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Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data

BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate well-characterized CNVs such as GSTM1 (1p13.3) deletion provides an important o...

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Autores principales: Marenne, Gaëlle, Real, Francisco X, Rothman, Nathaniel, Rodríguez-Santiago, Benjamin, Pérez-Jurado, Luis, Kogevinas, Manolis, García-Closas, Montse, Silverman, Debra T, Chanock, Stephen J, Génin, Emmanuelle, Malats, Núria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425254/
https://www.ncbi.nlm.nih.gov/pubmed/22817656
http://dx.doi.org/10.1186/1471-2164-13-326
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author Marenne, Gaëlle
Real, Francisco X
Rothman, Nathaniel
Rodríguez-Santiago, Benjamin
Pérez-Jurado, Luis
Kogevinas, Manolis
García-Closas, Montse
Silverman, Debra T
Chanock, Stephen J
Génin, Emmanuelle
Malats, Núria
author_facet Marenne, Gaëlle
Real, Francisco X
Rothman, Nathaniel
Rodríguez-Santiago, Benjamin
Pérez-Jurado, Luis
Kogevinas, Manolis
García-Closas, Montse
Silverman, Debra T
Chanock, Stephen J
Génin, Emmanuelle
Malats, Núria
author_sort Marenne, Gaëlle
collection PubMed
description BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate well-characterized CNVs such as GSTM1 (1p13.3) deletion provides an important opportunity to assess their performance. RESULTS: 773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the GSTM1 region using TaqMan, Multiplex Ligation-dependent Probe Amplification (MLPA), and Illumina Infinium 1 M SNP-array platforms. CNV callings provided by TaqMan and MLPA were highly concordant and replicated the association between GSTM1 and bladder cancer. This was not the case when CNVs were called using Illumina 1 M data through available algorithms since no deletion was detected across the study samples. In contrast, when the Log R Ratio (LRR) was used as a continuous measure for the 5 probes contained in this locus, we were able to detect their association with bladder cancer using simple regression models or more sophisticated methods such as the ones implemented in the CNVtools package. CONCLUSIONS: This study highlights an important limitation in the CNV calling from SNP-array data in regions of common aberrations and suggests that there may be added advantage for using LRR as a continuous measure in association tests rather than relying on calling algorithms.
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spelling pubmed-34252542012-08-23 Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data Marenne, Gaëlle Real, Francisco X Rothman, Nathaniel Rodríguez-Santiago, Benjamin Pérez-Jurado, Luis Kogevinas, Manolis García-Closas, Montse Silverman, Debra T Chanock, Stephen J Génin, Emmanuelle Malats, Núria BMC Genomics Methodology Article BACKGROUND: Structural variations such as copy number variants (CNV) influence the expression of different phenotypic traits. Algorithms to identify CNVs through SNP-array platforms are available. The ability to evaluate well-characterized CNVs such as GSTM1 (1p13.3) deletion provides an important opportunity to assess their performance. RESULTS: 773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the GSTM1 region using TaqMan, Multiplex Ligation-dependent Probe Amplification (MLPA), and Illumina Infinium 1 M SNP-array platforms. CNV callings provided by TaqMan and MLPA were highly concordant and replicated the association between GSTM1 and bladder cancer. This was not the case when CNVs were called using Illumina 1 M data through available algorithms since no deletion was detected across the study samples. In contrast, when the Log R Ratio (LRR) was used as a continuous measure for the 5 probes contained in this locus, we were able to detect their association with bladder cancer using simple regression models or more sophisticated methods such as the ones implemented in the CNVtools package. CONCLUSIONS: This study highlights an important limitation in the CNV calling from SNP-array data in regions of common aberrations and suggests that there may be added advantage for using LRR as a continuous measure in association tests rather than relying on calling algorithms. BioMed Central 2012-07-20 /pmc/articles/PMC3425254/ /pubmed/22817656 http://dx.doi.org/10.1186/1471-2164-13-326 Text en Copyright ©2012 Marenne et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Methodology Article
Marenne, Gaëlle
Real, Francisco X
Rothman, Nathaniel
Rodríguez-Santiago, Benjamin
Pérez-Jurado, Luis
Kogevinas, Manolis
García-Closas, Montse
Silverman, Debra T
Chanock, Stephen J
Génin, Emmanuelle
Malats, Núria
Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title_full Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title_fullStr Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title_full_unstemmed Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title_short Genome-wide CNV analysis replicates the association between GSTM1 deletion and bladder cancer: a support for using continuous measurement from SNP-array data
title_sort genome-wide cnv analysis replicates the association between gstm1 deletion and bladder cancer: a support for using continuous measurement from snp-array data
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3425254/
https://www.ncbi.nlm.nih.gov/pubmed/22817656
http://dx.doi.org/10.1186/1471-2164-13-326
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