High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison

Helen Davies; Ed Dicks; Philip Stephens; Charles Cox; Jon Teague; Chris Greenman; Graham Bignell; Sarah O'Meara; Sarah Edkins; Adrian Parker; Claire Stevens; Andrew Menzies; Matt Blow; Bill Bottomley; Mark Dronsfield; P. Andrew Futreal; Michael R. Stratton; Richard Wooster

doi:10.1016/j.ygeno.2005.11.008

High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison

Helen Davies, Ed Dicks, Philip Stephens, Charles Cox, Jon Teague, Chris Greenman, Graham Bignell, Sarah O'Meara, Sarah Edkins, Adrian Parker, Claire Stevens, Andrew Menzies, Matt Blow, Bill Bottomley, Mark Dronsfield, P. Andrew Futreal, Michael R. Stratton, Richard Wooster

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

33 Scopus citations

Abstract

We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.

Original language	English (US)
Pages (from-to)	427-432
Number of pages	6
Journal	Genomics
Volume	87
Issue number	3
DOIs	https://doi.org/10.1016/j.ygeno.2005.11.008
State	Published - Mar 2006
Externally published	Yes

Keywords

DNA sequencing
Heteroduplex
Mutation detection
Single-stranded confirmation polymorphism (SSCP)

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2005.11.008

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Davies, H., Dicks, E., Stephens, P., Cox, C., Teague, J., Greenman, C., Bignell, G., O'Meara, S., Edkins, S., Parker, A., Stevens, C., Menzies, A., Blow, M., Bottomley, B., Dronsfield, M., Futreal, P. A., Stratton, M. R., & Wooster, R. (2006). High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison. Genomics, 87(3), 427-432. https://doi.org/10.1016/j.ygeno.2005.11.008

Davies, H, Dicks, E, Stephens, P, Cox, C, Teague, J, Greenman, C, Bignell, G, O'Meara, S, Edkins, S, Parker, A, Stevens, C, Menzies, A, Blow, M, Bottomley, B, Dronsfield, M, Futreal, PA, Stratton, MR & Wooster, R 2006, 'High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison', Genomics, vol. 87, no. 3, pp. 427-432. https://doi.org/10.1016/j.ygeno.2005.11.008

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abstract = "We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.",

keywords = "DNA sequencing, Heteroduplex, Mutation detection, Single-stranded confirmation polymorphism (SSCP)",

author = "Helen Davies and Ed Dicks and Philip Stephens and Charles Cox and Jon Teague and Chris Greenman and Graham Bignell and Sarah O'Meara and Sarah Edkins and Adrian Parker and Claire Stevens and Andrew Menzies and Matt Blow and Bill Bottomley and Mark Dronsfield and Futreal, {P. Andrew} and Stratton, {Michael R.} and Richard Wooster",

note = "Funding Information: We thank the Wellcome Trust for funding this work. ",

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doi = "10.1016/j.ygeno.2005.11.008",

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AU - Davies, Helen

AU - Dicks, Ed

AU - Stephens, Philip

AU - Cox, Charles

AU - Teague, Jon

AU - Greenman, Chris

AU - Bignell, Graham

AU - O'Meara, Sarah

AU - Edkins, Sarah

AU - Parker, Adrian

AU - Stevens, Claire

AU - Menzies, Andrew

AU - Blow, Matt

AU - Bottomley, Bill

AU - Dronsfield, Mark

AU - Futreal, P. Andrew

AU - Stratton, Michael R.

AU - Wooster, Richard

N1 - Funding Information: We thank the Wellcome Trust for funding this work.

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N2 - We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.

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KW - DNA sequencing

KW - Heteroduplex

KW - Mutation detection

KW - Single-stranded confirmation polymorphism (SSCP)

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High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison

Abstract

Keywords

ASJC Scopus subject areas

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