Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer

Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density o...
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Autor*in:	Pio, Ruben [verfasserIn] Blanco, David Pajares, Maria Jose Aibar, Elena Durany, Olga Ezponda, Teresa Agorreta, Jackeline Gomez-Roman, Javier Anton, Miguel Angel Rubio, Angel Lozano, Maria D López-Picazo, Jose M Subirada, Francesc Maes, Tamara Montuenga, Luis M

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2010

Schlagwörter:	Alternative Splice Normal Lung Tissue Splice Form Alternative Splice Event Intron Retention

Anmerkung:	© Pio et al; licensee BioMed Central Ltd. 2010

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 11(2010), 1 vom: 03. Juni
Übergeordnetes Werk:	volume:11 ; year:2010 ; number:1 ; day:03 ; month:06

Links:	Volltext

DOI / URN:	10.1186/1471-2164-11-352

Katalog-ID:	SPR027054004

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245	1	0	\|a Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
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520			\|a Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies.
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author_variant	r p rp d b db m j p mj mjp e a ea o d od t e te j a ja j g r jgr m a a ma maa a r ar m d l md mdl j m l p jml jmlp f s fs t m tm l m m lm lmm
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publishDate	2010
allfields	10.1186/1471-2164-11-352 doi (DE-627)SPR027054004 (SPR)1471-2164-11-352-e DE-627 ger DE-627 rakwb eng Pio, Ruben verfasserin aut Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pio et al; licensee BioMed Central Ltd. 2010 Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213 Blanco, David aut Pajares, Maria Jose aut Aibar, Elena aut Durany, Olga aut Ezponda, Teresa aut Agorreta, Jackeline aut Gomez-Roman, Javier aut Anton, Miguel Angel aut Rubio, Angel aut Lozano, Maria D aut López-Picazo, Jose M aut Subirada, Francesc aut Maes, Tamara aut Montuenga, Luis M aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 03. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:03 month:06 https://dx.doi.org/10.1186/1471-2164-11-352 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 03 06
spelling	10.1186/1471-2164-11-352 doi (DE-627)SPR027054004 (SPR)1471-2164-11-352-e DE-627 ger DE-627 rakwb eng Pio, Ruben verfasserin aut Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pio et al; licensee BioMed Central Ltd. 2010 Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213 Blanco, David aut Pajares, Maria Jose aut Aibar, Elena aut Durany, Olga aut Ezponda, Teresa aut Agorreta, Jackeline aut Gomez-Roman, Javier aut Anton, Miguel Angel aut Rubio, Angel aut Lozano, Maria D aut López-Picazo, Jose M aut Subirada, Francesc aut Maes, Tamara aut Montuenga, Luis M aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 03. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:03 month:06 https://dx.doi.org/10.1186/1471-2164-11-352 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 03 06
allfields_unstemmed	10.1186/1471-2164-11-352 doi (DE-627)SPR027054004 (SPR)1471-2164-11-352-e DE-627 ger DE-627 rakwb eng Pio, Ruben verfasserin aut Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pio et al; licensee BioMed Central Ltd. 2010 Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213 Blanco, David aut Pajares, Maria Jose aut Aibar, Elena aut Durany, Olga aut Ezponda, Teresa aut Agorreta, Jackeline aut Gomez-Roman, Javier aut Anton, Miguel Angel aut Rubio, Angel aut Lozano, Maria D aut López-Picazo, Jose M aut Subirada, Francesc aut Maes, Tamara aut Montuenga, Luis M aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 03. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:03 month:06 https://dx.doi.org/10.1186/1471-2164-11-352 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 03 06
allfieldsGer	10.1186/1471-2164-11-352 doi (DE-627)SPR027054004 (SPR)1471-2164-11-352-e DE-627 ger DE-627 rakwb eng Pio, Ruben verfasserin aut Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pio et al; licensee BioMed Central Ltd. 2010 Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213 Blanco, David aut Pajares, Maria Jose aut Aibar, Elena aut Durany, Olga aut Ezponda, Teresa aut Agorreta, Jackeline aut Gomez-Roman, Javier aut Anton, Miguel Angel aut Rubio, Angel aut Lozano, Maria D aut López-Picazo, Jose M aut Subirada, Francesc aut Maes, Tamara aut Montuenga, Luis M aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 03. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:03 month:06 https://dx.doi.org/10.1186/1471-2164-11-352 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 03 06
