Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation
Summary The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to s...
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| Veröffentlicht in: | International journal of immunogenetics 2017-06, Vol.44 (3), p.135-144 |
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| container_title | International journal of immunogenetics |
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| creator | Valverde‐Villegas, J. M. Medeiros, R. M. Almeida, S. E. M. Chies, J. A. B. |
| description | Summary
The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNPs in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNPs were displayed in two separate panels (panel 1—IL2 rs2069762, TNFα rs1800629, rs361525; IL4 rs2243250; IL6 rs1800795; IL10 rs1800896, rs1800872; IL17A rs8193036, rs2275913 and panel 2—CCR3 rs309125, CCR4 rs6770096, rs2228428; CCR6 rs968334; CCR8 rs2853699; CXCR3 rs34334103, rs2280964;CXCR6 rs223435, rs2234358; CCL20 rs13034664, rs6749704; CCL22 rs4359426; CXCL10/IP‐10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNPs, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies. |
| doi_str_mv | 10.1111/iji.12314 |
| format | Article |
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The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNPs in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNPs were displayed in two separate panels (panel 1—IL2 rs2069762, TNFα rs1800629, rs361525; IL4 rs2243250; IL6 rs1800795; IL10 rs1800896, rs1800872; IL17A rs8193036, rs2275913 and panel 2—CCR3 rs309125, CCR4 rs6770096, rs2228428; CCR6 rs968334; CCR8 rs2853699; CXCR3 rs34334103, rs2280964;CXCR6 rs223435, rs2234358; CCL20 rs13034664, rs6749704; CCL22 rs4359426; CXCL10/IP‐10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNPs, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies.</description><identifier>ISSN: 1744-3121</identifier><identifier>EISSN: 1744-313X</identifier><identifier>DOI: 10.1111/iji.12314</identifier><identifier>PMID: 28374494</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Autoimmune diseases ; Autoimmune Diseases - genetics ; Autoimmune Diseases - immunology ; Autoimmune Diseases - physiopathology ; Cancer ; CCL20 protein ; CCL22 protein ; CCR6 protein ; CCR8 protein ; chemokine ; Chemokines ; Communicable Diseases - genetics ; Communicable Diseases - immunology ; Communicable Diseases - physiopathology ; CXCL10 protein ; CXCR3 protein ; cytokine ; Cytokines ; Cytokines - genetics ; Deoxyribonucleic acid ; DNA ; Genetic Association Studies ; Genetic Predisposition to Disease ; Genetic testing ; Genotype ; Genotypes ; Genotyping ; Humans ; Immunogenetics ; Immunogenetics - methods ; Infectious diseases ; Interleukin 1 ; Interleukin 10 ; Interleukin 2 ; Interleukin 4 ; Interleukin 6 ; IP-10 protein ; Ligands ; Male ; minisequencing ; Neoplasms - genetics ; Neoplasms - immunology ; Neoplasms - physiopathology ; Polymorphism ; Polymorphism, Single Nucleotide ; Receptors, Chemokine - genetics ; Sequence Analysis, DNA - methods ; Single-nucleotide polymorphism ; SNPs ; susceptibility markers ; Tumor necrosis factor</subject><ispartof>International journal of immunogenetics, 2017-06, Vol.44 (3), p.135-144</ispartof><rights>2017 John Wiley & Sons Ltd</rights><rights>2017 John Wiley & Sons Ltd.</rights><rights>Copyright © 2017 John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0001-7025-0660</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fiji.12314$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fiji.12314$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28374494$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Valverde‐Villegas, J. M.</creatorcontrib><creatorcontrib>Medeiros, R. M.</creatorcontrib><creatorcontrib>Almeida, S. E. M.</creatorcontrib><creatorcontrib>Chies, J. A. B.</creatorcontrib><title>Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation</title><title>International journal of immunogenetics</title><addtitle>Int J Immunogenet</addtitle><description>Summary
