MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India
MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a ve...
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| creator | Shah, Ruchi Sharma, Varun Bhat, Amrita Singh, Hemender Sharma, Indu Verma, Sonali Bhat, Gh Rasool Sharma, Bhanu Bakshi, Divya Kumar, Rakesh Dar, Nazir Ahmed |
| description | MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a very high potential of discovering disease-gene relationships. SNP-genotyping through MassARRAY is not only a cost-effective genotyping method but also provides a platform to validate variants observed through a high-throughput Next-generation sequencing (NGS).
In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature.
This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09-1.8 at 95% CI, p = 0.008) and 1.54 (1.21-2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir.
We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility. |
| doi_str_mv | 10.1186/s12885-020-06991-2 |
| format | Article |
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In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature.
This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09-1.8 at 95% CI, p = 0.008) and 1.54 (1.21-2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir.
We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility.</description><identifier>ISSN: 1471-2407</identifier><identifier>EISSN: 1471-2407</identifier><identifier>DOI: 10.1186/s12885-020-06991-2</identifier><identifier>PMID: 32487238</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Adult ; Aged ; Analysis ; Biomarkers, Tumor - genetics ; Case-Control Studies ; Confidence intervals ; Deoxyribonucleic acid ; DNA ; Environmental factors ; Esophageal cancer ; Esophageal Neoplasms - genetics ; Esophageal Neoplasms - pathology ; Esophageal Squamous Cell Carcinoma - genetics ; Esophageal Squamous Cell Carcinoma - pathology ; Esophagus ; Family medical history ; Female ; Gene amplification ; Gene expression ; Gene-Environment Interaction ; Genes ; Genetic aspects ; Genetic Predisposition to Disease ; Genetics ; Genotyping ; Genotyping Techniques - methods ; Healthy Volunteers ; High-Throughput Screening Assays - methods ; Humans ; India ; Ionization ; Male ; Mass spectrometry ; Mass spectroscopy ; Middle Aged ; Next-generation sequencing ; Polymerase Chain Reaction - methods ; Polymorphism, Single Nucleotide ; Population ; Population studies ; Risk factors ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods ; Squamous cell carcinoma ; Statistical analysis ; Studies</subject><ispartof>BMC cancer, 2020-06, Vol.20 (1), p.497-497, Article 497</ispartof><rights>COPYRIGHT 2020 BioMed Central Ltd.</rights><rights>2020. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c562t-c2012cf48f9b8e2f9805c0e1c5d5aa76cebcd14d827a60def6dc15ca3209f2293</citedby><cites>FETCH-LOGICAL-c562t-c2012cf48f9b8e2f9805c0e1c5d5aa76cebcd14d827a60def6dc15ca3209f2293</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268327/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268327/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,27907,27908,53774,53776</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32487238$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shah, Ruchi</creatorcontrib><creatorcontrib>Sharma, Varun</creatorcontrib><creatorcontrib>Bhat, Amrita</creatorcontrib><creatorcontrib>Singh, Hemender</creatorcontrib><creatorcontrib>Sharma, Indu</creatorcontrib><creatorcontrib>Verma, Sonali</creatorcontrib><creatorcontrib>Bhat, Gh Rasool</creatorcontrib><creatorcontrib>Sharma, Bhanu</creatorcontrib><creatorcontrib>Bakshi, Divya</creatorcontrib><creatorcontrib>Kumar, Rakesh</creatorcontrib><creatorcontrib>Dar, Nazir Ahmed</creatorcontrib><title>MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India</title><title>BMC cancer</title><addtitle>BMC Cancer</addtitle><description>MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a very high potential of discovering disease-gene relationships. SNP-genotyping through MassARRAY is not only a cost-effective genotyping method but also provides a platform to validate variants observed through a high-throughput Next-generation sequencing (NGS).
In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature.
This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09-1.8 at 95% CI, p = 0.008) and 1.54 (1.21-2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir.
