physicochemical
fundamentals of dna hybridizations on surfaces
as applied to
microarrays and bead-based sequencing technologies
international
workshop
Organizers
Dr. Alexander Pozhitkov, Max-Planck Institute for
Evolutionary
Prof. Peter A. Noble,
Prof. Hans Binder,
Sponsorship
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Contact
alexander.pozhitkov@evolbio.mpg.de
+1-206-543-3641
Abstract
Many fields of biological science depend upon accurate identification and quantification of nucleic acid targets because these targets indirectly reflect the state of a biological system. Oligonucleotide microarrays were once thought to be the big hope for the high-throughput identification and quantification of nucleic acids. At that time, it was believed that designing probes for microarrays and interpreting results was mostly a bioinformatics/statistical exercise. However, it turned out, that interpreting the signal from microarrays was a major challenge in terms of surface chemistry because many details, such as the interactions between nucleic acid targets in solution and oligonucleotide probes on a microarray surface, were not well understood. We consider microarray technology as an instrument for measuring concentrations in multicomponent mixtures of DNA or RNA species. From this point of view, selectivity, response function and reproducibility must be known for appropriate analytics in real world applications. Other laboratories devised ad hoc approaches to make biological sense of microarray signals. These approaches have been extensively implemented and are now widely accepted in the published literature. Recent significant advancements in the understanding of nucleic acid hybridization and dissociation on microarray surfaces have revealed a number of inconsistencies between physical chemistry and the ad hoc approaches. The purpose of this workshop is three-fold: (i) to update developments in the understanding and application of microarrays, (ii) to identify and resolve inconsistencies in microarray analytics, and (iii) to discuss the future of microarray technology from the perspective of measuring principles and potential applications. We believe that this workshop is essential for moving forward microarray research and also for the advancement of new technologies such as ‘next-generation’ sequencing, which depend upon surface-hybridizations and array capture.
Objectives
1. Recognize contradictions in the theoretical foundation of hybridization-based technologies.
2. Identify gaps in factual experimental basis of the existing theories.
3. Suggest future experiments to fill up the gaps.
Participants
Group
photo
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Name, address |
Keywords |
Refs |
Presentation |
|
Dr. Binder, H. University of Leipzig, Germany |
hook-calibration,
Affymetrix, nonspecific hybridization, mismatch, SNP detection, sequence
effects |
4, 5, 6, 7,
8, 9, 10, 12, 18 |
|
|
Dr. Buhot, A. Institut Nanoscience et Cryogénie, France |
hybridization isotherms,
brush effects, thermodynamics, surface effects, spacers |
21, 22, 27, 28, 29, 30, 31 |
|
|
Dr. Burden, C. The Australian National University, Australia |
Langmuir models, analysis
of spiked-in experiments, physic-chemistry of hybridization, statistics |
11, 12, 13, 14 |
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Dr. Carlon, E. Katolieke |
labeling, binding,
thermodynamics, Affymetrix, mismatches, nearest neighbor, background
subtraction, inverse Langmuir |
15, 16, 20, 19, 35, 36, 37, 38, 46, 47, 58, 93 |
|
|
Dr. Gibas, C Department of Bioinformatics and Genomics UNC – Charlotte |
hybridization modeling,
background correction |
23, 24,
75 |
|
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Dr. Gamble, L University of Washigton |
surface chemistry, direct
probing of surface tethered DNA |
17, 49, 50, 79 |
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Dr. Halperin, A. Université Joseph Fourier,
France. |
hybridization isotherms,
brush effects, thermodynamics, surface effects |
27, 28, 29, 30, 31, 32 |
|
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Dr. Harrison, A.P. |
image processing,
calibration, Affymetrix, probes, chimeric transcripts, probe sets, outliers |
1, 2, 33, 34, 48, 55, 76, 78, 80, 83, 86, 87 |
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Dr. Hooyberghs, J. VITO,
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thermodynamic
equilibrium, nearest neighbor model |
37, 38 |
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Dr. Kreil, D. |
gene expression profiling,
low-level data modelling, idenfication and removal of measurement artefacts,
thermodynamic modelling for probe design and signal read-out, signal
extraction and normalization |
3, 42,
44,
45,
51,
57 |
|
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Dr. Levicky, R. |
surface hybridization,
complementary metal oxide semiconductor |
25, 26, 40, 41, 43, 52, 53, 81, 82, 84, 85 |
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Dr. Ott, A.
Universität des |
surface hybridization,
hybridization affinity, mismatches and base bulges |
56, 59, 60, 61, 62 |
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Dr. Pettitt, B.M. University of Houston, USA. |
surface effects, melting,
surface electrostatic effects |
39, 74, 90, 91, 92 |
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Dr. Pozhitkov, A.E. Max-Planck Institute for
Evolutionary Dr. Noble, P.A. |
competitive hybridization
model, gel-pad oligonucleotide microarrays, probe design, oligonucleotide
probes behavior, variability in melting, nonequilibrium thermal dissociation,
stringent washing, quantification of multiple nucleic acid targets,
nonspecific hybridization, hybridization isotherms, scanner calibration,
nearest neighbor |
54, 63, 64, 65,
66, 67, 68, 69, 70, 71, 72, 73,
77, 88,
89
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