Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies
Objectives Previous association studies have identified genetic variants in the human leukocyte antigen (HLA) complex as substantial risk factors for idiopathic inflammatory myopathies (IIMs). However, a great number of genes are located in the HLA region, and thus fine mapping is quite necessary. M...
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| Veröffentlicht in: | International journal of rheumatic diseases 2018-08, Vol.21 (8), p.1619-1626 |
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| container_title | International journal of rheumatic diseases |
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| creator | Peng, Qing‐Lin Lin, Jin‐Ming Zhang, Yong‐Biao Zhang, Xue‐Zhi Wang, Pan‐Pan Wu, Ting‐Ting Yu, Jun Dong, Xiao‐Qun Gu, Ming‐Liang Wang, Guo‐Chun |
| description | Objectives
Previous association studies have identified genetic variants in the human leukocyte antigen (HLA) complex as substantial risk factors for idiopathic inflammatory myopathies (IIMs). However, a great number of genes are located in the HLA region, and thus fine mapping is quite necessary.
Methods
Targeted capture sequencing were performed on the whole HLA region in 42 IIM patients and 24 healthy controls. A microarray analysis was applied to analyze gene expression profiles in additional 20 newly diagnosed IIM and five healthy controls.
Results
The HLA region was confirmed to be associated with IIMs in Chinese patients. By gene expression profiling and pathway analysis, several genes were identified as candidates for IIM risk factors, including HLA‐A, HLA‐B, HLA‐DRB5, HLA‐DRB1, HLA‐DQA1, HLA‐DQB1 and HLA‐DQB2. Interestingly, p.Y107V of the HLA‐DRB1 was predicted to be a potential causal non‐synonymous variation for IIMs that may affect the antigen‐binding groove of the HLA‐II molecule.
Conclusions
Our data have revealed novel genetic variations in the HLA region of IIM patients and provide new insight into the pathogenesis and diagnosis of IIMs. |
| doi_str_mv | 10.1111/1756-185X.13350 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2094427391</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2094427391</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3710-c8e62a9fec957ecd826e475c555d5f39cd88e820c7033f6b8a361920e1abf23</originalsourceid><addsrcrecordid>eNqFkTtPwzAUhS0EouUxsyFLLCxt7Th2krGqeEmVQKIDm-U6N62rxCl20qriz-OS0oEFL9c6-s6RfQ9CN5QMaTgjmnAxoCn_GFLGODlB_aNyerzHtIcuvF8RIigTyTnqMUJjkbC0j75myi2ggRxrtW5aB9jDZwtWG7vAJgfbmMKAx7beQIkXYKExGm-UM6oxtfXYWDxZGgse8DpIweDx1jTLYDZ1UJYBN7YoVVWppnY7XO06GfwVOitU6eH6MC_R--PDbPI8mL4-vUzG04FmCSUDnYKIVFaAzngCOk8jAXHCNec85wXLgpJCGhGdEMYKMU8VEzSLCFA1LyJ2ie671LWrw898IyvjNZSlslC3XkYki-MoYRkN6N0fdFW3zoa37SlGI5YKEahRR2lXe--gkGtnKuV2khK5b0Xu9y73HcifVoLj9pDbzivIj_xvDQHgHbA1Jez-y5Pjt2kX_A2n95ma</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2093123866</pqid></control><display><type>article</type><title>Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies</title><source>MEDLINE</source><source>Wiley Online Library All Journals</source><creator>Peng, Qing‐Lin ; Lin, Jin‐Ming ; Zhang, Yong‐Biao ; Zhang, Xue‐Zhi ; Wang, Pan‐Pan ; Wu, Ting‐Ting ; Yu, Jun ; Dong, Xiao‐Qun ; Gu, Ming‐Liang ; Wang, Guo‐Chun</creator><creatorcontrib>Peng, Qing‐Lin ; Lin, Jin‐Ming ; Zhang, Yong‐Biao ; Zhang, Xue‐Zhi ; Wang, Pan‐Pan ; Wu, Ting‐Ting ; Yu, Jun ; Dong, Xiao‐Qun ; Gu, Ming‐Liang ; Wang, Guo‐Chun</creatorcontrib><description>Objectives
Previous association studies have identified genetic variants in the human leukocyte antigen (HLA) complex as substantial risk factors for idiopathic inflammatory myopathies (IIMs). However, a great number of genes are located in the HLA region, and thus fine mapping is quite necessary.
