A genome-wide DNA methylation study in colorectal carcinoma

<p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium m...
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Autor*in:	Dodsworth Charlotte [verfasserIn] Rahaman Ronald [verfasserIn] Paul-Brutus Rachelle [verfasserIn] Roy Shantanu [verfasserIn] Jasmine Farzana [verfasserIn] Raza Maruf [verfasserIn] Kibriya Muhammad G [verfasserIn] Rakibuz-Zaman Muhammad [verfasserIn] Kamal Mohammed [verfasserIn] Ahsan Habibul [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: BMC Medical Genomics - BMC, 2008, 4(2011), 1, p 50
Übergeordnetes Werk:	volume:4 ; year:2011 ; number:1, p 50

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1755-8794-4-50

Katalog-ID:	DOAJ05150877X

Internformat


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allfields	10.1186/1755-8794-4-50 doi (DE-627)DOAJ05150877X (DE-599)DOAJf1456e1ef26b4d278b65cd814e406a88 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Dodsworth Charlotte verfasserin aut A genome-wide DNA methylation study in colorectal carcinoma 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p< Internal medicine Genetics Rahaman Ronald verfasserin aut Paul-Brutus Rachelle verfasserin aut Roy Shantanu verfasserin aut Jasmine Farzana verfasserin aut Raza Maruf verfasserin aut Kibriya Muhammad G verfasserin aut Rakibuz-Zaman Muhammad verfasserin aut Kamal Mohammed verfasserin aut Ahsan Habibul verfasserin aut In BMC Medical Genomics BMC, 2008 4(2011), 1, p 50 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:4 year:2011 number:1, p 50 https://doi.org/10.1186/1755-8794-4-50 kostenfrei https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 kostenfrei http://www.biomedcentral.com/1755-8794/4/50 kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 4 2011 1, p 50
spelling	10.1186/1755-8794-4-50 doi (DE-627)DOAJ05150877X (DE-599)DOAJf1456e1ef26b4d278b65cd814e406a88 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Dodsworth Charlotte verfasserin aut A genome-wide DNA methylation study in colorectal carcinoma 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p< Internal medicine Genetics Rahaman Ronald verfasserin aut Paul-Brutus Rachelle verfasserin aut Roy Shantanu verfasserin aut Jasmine Farzana verfasserin aut Raza Maruf verfasserin aut Kibriya Muhammad G verfasserin aut Rakibuz-Zaman Muhammad verfasserin aut Kamal Mohammed verfasserin aut Ahsan Habibul verfasserin aut In BMC Medical Genomics BMC, 2008 4(2011), 1, p 50 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:4 year:2011 number:1, p 50 https://doi.org/10.1186/1755-8794-4-50 kostenfrei https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 kostenfrei http://www.biomedcentral.com/1755-8794/4/50 kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 4 2011 1, p 50
allfields_unstemmed	10.1186/1755-8794-4-50 doi (DE-627)DOAJ05150877X (DE-599)DOAJf1456e1ef26b4d278b65cd814e406a88 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Dodsworth Charlotte verfasserin aut A genome-wide DNA methylation study in colorectal carcinoma 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p< Internal medicine Genetics Rahaman Ronald verfasserin aut Paul-Brutus Rachelle verfasserin aut Roy Shantanu verfasserin aut Jasmine Farzana verfasserin aut Raza Maruf verfasserin aut Kibriya Muhammad G verfasserin aut Rakibuz-Zaman Muhammad verfasserin aut Kamal Mohammed verfasserin aut Ahsan Habibul verfasserin aut In BMC Medical Genomics BMC, 2008 4(2011), 1, p 50 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:4 year:2011 number:1, p 50 https://doi.org/10.1186/1755-8794-4-50 kostenfrei https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 kostenfrei http://www.biomedcentral.com/1755-8794/4/50 kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 4 2011 1, p 50
allfieldsGer	10.1186/1755-8794-4-50 doi (DE-627)DOAJ05150877X (DE-599)DOAJf1456e1ef26b4d278b65cd814e406a88 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Dodsworth Charlotte verfasserin aut A genome-wide DNA methylation study in colorectal carcinoma 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p< Internal medicine Genetics Rahaman Ronald verfasserin aut Paul-Brutus Rachelle verfasserin aut Roy Shantanu verfasserin aut Jasmine Farzana verfasserin aut Raza Maruf verfasserin aut Kibriya Muhammad G verfasserin aut Rakibuz-Zaman Muhammad verfasserin aut Kamal Mohammed verfasserin aut Ahsan Habibul verfasserin aut In BMC Medical Genomics BMC, 2008 4(2011), 1, p 50 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:4 year:2011 number:1, p 50 https://doi.org/10.1186/1755-8794-4-50 kostenfrei https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 kostenfrei http://www.biomedcentral.com/1755-8794/4/50 kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 4 2011 1, p 50