allfieldsSound	10.1186/1471-2164-11-352 doi (DE-627)SPR027054004 (SPR)1471-2164-11-352-e DE-627 ger DE-627 rakwb eng Pio, Ruben verfasserin aut Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Pio et al; licensee BioMed Central Ltd. 2010 Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213 Blanco, David aut Pajares, Maria Jose aut Aibar, Elena aut Durany, Olga aut Ezponda, Teresa aut Agorreta, Jackeline aut Gomez-Roman, Javier aut Anton, Miguel Angel aut Rubio, Angel aut Lozano, Maria D aut López-Picazo, Jose M aut Subirada, Francesc aut Maes, Tamara aut Montuenga, Luis M aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 03. Juni (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:03 month:06 https://dx.doi.org/10.1186/1471-2164-11-352 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2010 1 03 06
language	English
source	Enthalten in BMC genomics 11(2010), 1 vom: 03. Juni volume:11 year:2010 number:1 day:03 month:06
sourceStr	Enthalten in BMC genomics 11(2010), 1 vom: 03. Juni volume:11 year:2010 number:1 day:03 month:06
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Alternative Splice Normal Lung Tissue Splice Form Alternative Splice Event Intron Retention
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Pio, Ruben @@aut@@ Blanco, David @@aut@@ Pajares, Maria Jose @@aut@@ Aibar, Elena @@aut@@ Durany, Olga @@aut@@ Ezponda, Teresa @@aut@@ Agorreta, Jackeline @@aut@@ Gomez-Roman, Javier @@aut@@ Anton, Miguel Angel @@aut@@ Rubio, Angel @@aut@@ Lozano, Maria D @@aut@@ López-Picazo, Jose M @@aut@@ Subirada, Francesc @@aut@@ Maes, Tamara @@aut@@ Montuenga, Luis M @@aut@@
publishDateDaySort_date	2010-06-03T00:00:00Z
hierarchy_top_id	326644954
id	SPR027054004
language_de	englisch
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author	Pio, Ruben
spellingShingle	Pio, Ruben misc Alternative Splice misc Normal Lung Tissue misc Splice Form misc Alternative Splice Event misc Intron Retention Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
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topic_title	Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer Alternative Splice (dpeaa)DE-He213 Normal Lung Tissue (dpeaa)DE-He213 Splice Form (dpeaa)DE-He213 Alternative Splice Event (dpeaa)DE-He213 Intron Retention (dpeaa)DE-He213
topic	misc Alternative Splice misc Normal Lung Tissue misc Splice Form misc Alternative Splice Event misc Intron Retention
topic_unstemmed	misc Alternative Splice misc Normal Lung Tissue misc Splice Form misc Alternative Splice Event misc Intron Retention
topic_browse	misc Alternative Splice misc Normal Lung Tissue misc Splice Form misc Alternative Splice Event misc Intron Retention
format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
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title_full	Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
author_sort	Pio, Ruben
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author_browse	Pio, Ruben Blanco, David Pajares, Maria Jose Aibar, Elena Durany, Olga Ezponda, Teresa Agorreta, Jackeline Gomez-Roman, Javier Anton, Miguel Angel Rubio, Angel Lozano, Maria D López-Picazo, Jose M Subirada, Francesc Maes, Tamara Montuenga, Luis M
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format_se	Elektronische Aufsätze
author-letter	Pio, Ruben
doi_str_mv	10.1186/1471-2164-11-352
title_sort	development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
title_auth	Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
abstract	Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. © Pio et al; licensee BioMed Central Ltd. 2010
abstractGer	Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. © Pio et al; licensee BioMed Central Ltd. 2010
abstract_unstemmed	Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. © Pio et al; licensee BioMed Central Ltd. 2010
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title_short	Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
url	https://dx.doi.org/10.1186/1471-2164-11-352
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author2	Blanco, David Pajares, Maria Jose Aibar, Elena Durany, Olga Ezponda, Teresa Agorreta, Jackeline Gomez-Roman, Javier Anton, Miguel Angel Rubio, Angel Lozano, Maria D López-Picazo, Jose M Subirada, Francesc Maes, Tamara Montuenga, Luis M
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Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer

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