We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility.</description><subject>Adult</subject><subject>Aged</subject><subject>Analysis</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Case-Control Studies</subject><subject>Confidence intervals</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Environmental factors</subject><subject>Esophageal cancer</subject><subject>Esophageal Neoplasms - genetics</subject><subject>Esophageal Neoplasms - pathology</subject><subject>Esophageal Squamous Cell Carcinoma - genetics</subject><subject>Esophageal Squamous Cell Carcinoma - pathology</subject><subject>Esophagus</subject><subject>Family medical history</subject><subject>Female</subject><subject>Gene amplification</subject><subject>Gene expression</subject><subject>Gene-Environment Interaction</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Predisposition to Disease</subject><subject>Genetics</subject><subject>Genotyping</subject><subject>Genotyping Techniques - methods</subject><subject>Healthy Volunteers</subject><subject>High-Throughput Screening Assays - methods</subject><subject>Humans</subject><subject>India</subject><subject>Ionization</subject><subject>Male</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Middle Aged</subject><subject>Next-generation sequencing</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population studies</subject><subject>Risk factors</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</subject><subject>Squamous cell carcinoma</subject><subject>Statistical analysis</subject><subject>Studies</subject><issn>1471-2407</issn><issn>1471-2407</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><recordid>eNptkl1rFDEUhgdRbK3-AS8kIBQFpyaZr8yNsBQ_VusHW73wKpzNnOymZJJtMlPtvzfj1rorkouE5Dnv4bx5s-wxoyeMifplZFyIKqec5rRuW5bzO9khK5t0KGlzd-d8kD2I8YJS1ggq7mcHBS9FwwtxmHUfIcbZYjH7TsCBvY4mEq_J8APtFRIFTmEgAS0M2JHzT18iMY5g9Js1rBAsiZcj9H6MRKG1iQ_KON_DRL0__vCCzF1n4GF2T4ON-OhmP8q-vXn99fRdfvb57fx0dparquZDrjhlXOlS6HYpkOtW0EpRZKrqKoCmVrhUHSs7wRuoaYe67hSrFBSctprztjjKXm11N-Oyx06hGwJYuQmmh3AtPRi5_-LMWq78lWx4LQreJIFnNwLBX44YB9mbOE0GDtOQMnnZMtFWJU_o03_QCz-GZOFEsVJMFpd_qRVYlMZpn_qqSVTO6tRQcF4XiTr5D5VWh71R3qE26X6v4PleQWIG_DmsYIxRzs8X--zxDrtOnzaso7fjYLyL-yDfgir4GAPqW-MYlVPg5DZwMgVO_g6cnGx4smv5bcmfhBW_AEATzgE</recordid><startdate>20200601</startdate><enddate>20200601</enddate><creator>Shah, Ruchi</creator><creator>Sharma, Varun</creator><creator>Bhat, Amrita</creator><creator>Singh, Hemender</creator><creator>Sharma, Indu</creator><creator>Verma, Sonali</creator><creator>Bhat, Gh Rasool</creator><creator>Sharma, Bhanu</creator><creator>Bakshi, Divya</creator><creator>Kumar, Rakesh</creator><creator>Dar, Nazir Ahmed</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7TO</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>H94</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20200601</creationdate><title>MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India</title><author>Shah, Ruchi ; Sharma, Varun ; Bhat, Amrita ; Singh, Hemender ; Sharma, Indu ; Verma, Sonali ; Bhat, Gh Rasool ; Sharma, Bhanu ; Bakshi, Divya ; Kumar, Rakesh ; Dar, Nazir Ahmed</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c562t-c2012cf48f9b8e2f9805c0e1c5d5aa76cebcd14d827a60def6dc15ca3209f2293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adult</topic><topic>Aged</topic><topic>Analysis</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Case-Control Studies</topic><topic>Confidence intervals</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Environmental factors</topic><topic>Esophageal cancer</topic><topic>Esophageal Neoplasms - genetics</topic><topic>Esophageal Neoplasms - pathology</topic><topic>Esophageal Squamous Cell Carcinoma - genetics</topic><topic>Esophageal Squamous Cell Carcinoma - pathology</topic><topic>Esophagus</topic><topic>Family medical history</topic><topic>Female</topic><topic>Gene amplification</topic><topic>Gene expression</topic><topic>Gene-Environment Interaction</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic Predisposition to Disease</topic><topic>Genetics</topic><topic>Genotyping</topic><topic>Genotyping Techniques - methods</topic><topic>Healthy Volunteers</topic><topic>High-Throughput Screening Assays - methods</topic><topic>Humans</topic><topic>India</topic><topic>Ionization</topic><topic>Male</topic><topic>Mass spectrometry</topic><topic>Mass spectroscopy</topic><topic>Middle Aged</topic><topic>Next-generation sequencing</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Population</topic><topic>Population studies</topic><topic>Risk