allfieldsSound	10.1186/1755-8794-4-50 doi (DE-627)DOAJ05150877X (DE-599)DOAJf1456e1ef26b4d278b65cd814e406a88 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Dodsworth Charlotte verfasserin aut A genome-wide DNA methylation study in colorectal carcinoma 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p< Internal medicine Genetics Rahaman Ronald verfasserin aut Paul-Brutus Rachelle verfasserin aut Roy Shantanu verfasserin aut Jasmine Farzana verfasserin aut Raza Maruf verfasserin aut Kibriya Muhammad G verfasserin aut Rakibuz-Zaman Muhammad verfasserin aut Kamal Mohammed verfasserin aut Ahsan Habibul verfasserin aut In BMC Medical Genomics BMC, 2008 4(2011), 1, p 50 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:4 year:2011 number:1, p 50 https://doi.org/10.1186/1755-8794-4-50 kostenfrei https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 kostenfrei http://www.biomedcentral.com/1755-8794/4/50 kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 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_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 4 2011 1, p 50
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topic_title	RC31-1245 QH426-470 A genome-wide DNA methylation study in colorectal carcinoma
topic	misc RC31-1245 misc QH426-470 misc Internal medicine misc Genetics
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title	A genome-wide DNA methylation study in colorectal carcinoma
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title_full	A genome-wide DNA methylation study in colorectal carcinoma
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author_browse	Dodsworth Charlotte Rahaman Ronald Paul-Brutus Rachelle Roy Shantanu Jasmine Farzana Raza Maruf Kibriya Muhammad G Rakibuz-Zaman Muhammad Kamal Mohammed Ahsan Habibul
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title_sort	genome-wide dna methylation study in colorectal carcinoma
callnumber	RC31-1245
title_auth	A genome-wide DNA methylation study in colorectal carcinoma
abstract	<p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<We performed a genome-wide scan of 27,578 CpG loci covering 14,475 genes to identify differentially methylated loci (DML) in colorectal carcinoma (CRC).</p< <p<Methods</p< <p<We used Illumina's Infinium methylation assay in paired DNA samples extracted from 24 fresh frozen CRC tissues and their corresponding normal colon tissues from 24 consecutive diagnosed patients at a tertiary medical center.</p< <p<Results</p< <p<We found a total of 627 DML in CRC covering 513 genes, of which 535 are novel DML covering 465 genes. We also validated the Illumina Infinium methylation data for top-ranking genes by non-bisulfite conversion q-PCR-based methyl profiler assay in a subset of the same samples. We also carried out integration of genome-wide copy number and expression microarray along with methylation profiling to see the functional effect of methylation. Gene Set Enrichment Analysis (GSEA) showed that among the major "gene sets" that are hypermethylated in CRC are the sets: "inhibition of adenylate cyclase activity by G-protein signaling", "Rac guanyl-nucleotide exchange factor activity", "regulation of retinoic acid receptor signaling pathway" and "estrogen receptor activity". Two-level nested cross validation showed that DML-based predictive models may offer reasonable sensitivity (around 89%), specificity (around 95%), positive predictive value (around 95%) and negative predictive value (around 89%), suggesting that these markers may have potential clinical application.</p< <p<Conclusion</p< <p<Our genome-wide methylation study in CRC clearly supports most of the previous findings; additionally we found a large number of novel DML in CRC tissue. If confirmed in future studies, these findings may lead to identification of genomic markers for potential clinical application.</p<
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title_short	A genome-wide DNA methylation study in colorectal carcinoma
url	https://doi.org/10.1186/1755-8794-4-50 https://doaj.org/article/f1456e1ef26b4d278b65cd814e406a88 http://www.biomedcentral.com/1755-8794/4/50 https://doaj.org/toc/1755-8794
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up_date	2024-07-03T20:45:37.951Z
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