Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome
Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by SCN5A mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through in vitro studies. Therefore, we developed a new approach by combining multiple in sil...
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| Veröffentlicht in: | Scientific reports 2014-01, Vol.4 (1), p.3850-3850, Article 3850 |
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| creator | Juang, Jyh-Ming Jimmy Lu, Tzu-Pin Lai, Liang-Chuan Hsueh, Chia-Hsiang Liu, Yen-Bin Tsai, Chia-Ti Lin, Lian-Yu Yu, Chih-Chieh Hwang, Juey-Jen Chiang, Fu-Tien Yeh, Sherri Shih-Fan Chen, Wen-Pin Chuang, Eric Y. Lai, Ling-Ping Lin, Jiunn-Lee |
| description | Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by
SCN5A
mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through
in vitro
studies. Therefore, we developed a new approach by combining multiple
in silico
analyses to predict functional and structural changes of candidate
SCN5A
variants in BrS before conducting
in vitro
studies. Five
SCN5A
non-synonymous variants (1651G>A, 1776C>G, 1673A>G, 3269C>T and 3578G>A) were identified in 14 BrS patients using direct DNA sequencing. Several bioinformatics algorithms were applied and predicted that 1651G>A (A551T) and 1776C>G (N592K) were high-risk
SCN5A
variants (odds ratio 59.59 and 23.93). The results were validated by Mass spectrometry and
in vitro
electrophysiological assays. We concluded that integrating sequence-based information and secondary protein structures elements may help select highly potential variants in BrS before conducting time-consuming electrophysiological studies and two novel
SCN5A
mutations were validated. |
| doi_str_mv | 10.1038/srep03850 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3902491</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1897803511</sourcerecordid><originalsourceid>FETCH-LOGICAL-c438t-e9a2bb3591081252633c14dadfeb7366be2c7a1c209975774f1d37346f2f3ddf3</originalsourceid><addsrcrecordid>eNplkUtrGzEUhUVoaUKaRf9AEXTTBtzqORptCq7JC9Kk4CZboRlpXAVZciRNwPn1lXFq3FabK-79dO5BB4B3GH3GiLZfcrKrWjk6AEcEMT4hlJBXe_dDcJLzA6qHE8mwfAMOCWMN5aI9AuauOO-eXVjA76MvbuUtdAHOa7OPcBq0X2ebYYnwythQ3LCGP8aii3uycKbHrD2cz274FN7r5HQoefP6WxoX2mg4XweT4tK-Ba8H7bM9eanH4O787OfscnJ9e3E1m15PekbbMrFSk66jXGLUYsJJQ2mPmdFmsJ2gTdNZ0guNe4KkFFwINmBDBWXNQAZqzECPwdet7mrsltb01XDSXq2SW-q0VlE79fckuF9qEZ8UlYgwiavAxxeBFB9Hm4tautxb73WwccwKM0kEaitb0Q__oA9xTPW_KtVK0SLK8Ubw05bqU8w1qWFnBiO1iU_t4qvs-333O_JPWBU43QK5jsLCpr2V_6n9BinXpAU</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1897803511</pqid></control><display><type>article</type><title>Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome</title><source>MEDLINE</source><source>Nature Free</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><source>Springer Nature OA Free Journals</source><creator>Juang, Jyh-Ming Jimmy ; Lu, Tzu-Pin ; Lai, Liang-Chuan ; Hsueh, Chia-Hsiang ; Liu, Yen-Bin ; Tsai, Chia-Ti ; Lin, Lian-Yu ; Yu, Chih-Chieh ; Hwang, Juey-Jen ; Chiang, Fu-Tien ; Yeh, Sherri Shih-Fan ; Chen, Wen-Pin ; Chuang, Eric Y. ; Lai, Ling-Ping ; Lin, Jiunn-Lee</creator><creatorcontrib>Juang, Jyh-Ming Jimmy ; Lu, Tzu-Pin ; Lai, Liang-Chuan ; Hsueh, Chia-Hsiang ; Liu, Yen-Bin ; Tsai, Chia-Ti ; Lin, Lian-Yu ; Yu, Chih-Chieh ; Hwang, Juey-Jen ; Chiang, Fu-Tien ; Yeh, Sherri Shih-Fan ; Chen, Wen-Pin ; Chuang, Eric Y. ; Lai, Ling-Ping ; Lin, Jiunn-Lee</creatorcontrib><description>Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by
SCN5A
mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through