The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNPs in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNPs were displayed in two separate panels (panel 1—IL2 rs2069762, TNFα rs1800629, rs361525; IL4 rs2243250; IL6 rs1800795; IL10 rs1800896, rs1800872; IL17A rs8193036, rs2275913 and panel 2—CCR3 rs309125, CCR4 rs6770096, rs2228428; CCR6 rs968334; CCR8 rs2853699; CXCR3 rs34334103, rs2280964;CXCR6 rs223435, rs2234358; CCL20 rs13034664, rs6749704; CCL22 rs4359426; CXCL10/IP‐10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNPs, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies.</description><subject>Autoimmune diseases</subject><subject>Autoimmune Diseases - genetics</subject><subject>Autoimmune Diseases - immunology</subject><subject>Autoimmune Diseases - physiopathology</subject><subject>Cancer</subject><subject>CCL20 protein</subject><subject>CCL22 protein</subject><subject>CCR6 protein</subject><subject>CCR8 protein</subject><subject>chemokine</subject><subject>Chemokines</subject><subject>Communicable Diseases - genetics</subject><subject>Communicable Diseases - immunology</subject><subject>Communicable Diseases - physiopathology</subject><subject>CXCL10 protein</subject><subject>CXCR3 protein</subject><subject>cytokine</subject><subject>Cytokines</subject><subject>Cytokines - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Genetic Association Studies</subject><subject>Genetic Predisposition to Disease</subject><subject>Genetic testing</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Humans</subject><subject>Immunogenetics</subject><subject>Immunogenetics - methods</subject><subject>Infectious diseases</subject><subject>Interleukin 1</subject><subject>Interleukin 10</subject><subject>Interleukin 2</subject><subject>Interleukin 4</subject><subject>Interleukin 6</subject><subject>IP-10 protein</subject><subject>Ligands</subject><subject>Male</subject><subject>minisequencing</subject><subject>Neoplasms - genetics</subject><subject>Neoplasms - immunology</subject><subject>Neoplasms - physiopathology</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Receptors, Chemokine - genetics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Single-nucleotide polymorphism</subject><subject>SNPs</subject><subject>susceptibility markers</subject><subject>Tumor necrosis factor</subject><issn>1744-3121</issn><issn>1744-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdkctOwzAQRS0E4r3gB5AlNiwo9YvEZod4FiFAAiR2lomnrUtihzgB9Tf4YtwWusAb39EcX834IrRHyTFNp-8m7pgyTsUK2qS5ED1O-evqUjO6gbZinBDCMyHIOtpgkqeWEpvoe1BVnQ8j8NC6AtdNGLrS-REOQ8w4frp_jDNZTNvw7jxg4y0uxlAtqgYKqNvQ4Nn7iNtxE7rRGBtcOe8ifHTgi5lZC8XYu1Se4guIbuSPsIVPKENdgW_npp-mdNa0LvgdtDY0ZYTd33sbvVxdPp_f9O4ergfnZ3e9muVK9BTLrciUIsIIlXPF8yGzhhgQBDiRNrNG0ZxwTjJCQGSESWmpPFGQJ4xLvo0OF75p6TRabHXlYgFlaTyELmoqpaCZzFiW0IN_6CR0jU_TaaoYEZLxE5ao_V-qe6vA6rpxlWmm-u-3E9BfAF-uhOmyT4mexahTjHoeox7cDuaC_wBpGI8l</recordid><startdate>201706</startdate><enddate>201706</enddate><creator>Valverde‐Villegas, J. M.</creator><creator>Medeiros, R. M.</creator><creator>Almeida, S. E. M.</creator><creator>Chies, J. A. B.</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7T5</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-7025-0660</orcidid></search><sort><creationdate>201706</creationdate><title>Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation</title><author>Valverde‐Villegas, J. M. ; Medeiros, R. M. ; Almeida, S. E. M. ; Chies, J. A. B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p2794-927d469904a4973937f2da0ae40e308d6da9170330600e460288d1859e7da0383</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Autoimmune diseases</topic><topic>Autoimmune Diseases - genetics</topic><topic>Autoimmune Diseases - immunology</topic><topic>Autoimmune Diseases - physiopathology</topic><topic>Cancer</topic><topic>CCL20 protein</topic><topic>CCL22 protein</topic><topic>CCR6 protein</topic><topic>CCR8 