Transcript Floorplan Evaluation with Timing

Integrated Design Flow for Universal DNA Tag Arrays
N.
1
Hundewale ,
1CS
– In which cell tissues and under what environmental conditions is each
gene active?
– How does the activity level of a gene change with: cell cycle stage,
environmental conditions, disease, etc.?
– What genes seem to be regulated together?
• Universal tag arrays (UTAs) technology
– Provides unprecedented assay customization flexibility while
maintaining a high degree of multiplexing and low unit cost
• In this poster we describe an integrated design flow for
genomic assays based on UTAs
– We use the proposed flow to design UTA-based assays for
measuring Herpes B viral gene expression in cells derived from
macaque and human hosts
– After defining a “B virus molecular signature”, the assay can provide a
sensitive tool for early B virus infection diagnosis and differentiation
between B herpes and the closely related herpes simplex viruses
Design Flow
• “Programmable” Array Format [Brenner 97, Morris et al. 98]
– Array consists of application independent oligonucleotides called tags
– Two-part reporter probes: aplication specific primers ligated to antitags
– Detection carried by a sequence of reactions separately involving the
primer and the antitag part of reporter probes
• Tag/Antitag Hybridization Constraints
(H1) Antitags hybridize strongly to complementary tags
(H2) No antitag hybridezes to a non-complementary tag
(H3) Antitags do not cross-hybridize to each other
t1 t1
t2 t2
t1
t1 t2
• Open reading frames (ORFs)
Bioperl
GenMark/
ORF Finder
ORFs in Fasta format
Promide
PerTags
and A.
1
Zelikovsky
ORF and Primer Selection
Genomic IDs
Probe pools
Tag/antitag sequences
C.
2
Prajescu ,
Universal DNA Tag Arrays
• DNA microarrays provide a tool for answering a wide
variety of questions about the dynamics of cells
Assay
parameters
L.
3
Perelygina ,
Department, GSU, 2CSE Department, UCONN, 3Department of Biology, GSU
Abstract
Sequences in FASTA format
I.
2
Mandoiu ,
PrimerDel+
Reporter probes
– ORFs are regions of genetic material beginning with a start codon and
ending with a stop codon that might code for a protein
– ORFs can be extracted by means of the genome's sequence or id
using ORF Finder. A second approach is to use the GenMark family of
statistical gene prediction programs [Borodovsky]
•Primer selection
-Constraints:
- Homogeneity: Each primer must hybridize to its target site at the
temperature selected for the experiment
- Sensitivity: Must avoid self-hybridization and ensure that primers do
not form secondary structures
- Specificity: Each primer must hybridize to one particular ORF
-Selection tools:
Hybridization Experiment and Analysis
- Primer and microarray probe selection are well studied; we use the
Promide tool [Rahmann 03] for selecting pools of primer candidates
meeting the above constraints for each ORF
Conclusions
• We have described a suite of software tools for designing
genomic assays based on UTAs
– Integrating design flow optimization steps yields higher multiplexing
rates and leads to reduced assay costs
• In future work we will make the entire software suite
available as an online web server
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References
Aymetrix, Inc., GeneFlex tag array probe set, available at the NetAffx™ Analysis Center,
http://www.affymetrix.com/analysis/
M. Atlas, N. Hundewale, L. Perelygina, and A. Zelikovsky, Proc. International Conf. of the IEEE
Engineering in Medicine and Biology (EMBC), pp. 172-175, 2004.
A. BenDor, T. Hartman, B. Schwikowski, R. Sharan, and Z. Yakhini. Towards optimally multiplexed
applications of universal DNA tag systems. Proc. 7th Annual International Conference on Research in
Computational Molecular Biology (RECOMB), pp. 48-56, 2003
S. Brenner. Methods for sorting polynucleotides using oligonucleotide tags. US Patent 5,604,097, 1997.
I.I. Mandoiu and D. Trinca. Exact and approximation algorithms for DNA tag set design. Proc. 16th Annual
Symposium on Combinatorial Pattern Matching (CPM), pp. 383-393, 2005.
I.I. Mandoiu, C. Prajescu, and D. Trinca. Improved tag set design and multiplexing algorithms for universal
arrays. Proc. 5th Int. Conf. on Computational Science (ICCS 2005), Part II, pp. 994-1002, 2005.
M. Borodovsky, Genemark, http://opal.biology.gatech.edu/GeneMark
ORF finder, http://www.ncbi.nih.gov/gorf/gorf.html.
S. Rahmann, Rapid large-scale oligonucleotide selection for microarrays, Proc. IEEE Computer Society
Bioinformatics Conference (CSB), 2002.
RECOMB 2005, Poster Session A, Bay 43