Methods
Targeted capture sequencing were performed on the whole HLA region in 42 IIM patients and 24 healthy controls. A microarray analysis was applied to analyze gene expression profiles in additional 20 newly diagnosed IIM and five healthy controls.
Results
The HLA region was confirmed to be associated with IIMs in Chinese patients. By gene expression profiling and pathway analysis, several genes were identified as candidates for IIM risk factors, including HLA‐A, HLA‐B, HLA‐DRB5, HLA‐DRB1, HLA‐DQA1, HLA‐DQB1 and HLA‐DQB2. Interestingly, p.Y107V of the HLA‐DRB1 was predicted to be a potential causal non‐synonymous variation for IIMs that may affect the antigen‐binding groove of the HLA‐II molecule.
Conclusions
Our data have revealed novel genetic variations in the HLA region of IIM patients and provide new insight into the pathogenesis and diagnosis of IIMs.</description><identifier>ISSN: 1756-1841</identifier><identifier>EISSN: 1756-185X</identifier><identifier>DOI: 10.1111/1756-185X.13350</identifier><identifier>PMID: 30146738</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>Adult ; Antigens ; Asian Continental Ancestry Group - genetics ; Case-Control Studies ; China - epidemiology ; dermatomyositis ; DNA microarrays ; DQA1 protein ; Drb1 protein ; Female ; Gene expression ; Gene Expression Profiling - methods ; Gene mapping ; gene polymorphism ; Genetic Association Studies ; Genetic diversity ; Genetic Predisposition to Disease ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Histocompatibility antigen HLA ; HLA Antigens - genetics ; HLA Antigens - immunology ; human leukocyte antigen polymyositis ; Humans ; Inflammation ; Male ; Middle Aged ; Myositis - diagnosis ; Myositis - ethnology ; Myositis - genetics ; Myositis - immunology ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Predictive Value of Tests ; Risk Factors ; Transcriptome</subject><ispartof>International journal of rheumatic diseases, 2018-08, Vol.21 (8), p.1619-1626</ispartof><rights>2018 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd</rights><rights>2018 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.</rights><rights>International Journal of Rheumatic Diseases © 2018 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3710-c8e62a9fec957ecd826e475c555d5f39cd88e820c7033f6b8a361920e1abf23</citedby><cites>FETCH-LOGICAL-c3710-c8e62a9fec957ecd826e475c555d5f39cd88e820c7033f6b8a361920e1abf23</cites><orcidid>0000-0002-1271-1729</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%2F1756-185X.13350$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1756-185X.13350$$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/30146738$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Peng, Qing‐Lin</creatorcontrib><creatorcontrib>Lin, Jin‐Ming</creatorcontrib><creatorcontrib>Zhang, Yong‐Biao</creatorcontrib><creatorcontrib>Zhang, Xue‐Zhi</creatorcontrib><creatorcontrib>Wang, Pan‐Pan</creatorcontrib><creatorcontrib>Wu, Ting‐Ting</creatorcontrib><creatorcontrib>Yu, Jun</creatorcontrib><creatorcontrib>Dong, Xiao‐Qun</creatorcontrib><creatorcontrib>Gu, Ming‐Liang</creatorcontrib><creatorcontrib>Wang, Guo‐Chun</creatorcontrib><title>Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies</title><title>International journal of rheumatic diseases</title><addtitle>Int J Rheum Dis</addtitle><description>Objectives
Previous association studies have identified genetic variants in the human leukocyte antigen (HLA) complex as substantial risk factors for idiopathic inflammatory myopathies (IIMs). However, a great number of genes are located in the HLA region, and thus fine mapping is quite necessary.
Methods
Targeted capture sequencing were performed on the whole HLA region in 42 IIM patients and 24 healthy controls. A microarray analysis was applied to analyze gene expression profiles in additional 20 newly diagnosed IIM and five healthy controls.
Results
The HLA region was confirmed to be associated with IIMs in Chinese patients. By gene expression profiling and pathway analysis, several genes were identified as candidates for IIM risk factors, including HLA‐A, HLA‐B, HLA‐DRB5, HLA‐DRB1, HLA‐DQA1, HLA‐DQB1 and HLA‐DQB2. Interestingly, p.Y107V of the HLA‐DRB1 was predicted to be a potential causal non‐synonymous variation for IIMs that may affect the antigen‐binding groove of the HLA‐II molecule.