in vitro
studies. Therefore, we developed a new approach by combining multiple
in silico
analyses to predict functional and structural changes of candidate
SCN5A
variants in BrS before conducting
in vitro
studies. Five
SCN5A
non-synonymous variants (1651G>A, 1776C>G, 1673A>G, 3269C>T and 3578G>A) were identified in 14 BrS patients using direct DNA sequencing. Several bioinformatics algorithms were applied and predicted that 1651G>A (A551T) and 1776C>G (N592K) were high-risk
SCN5A
variants (odds ratio 59.59 and 23.93). The results were validated by Mass spectrometry and
in vitro
electrophysiological assays. We concluded that integrating sequence-based information and secondary protein structures elements may help select highly potential variants in BrS before conducting time-consuming electrophysiological studies and two novel
SCN5A
mutations were validated.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep03850</identifier><identifier>PMID: 24463578</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>101/58 ; 38/47 ; 38/77 ; 631/114 ; 692/699/75/29 ; 9/74 ; Adult ; Algorithms ; Bioinformatics ; Brugada Syndrome - genetics ; Cardiac arrhythmia ; Coronary artery disease ; DNA sequencing ; Female ; Genetic Predisposition to Disease ; Heart diseases ; Humanities and Social Sciences ; Humans ; Male ; Mass spectroscopy ; Middle Aged ; multidisciplinary ; Mutation ; NAV1.5 Voltage-Gated Sodium Channel - chemistry ; NAV1.5 Voltage-Gated Sodium Channel - genetics ; Patch-Clamp Techniques ; Protein Structure, Secondary ; Science ; Structure-function relationships</subject><ispartof>Scientific reports, 2014-01, Vol.4 (1), p.3850-3850, Article 3850</ispartof><rights>The Author(s) 2014</rights><rights>Copyright Nature Publishing Group Jan 2014</rights><rights>Copyright © 2014, Macmillan Publishers Limited. All rights reserved 2014 Macmillan Publishers Limited. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c438t-e9a2bb3591081252633c14dadfeb7366be2c7a1c209975774f1d37346f2f3ddf3</citedby><cites>FETCH-LOGICAL-c438t-e9a2bb3591081252633c14dadfeb7366be2c7a1c209975774f1d37346f2f3ddf3</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/PMC3902491/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902491/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27903,27904,41098,42167,51553,53768,53770</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24463578$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Juang, Jyh-Ming Jimmy</creatorcontrib><creatorcontrib>Lu, Tzu-Pin</creatorcontrib><creatorcontrib>Lai, Liang-Chuan</creatorcontrib><creatorcontrib>Hsueh, Chia-Hsiang</creatorcontrib><creatorcontrib>Liu, Yen-Bin</creatorcontrib><creatorcontrib>Tsai, Chia-Ti</creatorcontrib><creatorcontrib>Lin, Lian-Yu</creatorcontrib><creatorcontrib>Yu, Chih-Chieh</creatorcontrib><creatorcontrib>Hwang, Juey-Jen</creatorcontrib><creatorcontrib>Chiang, Fu-Tien</creatorcontrib><creatorcontrib>Yeh, Sherri Shih-Fan</creatorcontrib><creatorcontrib>Chen, Wen-Pin</creatorcontrib><creatorcontrib>Chuang, Eric Y.</creatorcontrib><creatorcontrib>Lai, Ling-Ping</creatorcontrib><creatorcontrib>Lin, Jiunn-Lee</creatorcontrib><title>Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by
SCN5A
mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through
in vitro
studies. Therefore, we developed a new approach by combining multiple
in silico
analyses to predict functional and structural changes of candidate
SCN5A
variants in BrS before conducting
in vitro
studies. Five
SCN5A
