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Probe Selection Strategies for Microarrays
Considerations and Pitfalls
Kay Hofmann
MEMOREC Stoffel GmbH
Cologne/Germany
Probe selection wish list
Probe selection strategy should ensure
Biologically meaningful results (The truth...)
Coverage, Sensitivity (... The whole truth...)
Specificity (... And nothing but the truth)
Annotation
Reproducability
Technology
Probe immobilization
Oligonucleotide coupling
Synthesis with linker, covalent coupling to surface
Oligonucleotide photolithography
ds-cDNA coupling
cDNA generated by PCR, nonspecific binding to surface
ss-cDNA coupling
PCR with one modified primer, covalent coupling, 2nd strand removal
Spotting
With contact (pin-based systems)
Without contact (ink jet technology)
Technology-specific requirements
General
Not too short (sensitivity, selectivity)
Not too long (viscosity, surface properties)
Not too heterogeneous (robustness)
Degree of importance depends on method
Single strand methods (Oligos, ss-cDNA)
Orientation must be known
ss-cDNA methods are not perfect
ds-cDNA methods don’t care
Probe selection approaches
Accuracy
Throughput
Selected
Genes
Selected Gene
Regions
ESTs
Cluster
Representatives
Anonymous
Non-Selective Approaches
Anonmymous (blind) spotting
Using clones from a library without prior sequencing
Only clones with interesting expression pattern are sequenced
Normalization of library highly recommended
Typical uses:
HT-arrays of ‘exotic’ organisms or tissues
Large-scale verification of DD clones
EST spotting
Using clones from a library after sequencing
Little justification since sequence availability allow selection
Spotting of cluster representatives
Sequence Clustering
For human / mouse / rat EST clones: public cluster libraries
Unigene (NCBI)
THC (TIGR)
For custom sequence: clustering tools
STACK_PACK (SANBI)
JESAM (HGMP)
PCP (Paracel, commercial)
A benign clustering situation
!
In the absence of 5‘-3‘ links
Two clusters corresponding to one gene
!
Overlap too short
Three clusters corresponding to one gene
!
!
Chimeric ESTs
One cluster corresponding to two genes
Chimeric ESTs .. continued
Chimeric ESTs are quite common
Chimeric ESTs are a major nuisance for array probe selection
One of the fusion partners is usually a highly expressed mRNA
Double-picking of chimeric ESTs can fool even cautious clustering
programs.
Unigene contains several chimeric clusters
The annotation of chimeric clusters is erratic
Chimeric ESTs can be detected by genome comparison
There is one particularly bad class of chimeric sequences that will
be subject of the exercises.
How to select a cluster representative
If possible, pick a clone with completely known sequence
Avoid problematic regions
Alu-repeats, B1, B2 and other SINEs
LINEs
Endogenous retroviruses
Microsatellite repeats
Avoid regions with high similarity to non-identical sequences
In many clusters, orientation and position relative to ORF are
unknown and cannot be selected for.
Test selected clone for sequence correctness
Test selected clone for chimerism
Some commercial providers offer sequence verified UNIGENE
cluster representatives
Selection of genes
If possible, use all of them
Biased selection
Selection by tissue
Selection by topic
Selection by visibility
Selection by known expression properties
Selection from unbiased pre-screen
Use sources of expression information
EST frequency
Published array studies
SAGE data
Selection of gene regions
3‘ UTR
ORF
5‘ UTR
Alternative polyadenylation
Alternative polyadenylation
Constitutive polyA heterogeneity
3’-Fragments: reduced sensitivity
no impact on expression ratio
Regulated polyA heterogeneity
Fragment choice influences expression ratio
Multiple fragments necessary
Detection of cryptic polyA signals
Prediction (AATAAA)
Polyadenylated ESTs
SAGE tags
Alternative splicing
Alternative splicing
Constitutive splice form heterogeneity
Fragment in alternative exon: reduced sensitivity
No impact on expression ratio
Regulated splice form heterogeneity
Fragment choice influences expression ratio
Multiple fragments necessary
Detection of alternative splicing events
Hard/Impossible to predict
EST analysis (beware of pre-mRNA)
Literature
Alternative promoter usage
Alternative promotor usage
What is the desired readout?
If promoter activity matters most: multiple fragments
If overall mRNA level matters most: downstream fragment
Detection of alternative promoter usage
Prediction difficult (possible?)
EST analysis
Literature
UDP-Glucuronosyltransferases
UGT1A8
UGT1A7
Selection of gene regions
Coding region (ORF)
Annotation relatively safe
No problems with alternative polyA sites
No repetitive elements or other funny sequences
danger of close isoforms
danger of alternative splicing
might be missing in short RT products
3’ untranslated region
Annotation less safe
danger of alternative polyA sites
danger of repetitive elements
less likely to cross-hybridize with isoforms
little danger of alternative splicing
5’ untranslated region
close linkage to promoter
frequently not available
Pick a gene
Try get a complete cDNA sequence
Verify sequence architecture (e.g. cross-species comparison)
Mask repetitive elements (and vector!)
If possible, discard 3’-UTR beyond first polyA signal
Look for alternative splice events
Use remaining region of interest for similarity searches
Mask regions that could cross-hybridize
Use the remaining region for probe amplification or EST selection
When working with ESTs, use sequence-verified clones
Some useful URLs
Exercises
1) Assume that you are interested in the p53-homolog p63, also known as
Ket (TrEMBL: Q9UE10) What kind of fragment(s) would you use for
expression analysis? Why?
2) The cytochrome P450 family is very important for toxicological
microarray analysis since most isoforms repond to different toxic
compounds. Is it possible to design a cDNA fragment (minimal size 200 bp)
that would be able to separate CYP2A6 and CYP2A7? What is the
situation with CYP1A1 and CYP1A2? What region should be used?
3) Name a few possible reasons why, for some genes, an Affymetrixtype panel of oligonucleotides give very heterogeneous results.
4) Two (hypothetical) papers using different types of microarrays report
very different results for the regulation of the thyroid receptor alpha-2
(Swissprot: THA2_HUMAN). Can you think of a possible explanation?
What could you do to resolve this issue?
Tools for Exercises
Literature search with Pubmed:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Sequence search & retrieval (SwissProt, Entrez)
http://www.expasy.ch/sprot/
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide
BLAST searches at SIB
http://www.ch.embnet.org/software/aBLAST.html
Use specific subdatabase! Mind the ‘repsim‘ filter
Two-way sequence alignment
http://www.ch.embnet.org/software/LALIGN_form.html