custom
ver.12
Array formats mini-array (format 400)
4 identical sense probes for each miRNA
8x15K
Human: 866 + 89
human viral
Mouse: 627 + 39 mouse viral
Rat: 350
12 sample BeadChip
Human: 1146
Mouse: 656

* DASL assay: cDNA-mediated Annealing, Selection, extension, Ligation assay
 

Array CGH.*

 
Agilent
NimbleGen
Amount of genomic DNA requested for service 3 µg 1-5 µg
Amount of DNA required for amplification method, if available 100 ng N/A
Probe size 60-mer 50-75-mer
Species for which catalogue arrays are available (Custom printing is available on both platforms) Human
Mouse
Rat
Human
Mouse
Rat
Drosophila
C. elegans
S. cerevisiae
S. pombe
Zebrafish
Chicken
Cow
P. falciparum 3D7
Array formats 244K, 2x105K, 4x44K Human: 2.1M, 385K, 12x135K, 4x72K;
Mouse & others: mostly 385K

* cDNA arrays can also be used for aCGH, read more
 

cDNA Microarrays

Advantages
Disadvantages
Increased detection sensitivity due to longer sequences Cross-hybridisation can be a problem
Affordable (production cost is lower than for oligonucleotide arrays) Maintaining clones and PCR amplification is labour-intensive (not a problem if you are purchasing printed arrays)
Allows representation of entire genome on one array
No prior knowledge of gene sequence required (use of clone library); no probe design involved
 

Oligonucleotide arrays (in general)

Advantages
Disadvantages
Higher specificity (less cross-hybridisation due to shorter probes) Decreased sensitivity due to shorter sequences (lower sensitivity compensated by use of multiple probes)
More uniform melting temperatures Expensive to design and manufacture
Detection of SNP and splice variants Prior knowledge of sequence required
Higher uniformity of spots (controlled amount of material per spot)
 

Affymetrix and Agilent Oligonucleotide arrays

Affymetrix
Agilent
Only 1-colour is offered Offers both 1- and 2-colour systems
Decreased sensitivity due to shorter sequences (25-mer); however, lower sensitivity compensated by the fact that multiple oligos represent each gene Longer 60-mers are more tolerant of sequence mismatches and thus are more suitable for analysis of highly polymorphic regions
RNA amplification is part of RNA labeling protocol; can be fairly expensive (compared with cDNA arrays) RNA amplification is part of RNA labeling protocol; can be fairly expensive (compared with cDNA arrays)
Additional equipment (specialised fluidics station and Affymetrix-specific scanner) required
 

Agilent 1-colour versus 2-colour

 

Table 1. The strengths and weaknesses of NGS and microarrays.
(This table was taken from Asmann et al. Gastroenterology 2008, 135:1466)

Microarray Analysis
Massively parallel, or next-generation, sequencing
Pros
Cons
Pros
Cons
Relatively inexpensive High background, low sensitivity Low background, very sensitive Expensive
Easy sample preparation Limited dynamic range Large dynamic range Complex sample preparation
Mature informatics and statistics Not quantitative Quantitative Limited bioinformatics
  Competitive hybridisation Massive information technology infrastructure required
Annotation of probes
 

Table 2. Comparison of Roche, Illumina, and Applied Biosystems NGS platforms.

Roche (454): Titanium series reagents (run on FLX Genome Sequencer)
Illumina: Genome Analyser II
Applied Biosystems: SOLiDTM
Sequencing chemistry pyrosequencing polymerase-based sequencing-by-synthesis Ligation-based sequencing
Amplification approach Emulsion PCR Bridge amplification Emulsion PCR
MB/run 400-600 MB 1300 MB 3000 MB
Time/run 10 hr 4 days 5 days
Read length 400 bp up to 75 bp 35 bp
 
Products List

 
Services List


Ordering Information

Order Placement.
Please use our order form to place an order. For questions about the ordering process feel free to contact us.
 
 
 
 

About Us  |  Products  |  Services   |   R&D Projects   |   Order Form   |   Contact Us © 1997-2014 DNAmicroarray, Inc. All rights reserved.