Genome-wide CNV analysis replicates the association between <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-07-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/326 |
| _version_ | 1818917558797991936 |
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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 | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>GSTM1</it> (1p13.3) deletion provides an important opportunity to assess their performance.</p> <p>Results</p> <p>773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the <it>GSTM1</it> 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 <it>GSTM1</it> 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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-20T00:35:59Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T00:35:59Z |
| publishDate | 2012-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-803b69ed68a94a81837b7c34bc98a62d2022-12-21T19:59:46ZengBMCBMC Genomics1471-21642012-07-0113132610.1186/1471-2164-13-326Genome-wide CNV analysis replicates the association between <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array dataMarenne GaëlleReal Francisco XRothman NathanielRodríguez-Santiago BenjaminPérez-Jurado LuisKogevinas ManolisGarcía-Closas MontseSilverman Debra TChanock Stephen JGénin EmmanuelleMalats Núria<p>Abstract</p> <p>Background</p> <p>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 <it>GSTM1</it> (1p13.3) deletion provides an important opportunity to assess their performance.</p> <p>Results</p> <p>773 cases and 759 controls from the SBC/EPICURO Study were genotyped in the <it>GSTM1</it> 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 <it>GSTM1</it> 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/13/326Bladder cancer riskGlutathione <it>S</it>-transferase mu 1 (<it>GSTM1</it>)Copy number variation (CNV)SNP-array |
| spellingShingle | 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 <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data BMC Genomics Bladder cancer risk Glutathione <it>S</it>-transferase mu 1 (<it>GSTM1</it>) Copy number variation (CNV) SNP-array |
| title | Genome-wide CNV analysis replicates the association between <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data |
| title_full | Genome-wide CNV analysis replicates the association between <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data |
| title_fullStr | Genome-wide CNV analysis replicates the association between <it>GSTM1</it> 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 <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data |
| title_short | Genome-wide CNV analysis replicates the association between <it>GSTM1</it> deletion and bladder cancer: a support for using continuous measurement from SNP-array data |
| title_sort | genome wide cnv analysis replicates the association between it gstm1 it deletion and bladder cancer a support for using continuous measurement from snp array data |
| topic | Bladder cancer risk Glutathione <it>S</it>-transferase mu 1 (<it>GSTM1</it>) Copy number variation (CNV) SNP-array |
| url | http://www.biomedcentral.com/1471-2164/13/326 |
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