Conclusions
Our data have revealed novel genetic variations in the HLA region of IIM patients and provide new insight into the pathogenesis and diagnosis of IIMs.</description><subject>Adult</subject><subject>Antigens</subject><subject>Asian Continental Ancestry Group - genetics</subject><subject>Case-Control Studies</subject><subject>China - epidemiology</subject><subject>dermatomyositis</subject><subject>DNA microarrays</subject><subject>DQA1 protein</subject><subject>Drb1 protein</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene mapping</subject><subject>gene polymorphism</subject><subject>Genetic Association Studies</subject><subject>Genetic diversity</subject><subject>Genetic Predisposition to Disease</subject><subject>Genetic Variation</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Histocompatibility antigen HLA</subject><subject>HLA Antigens - genetics</subject><subject>HLA Antigens - immunology</subject><subject>human leukocyte antigen polymyositis</subject><subject>Humans</subject><subject>Inflammation</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Myositis - diagnosis</subject><subject>Myositis - ethnology</subject><subject>Myositis - genetics</subject><subject>Myositis - immunology</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Phenotype</subject><subject>Predictive Value of Tests</subject><subject>Risk Factors</subject><subject>Transcriptome</subject><issn>1756-1841</issn><issn>1756-185X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkTtPwzAUhS0EouUxsyFLLCxt7Th2krGqeEmVQKIDm-U6N62rxCl20qriz-OS0oEFL9c6-s6RfQ9CN5QMaTgjmnAxoCn_GFLGODlB_aNyerzHtIcuvF8RIigTyTnqMUJjkbC0j75myi2ggRxrtW5aB9jDZwtWG7vAJgfbmMKAx7beQIkXYKExGm-UM6oxtfXYWDxZGgse8DpIweDx1jTLYDZ1UJYBN7YoVVWppnY7XO06GfwVOitU6eH6MC_R--PDbPI8mL4-vUzG04FmCSUDnYKIVFaAzngCOk8jAXHCNec85wXLgpJCGhGdEMYKMU8VEzSLCFA1LyJ2ie671LWrw898IyvjNZSlslC3XkYki-MoYRkN6N0fdFW3zoa37SlGI5YKEahRR2lXe--gkGtnKuV2khK5b0Xu9y73HcifVoLj9pDbzivIj_xvDQHgHbA1Jez-y5Pjt2kX_A2n95ma</recordid><startdate>201808</startdate><enddate>201808</enddate><creator>Peng, Qing‐Lin</creator><creator>Lin, Jin‐Ming</creator><creator>Zhang, Yong‐Biao</creator><creator>Zhang, Xue‐Zhi</creator><creator>Wang, Pan‐Pan</creator><creator>Wu, Ting‐Ting</creator><creator>Yu, Jun</creator><creator>Dong, Xiao‐Qun</creator><creator>Gu, Ming‐Liang</creator><creator>Wang, Guo‐Chun</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>AAYXX</scope><scope>CITATION</scope><scope>7QP</scope><scope>7T5</scope><scope>H94</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1271-1729</orcidid></search><sort><creationdate>201808</creationdate><title>Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies</title><author>Peng, Qing‐Lin ; Lin, Jin‐Ming ; Zhang, Yong‐Biao ; Zhang, Xue‐Zhi ; Wang, Pan‐Pan ; Wu, Ting‐Ting ; Yu, Jun ; Dong, Xiao‐Qun ; Gu, Ming‐Liang ; Wang, Guo‐Chun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3710-c8e62a9fec957ecd826e475c555d5f39cd88e820c7033f6b8a361920e1abf23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Adult</topic><topic>Antigens</topic><topic>Asian Continental Ancestry Group - genetics</topic><topic>Case-Control Studies</topic><topic>China - epidemiology</topic><topic>dermatomyositis</topic><topic>DNA microarrays</topic><topic>DQA1 protein</topic><topic>Drb1 protein</topic><topic>Female</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene mapping</topic><topic>gene polymorphism</topic><topic>Genetic Association Studies</topic><topic>Genetic diversity</topic><topic>Genetic Predisposition to Disease</topic><topic>Genetic Variation</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Histocompatibility antigen HLA</topic><topic>HLA Antigens - genetics</topic><topic>HLA Antigens - immunology</topic><topic>human leukocyte antigen polymyositis</topic><topic>Humans</topic><topic>Inflammation</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Myositis - diagnosis</topic><topic>Myositis - ethnology</topic><topic>Myositis - genetics</topic><topic>Myositis - immunology</topic><topic>Oligonucleotide Array Sequence Analysis</topic><topic>Phenotype</topic><topic>Predictive Value of Tests</topic><topic>Risk Factors</topic><topic>Transcriptome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Peng, Qing‐Lin</creatorcontrib><creatorcontrib>Lin, Jin‐Ming</creatorcontrib><creatorcontrib>Zhang, Yong‐Biao</creatorcontrib><creatorcontrib>Zhang, Xue‐Zhi</creatorcontrib><creatorcontrib>Wang, Pan‐Pan</creatorcontrib><creatorcontrib>Wu, Ting‐Ting</creatorcontrib><creatorcontrib>Yu, Jun</creatorcontrib><creatorcontrib>Dong, Xiao‐Qun</creatorcontrib><creatorcontrib>Gu, Ming‐Liang</creatorcontrib><creatorcontrib>Wang, Guo‐Chun</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Immunology Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of rheumatic diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Peng, Qing‐Lin</au><au>Lin, Jin‐Ming</au><au>Zhang, Yong‐Biao</au><au>Zhang, Xue‐Zhi</au><au>Wang, Pan‐Pan</au><au>Wu, Ting‐Ting</au><au>Yu, Jun</au><au>Dong, Xiao‐Qun</au><au>Gu, Ming‐Liang</au><au>Wang, Guo‐Chun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies</atitle><jtitle>International journal of rheumatic diseases</jtitle><addtitle>Int J Rheum Dis</addtitle><date>2018-08</date><risdate>2018</risdate><volume>21</volume><issue>8</issue><spage>1619</spage><epage>1626</epage><pages>1619-1626</pages><issn>1756-1841</issn><eissn>1756-185X</eissn><abstract>Objectives
Previous association studies have identified genetic variants in the human leukocyte antigen (HLA) complex as substantial risk factors for idiopathic inflammatory myopathies (IIMs). However, a great number of genes are located in the HLA region, and thus fine mapping is quite necessary.
Methods
Targeted capture sequencing were performed on the whole HLA region in 42 IIM patients and 24 healthy controls. A microarray analysis was applied to analyze gene expression profiles in additional 20 newly diagnosed IIM and five healthy controls.
Results
The HLA region was confirmed to be associated with IIMs in Chinese patients. By gene expression profiling and pathway analysis, several genes were identified as candidates for IIM risk factors, including HLA‐A, HLA‐B, HLA‐DRB5, HLA‐DRB1, HLA‐DQA1, HLA‐DQB1 and HLA‐DQB2. Interestingly, p.Y107V of the HLA‐DRB1 was predicted to be a potential causal non‐synonymous variation for IIMs that may affect the antigen‐binding groove of the HLA‐II molecule.
Conclusions
Our data have revealed novel genetic variations in the HLA region of IIM patients and provide new insight into the pathogenesis and diagnosis of IIMs.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>30146738</pmid><doi>10.1111/1756-185X.13350</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-1271-1729</orcidid></addata></record> |
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| ispartof | International journal of rheumatic diseases, 2018-08, Vol.21 (8), p.1619-1626 |
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| subjects | Adult Antigens Asian Continental Ancestry Group - genetics Case-Control Studies China - epidemiology dermatomyositis DNA microarrays DQA1 protein Drb1 protein Female Gene expression Gene Expression Profiling - methods Gene mapping gene polymorphism Genetic Association Studies Genetic diversity Genetic Predisposition to Disease Genetic Variation High-Throughput Nucleotide Sequencing Histocompatibility antigen HLA HLA Antigens - genetics HLA Antigens - immunology human leukocyte antigen polymyositis Humans Inflammation Male Middle Aged Myositis - diagnosis Myositis - ethnology Myositis - genetics Myositis - immunology Oligonucleotide Array Sequence Analysis Phenotype Predictive Value of Tests Risk Factors Transcriptome |
| title | Targeted capture sequencing identifies novel genetic variations in Chinese patients with idiopathic inflammatory myopathies |
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