Smoothing waves in array CGH tumor profiles

Mark A. van de Wiel; Rebecca Brosens; Paul H.C. Eilers; Candy Kumps; Gerrit A. Meijer; Björn Menten; Erik Sistermans; Frank Speleman; Marieke E. Timmerman; Bauke Ylstra

doi:10.1093/bioinformatics/btp132

Smoothing waves in array CGH tumor profiles

Mark A. van de Wiel^*, Rebecca Brosens, Paul H.C. Eilers, Candy Kumps, Gerrit A. Meijer, Björn Menten, Erik Sistermans, Frank Speleman, Marieke E. Timmerman, Bauke Ylstra

^*Corresponding author for this work

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

59 Citations (Scopus)

Abstract

Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles.

Original language	English
Pages (from-to)	1099-1104
Number of pages	6
Journal	Bioinformatics
Volume	25
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btp132
Publication status	Published - 2009
Externally published	Yes

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10.1093/bioinformatics/btp132

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title = "Smoothing waves in array CGH tumor profiles",

abstract = "Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles.",

author = "{van de Wiel}, {Mark A.} and Rebecca Brosens and Eilers, {Paul H.C.} and Candy Kumps and Meijer, {Gerrit A.} and Bj{\"o}rn Menten and Erik Sistermans and Frank Speleman and Timmerman, {Marieke E.} and Bauke Ylstra",

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AU - van de Wiel, Mark A.

AU - Brosens, Rebecca

AU - Eilers, Paul H.C.

AU - Kumps, Candy

AU - Meijer, Gerrit A.

AU - Menten, Björn

AU - Sistermans, Erik

AU - Speleman, Frank

AU - Timmerman, Marieke E.

AU - Ylstra, Bauke

PY - 2009

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N2 - Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles.

AB - Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles.

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EP - 1104

JO - Bioinformatics

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ER -

Smoothing waves in array CGH tumor profiles

Abstract

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