factors</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</topic><topic>Squamous cell carcinoma</topic><topic>Statistical analysis</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shah, Ruchi</creatorcontrib><creatorcontrib>Sharma, Varun</creatorcontrib><creatorcontrib>Bhat, Amrita</creatorcontrib><creatorcontrib>Singh, Hemender</creatorcontrib><creatorcontrib>Sharma, Indu</creatorcontrib><creatorcontrib>Verma, Sonali</creatorcontrib><creatorcontrib>Bhat, Gh Rasool</creatorcontrib><creatorcontrib>Sharma, Bhanu</creatorcontrib><creatorcontrib>Bakshi, Divya</creatorcontrib><creatorcontrib>Kumar, Rakesh</creatorcontrib><creatorcontrib>Dar, Nazir Ahmed</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC cancer</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shah, Ruchi</au><au>Sharma, Varun</au><au>Bhat, Amrita</au><au>Singh, Hemender</au><au>Sharma, Indu</au><au>Verma, Sonali</au><au>Bhat, Gh Rasool</au><au>Sharma, Bhanu</au><au>Bakshi, Divya</au><au>Kumar, Rakesh</au><au>Dar, Nazir Ahmed</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India</atitle><jtitle>BMC cancer</jtitle><addtitle>BMC Cancer</addtitle><date>2020-06-01</date><risdate>2020</risdate><volume>20</volume><issue>1</issue><spage>497</spage><epage>497</epage><pages>497-497</pages><artnum>497</artnum><issn>1471-2407</issn><eissn>1471-2407</eissn><abstract>MassARRAY (Agena Bioscience™) combines competitive PCR with MALDI-TOF mass spectrometry (MS) analysis that gives highly accurate, sensitive, and high-throughput methods for the quantitative analysis of variation of gene expression in multiple samples. SNPs (Single Nucleotide Polymorphisms) have a very high potential of discovering disease-gene relationships. SNP-genotyping through MassARRAY is not only a cost-effective genotyping method but also provides a platform to validate variants observed through a high-throughput Next-generation sequencing (NGS).
In the present study, we have incorporated the use of matrix-assisted laser desorption/ionization-time of flight, mass spectrometry (MALDI-TOF) as a tool for differentiating genotypes based on the mass of variant. We have performed multiplex PCR and genotyped 12 SNPs in 758 samples (166 cases and 592 controls). The 12 studied SNPs were chosen with a rationale for their association with multiple cancers in literature.
This is the first study to explore these SNPs with esophageal cancer within the J&K population. Out of 12 SNPs, two SNPs rs12190287 of TCF21 and rs10046 of CYP19A1 were significantly associated with esophageal cancer with Odds Ratio (OR) 1.412 (1.09-1.8 at 95% CI, p = 0.008) and 1.54 (1.21-2.072 at 95% CI, p = 0.0007) within the population of Jammu and Kashmir.
We explored 12 SNPs that were found to be associated with multiple cancers in literature with esophageal cancer within the population of J&K. This is the first study to find the relation of these SNPs with ESCC within the studied population. This study explores the relation of genetic and environmental factors with the ESCC susceptibility.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>32487238</pmid><doi>10.1186/s12885-020-06991-2</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | BMC cancer, 2020-06, Vol.20 (1), p.497-497, Article 497 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central Open Access; Springer Nature OA Free Journals; Springer Nature - Complete Springer Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Adult Aged Analysis Biomarkers, Tumor - genetics Case-Control Studies Confidence intervals Deoxyribonucleic acid DNA Environmental factors Esophageal cancer Esophageal Neoplasms - genetics Esophageal Neoplasms - pathology Esophageal Squamous Cell Carcinoma - genetics Esophageal Squamous Cell Carcinoma - pathology Esophagus Family medical history Female Gene amplification Gene expression Gene-Environment Interaction Genes Genetic aspects Genetic Predisposition to Disease Genetics Genotyping Genotyping Techniques - methods Healthy Volunteers High-Throughput Screening Assays - methods Humans India Ionization Male Mass spectrometry Mass spectroscopy Middle Aged Next-generation sequencing Polymerase Chain Reaction - methods Polymorphism, Single Nucleotide Population Population studies Risk factors Single nucleotide polymorphisms Single-nucleotide polymorphism Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods Squamous cell carcinoma Statistical analysis Studies |
| title | MassARRAY analysis of twelve cancer related SNPs in esophageal squamous cell carcinoma in J&K, India |
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