non-synonymous variants (1651G>A, 1776C>G, 1673A>G, 3269C>T and 3578G>A) were identified in 14 BrS patients using direct DNA sequencing. Several bioinformatics algorithms were applied and predicted that 1651G>A (A551T) and 1776C>G (N592K) were high-risk
SCN5A
variants (odds ratio 59.59 and 23.93). The results were validated by Mass spectrometry and
in vitro
electrophysiological assays. We concluded that integrating sequence-based information and secondary protein structures elements may help select highly potential variants in BrS before conducting time-consuming electrophysiological studies and two novel
SCN5A
mutations were validated.</description><subject>101/58</subject><subject>38/47</subject><subject>38/77</subject><subject>631/114</subject><subject>692/699/75/29</subject><subject>9/74</subject><subject>Adult</subject><subject>Algorithms</subject><subject>Bioinformatics</subject><subject>Brugada Syndrome - genetics</subject><subject>Cardiac arrhythmia</subject><subject>Coronary artery disease</subject><subject>DNA sequencing</subject><subject>Female</subject><subject>Genetic Predisposition to Disease</subject><subject>Heart diseases</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Male</subject><subject>Mass spectroscopy</subject><subject>Middle Aged</subject><subject>multidisciplinary</subject><subject>Mutation</subject><subject>NAV1.5 Voltage-Gated Sodium Channel - chemistry</subject><subject>NAV1.5 Voltage-Gated Sodium Channel - genetics</subject><subject>Patch-Clamp Techniques</subject><subject>Protein Structure, Secondary</subject><subject>Science</subject><subject>Structure-function relationships</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkUtrGzEUhUVoaUKaRf9AEXTTBtzqORptCq7JC9Kk4CZboRlpXAVZciRNwPn1lXFq3FabK-79dO5BB4B3GH3GiLZfcrKrWjk6AEcEMT4hlJBXe_dDcJLzA6qHE8mwfAMOCWMN5aI9AuauOO-eXVjA76MvbuUtdAHOa7OPcBq0X2ebYYnwythQ3LCGP8aii3uycKbHrD2cz274FN7r5HQoefP6WxoX2mg4XweT4tK-Ba8H7bM9eanH4O787OfscnJ9e3E1m15PekbbMrFSk66jXGLUYsJJQ2mPmdFmsJ2gTdNZ0guNe4KkFFwINmBDBWXNQAZqzECPwdet7mrsltb01XDSXq2SW-q0VlE79fckuF9qEZ8UlYgwiavAxxeBFB9Hm4tautxb73WwccwKM0kEaitb0Q__oA9xTPW_KtVK0SLK8Ubw05bqU8w1qWFnBiO1iU_t4qvs-333O_JPWBU43QK5jsLCpr2V_6n9BinXpAU</recordid><startdate>20140127</startdate><enddate>20140127</enddate><creator>Juang, Jyh-Ming Jimmy</creator><creator>Lu, Tzu-Pin</creator><creator>Lai, Liang-Chuan</creator><creator>Hsueh, Chia-Hsiang</creator><creator>Liu, Yen-Bin</creator><creator>Tsai, Chia-Ti</creator><creator>Lin, Lian-Yu</creator><creator>Yu, Chih-Chieh</creator><creator>Hwang, Juey-Jen</creator><creator>Chiang, Fu-Tien</creator><creator>Yeh, Sherri Shih-Fan</creator><creator>Chen, Wen-Pin</creator><creator>Chuang, Eric Y.</creator><creator>Lai, Ling-Ping</creator><creator>Lin, Jiunn-Lee</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><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>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20140127</creationdate><title>Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome</title><author>Juang, Jyh-Ming Jimmy ; Lu, Tzu-Pin ; Lai, Liang-Chuan ; Hsueh, Chia-Hsiang ; Liu, Yen-Bin ; Tsai, Chia-Ti ; Lin, Lian-Yu ; Yu, Chih-Chieh ; Hwang, Juey-Jen ; Chiang, Fu-Tien ; Yeh, Sherri Shih-Fan ; Chen, Wen-Pin ; Chuang, Eric Y. ; Lai, Ling-Ping ; Lin, Jiunn-Lee</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c438t-e9a2bb3591081252633c14dadfeb7366be2c7a1c209975774f1d37346f2f3ddf3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>101/58</topic><topic>38/47</topic><topic>38/77</topic><topic>631/114</topic><topic>692/699/75/29</topic><topic>9/74</topic><topic>Adult</topic><topic>Algorithms</topic><topic>Bioinformatics</topic><topic>Brugada