protein</topic><topic>chemokine</topic><topic>Chemokines</topic><topic>Communicable Diseases - genetics</topic><topic>Communicable Diseases - immunology</topic><topic>Communicable Diseases - physiopathology</topic><topic>CXCL10 protein</topic><topic>CXCR3 protein</topic><topic>cytokine</topic><topic>Cytokines</topic><topic>Cytokines - genetics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Genetic Association Studies</topic><topic>Genetic Predisposition to Disease</topic><topic>Genetic testing</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Genotyping</topic><topic>Humans</topic><topic>Immunogenetics</topic><topic>Immunogenetics - methods</topic><topic>Infectious diseases</topic><topic>Interleukin 1</topic><topic>Interleukin 10</topic><topic>Interleukin 2</topic><topic>Interleukin 4</topic><topic>Interleukin 6</topic><topic>IP-10 protein</topic><topic>Ligands</topic><topic>Male</topic><topic>minisequencing</topic><topic>Neoplasms - genetics</topic><topic>Neoplasms - immunology</topic><topic>Neoplasms - physiopathology</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Receptors, Chemokine - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Single-nucleotide polymorphism</topic><topic>SNPs</topic><topic>susceptibility markers</topic><topic>Tumor necrosis factor</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Valverde‐Villegas, J. M.</creatorcontrib><creatorcontrib>Medeiros, R. M.</creatorcontrib><creatorcontrib>Almeida, S. E. M.</creatorcontrib><creatorcontrib>Chies, J. A. B.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of immunogenetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Valverde‐Villegas, J. M.</au><au>Medeiros, R. M.</au><au>Almeida, S. E. M.</au><au>Chies, J. A. B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation</atitle><jtitle>International journal of immunogenetics</jtitle><addtitle>Int J Immunogenet</addtitle><date>2017-06</date><risdate>2017</risdate><volume>44</volume><issue>3</issue><spage>135</spage><epage>144</epage><pages>135-144</pages><issn>1744-3121</issn><eissn>1744-313X</eissn><abstract>Summary
The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNPs in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNPs were displayed in two separate panels (panel 1—IL2 rs2069762, TNFα rs1800629, rs361525; IL4 rs2243250; IL6 rs1800795; IL10 rs1800896, rs1800872; IL17A rs8193036, rs2275913 and panel 2—CCR3 rs309125, CCR4 rs6770096, rs2228428; CCR6 rs968334; CCR8 rs2853699; CXCR3 rs34334103, rs2280964;CXCR6 rs223435, rs2234358; CCL20 rs13034664, rs6749704; CCL22 rs4359426; CXCL10/IP‐10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNPs, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>28374494</pmid><doi>10.1111/iji.12314</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-7025-0660</orcidid></addata></record> |
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| subjects | Autoimmune diseases Autoimmune Diseases - genetics Autoimmune Diseases - immunology Autoimmune Diseases - physiopathology Cancer CCL20 protein CCL22 protein CCR6 protein CCR8 protein chemokine Chemokines Communicable Diseases - genetics Communicable Diseases - immunology Communicable Diseases - physiopathology CXCL10 protein CXCR3 protein cytokine Cytokines Cytokines - genetics Deoxyribonucleic acid DNA Genetic Association Studies Genetic Predisposition to Disease Genetic testing Genotype Genotypes Genotyping Humans Immunogenetics Immunogenetics - methods Infectious diseases Interleukin 1 Interleukin 10 Interleukin 2 Interleukin 4 Interleukin 6 IP-10 protein Ligands Male minisequencing Neoplasms - genetics Neoplasms - immunology Neoplasms - physiopathology Polymorphism Polymorphism, Single Nucleotide Receptors, Chemokine - genetics Sequence Analysis, DNA - methods Single-nucleotide polymorphism SNPs susceptibility markers Tumor necrosis factor |
| title | Immunogenetic profiling of 23 SNPs of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation |
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