Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays

Catriona Rennie; Harry A Noyes; Stephen J Kemp; Helen Hulme; Andy Brass; David C Hoyle

doi:10.1186/1471-2164-9-317

Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays

Catriona Rennie, Harry A Noyes, Stephen J Kemp, Helen Hulme, Andy Brass, David C Hoyle

Royal (Dick) School of Veterinary Studies

Research output: Contribution to journal › Article › peer-review

Abstract

BACKGROUND: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.

RESULTS: We describe a large-scale investigation of microarray hybridisations to murine probes with known sequence mismatches, demonstrating that the effect of mismatches is strongly position-dependent and for small numbers of sequence mismatches is correlated with the maximum length of perfectly matched probe-target duplex. Length of perfect match explained 43% of the variance in log2 signal ratios between probes with one and two mismatches. The correlation with maximum length of perfect match does not conform to expectations based on considering the effect of mismatches purely in terms of reducing the binding energy. However, it can be explained qualitatively by considering the entropic contribution to duplex stability from configurations of differing perfect match length.

CONCLUSION: The results of this study have implications in terms of array design and analysis. They highlight the significant effect that short sequence mismatches can have upon microarray hybridisation intensities even for long oligonucleotide probes. All microarray data presented in this study are available from the GEO database 1, under accession number [GEO: GSE9669]

Original language	English
Pages (from-to)	317
Journal	BMC Genomics
Volume	9
DOIs	https://doi.org/10.1186/1471-2164-9-317
Publication status	Published - 3 Jul 2008

Keywords

Animals
Base Pair Mismatch
Base Pairing
DNA, Complementary
Fluorescent Dyes
Forecasting
Gene Dosage
Genetic Variation
Mice
Mice, Inbred A
Mice, Inbred BALB C
Mice, Inbred C57BL
Mice, Inbred Strains
Models, Theoretical
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
Oligonucleotide Probes
Polymorphism, Single Nucleotide
Sensitivity and Specificity

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10.1186/1471-2164-9-317

Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays
© 2008 Rennie et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 372 KBLicence: Creative Commons: Attribution (CC-BY)

http://www.biomedcentral.com/1471-2164/9/317

Cite this

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title = "Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays",

abstract = "BACKGROUND: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.RESULTS: We describe a large-scale investigation of microarray hybridisations to murine probes with known sequence mismatches, demonstrating that the effect of mismatches is strongly position-dependent and for small numbers of sequence mismatches is correlated with the maximum length of perfectly matched probe-target duplex. Length of perfect match explained 43% of the variance in log2 signal ratios between probes with one and two mismatches. The correlation with maximum length of perfect match does not conform to expectations based on considering the effect of mismatches purely in terms of reducing the binding energy. However, it can be explained qualitatively by considering the entropic contribution to duplex stability from configurations of differing perfect match length.CONCLUSION: The results of this study have implications in terms of array design and analysis. They highlight the significant effect that short sequence mismatches can have upon microarray hybridisation intensities even for long oligonucleotide probes. All microarray data presented in this study are available from the GEO database 1, under accession number [GEO: GSE9669]",

keywords = "Animals, Base Pair Mismatch, Base Pairing, DNA, Complementary, Fluorescent Dyes, Forecasting, Gene Dosage, Genetic Variation, Mice, Mice, Inbred A, Mice, Inbred BALB C, Mice, Inbred C57BL, Mice, Inbred Strains, Models, Theoretical, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotide Probes, Polymorphism, Single Nucleotide, Sensitivity and Specificity",

author = "Catriona Rennie and Noyes, {Harry A} and Kemp, {Stephen J} and Helen Hulme and Andy Brass and Hoyle, {David C}",

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T1 - Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays

AU - Rennie, Catriona

AU - Noyes, Harry A

AU - Kemp, Stephen J

AU - Hulme, Helen

AU - Brass, Andy

AU - Hoyle, David C

PY - 2008/7/3

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N2 - BACKGROUND: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.RESULTS: We describe a large-scale investigation of microarray hybridisations to murine probes with known sequence mismatches, demonstrating that the effect of mismatches is strongly position-dependent and for small numbers of sequence mismatches is correlated with the maximum length of perfectly matched probe-target duplex. Length of perfect match explained 43% of the variance in log2 signal ratios between probes with one and two mismatches. The correlation with maximum length of perfect match does not conform to expectations based on considering the effect of mismatches purely in terms of reducing the binding energy. However, it can be explained qualitatively by considering the entropic contribution to duplex stability from configurations of differing perfect match length.CONCLUSION: The results of this study have implications in terms of array design and analysis. They highlight the significant effect that short sequence mismatches can have upon microarray hybridisation intensities even for long oligonucleotide probes. All microarray data presented in this study are available from the GEO database 1, under accession number [GEO: GSE9669]

AB - BACKGROUND: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.RESULTS: We describe a large-scale investigation of microarray hybridisations to murine probes with known sequence mismatches, demonstrating that the effect of mismatches is strongly position-dependent and for small numbers of sequence mismatches is correlated with the maximum length of perfectly matched probe-target duplex. Length of perfect match explained 43% of the variance in log2 signal ratios between probes with one and two mismatches. The correlation with maximum length of perfect match does not conform to expectations based on considering the effect of mismatches purely in terms of reducing the binding energy. However, it can be explained qualitatively by considering the entropic contribution to duplex stability from configurations of differing perfect match length.CONCLUSION: The results of this study have implications in terms of array design and analysis. They highlight the significant effect that short sequence mismatches can have upon microarray hybridisation intensities even for long oligonucleotide probes. All microarray data presented in this study are available from the GEO database 1, under accession number [GEO: GSE9669]

KW - Animals

KW - Base Pair Mismatch

KW - Base Pairing

KW - DNA, Complementary

KW - Fluorescent Dyes

KW - Forecasting

KW - Gene Dosage

KW - Genetic Variation

KW - Mice

KW - Mice, Inbred A

KW - Mice, Inbred BALB C

KW - Mice, Inbred C57BL

KW - Mice, Inbred Strains

KW - Models, Theoretical

KW - Nucleic Acid Hybridization

KW - Oligonucleotide Array Sequence Analysis

KW - Oligonucleotide Probes

KW - Polymorphism, Single Nucleotide

KW - Sensitivity and Specificity

U2 - 10.1186/1471-2164-9-317

DO - 10.1186/1471-2164-9-317

M3 - Article

C2 - 18598341

VL - 9

SP - 317

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

ER -

Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays

Abstract

Keywords

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