Syndrome - genetics</topic><topic>Cardiac arrhythmia</topic><topic>Coronary artery disease</topic><topic>DNA sequencing</topic><topic>Female</topic><topic>Genetic Predisposition to Disease</topic><topic>Heart diseases</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Male</topic><topic>Mass spectroscopy</topic><topic>Middle Aged</topic><topic>multidisciplinary</topic><topic>Mutation</topic><topic>NAV1.5 Voltage-Gated Sodium Channel - chemistry</topic><topic>NAV1.5 Voltage-Gated Sodium Channel - genetics</topic><topic>Patch-Clamp Techniques</topic><topic>Protein Structure, Secondary</topic><topic>Science</topic><topic>Structure-function relationships</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Juang, Jyh-Ming Jimmy</creatorcontrib><creatorcontrib>Lu, Tzu-Pin</creatorcontrib><creatorcontrib>Lai, Liang-Chuan</creatorcontrib><creatorcontrib>Hsueh, Chia-Hsiang</creatorcontrib><creatorcontrib>Liu, Yen-Bin</creatorcontrib><creatorcontrib>Tsai, Chia-Ti</creatorcontrib><creatorcontrib>Lin, Lian-Yu</creatorcontrib><creatorcontrib>Yu, Chih-Chieh</creatorcontrib><creatorcontrib>Hwang, Juey-Jen</creatorcontrib><creatorcontrib>Chiang, Fu-Tien</creatorcontrib><creatorcontrib>Yeh, Sherri Shih-Fan</creatorcontrib><creatorcontrib>Chen, Wen-Pin</creatorcontrib><creatorcontrib>Chuang, Eric Y.</creatorcontrib><creatorcontrib>Lai, Ling-Ping</creatorcontrib><creatorcontrib>Lin, Jiunn-Lee</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</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 One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</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>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science 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>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Juang, Jyh-Ming Jimmy</au><au>Lu, Tzu-Pin</au><au>Lai, Liang-Chuan</au><au>Hsueh, Chia-Hsiang</au><au>Liu, Yen-Bin</au><au>Tsai, Chia-Ti</au><au>Lin, Lian-Yu</au><au>Yu, Chih-Chieh</au><au>Hwang, Juey-Jen</au><au>Chiang, Fu-Tien</au><au>Yeh, Sherri Shih-Fan</au><au>Chen, Wen-Pin</au><au>Chuang, Eric Y.</au><au>Lai, Ling-Ping</au><au>Lin, Jiunn-Lee</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2014-01-27</date><risdate>2014</risdate><volume>4</volume><issue>1</issue><spage>3850</spage><epage>3850</epage><pages>3850-3850</pages><artnum>3850</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Brugada syndrome (BrS) is an inheritable sudden cardiac death disease mainly caused by
SCN5A
mutations. Traditional approaches can be costly and time-consuming if all candidate variants need to be validated through
in vitro
studies. Therefore, we developed a new approach by combining multiple
in silico
analyses to predict functional and structural changes of candidate
SCN5A
variants in BrS before conducting
in vitro
studies. Five
SCN5A
non-synonymous variants (1651G>A, 1776C>G, 1673A>G, 3269C>T and 3578G>A) were identified in 14 BrS patients using direct DNA sequencing. Several bioinformatics algorithms were applied and predicted that 1651G>A (A551T) and 1776C>G (N592K) were high-risk
SCN5A
variants (odds ratio 59.59 and 23.93). The results were validated by Mass spectrometry and
in vitro
electrophysiological assays. We concluded that integrating sequence-based information and secondary protein structures elements may help select highly potential variants in BrS before conducting time-consuming electrophysiological studies and two novel
SCN5A
mutations were validated.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>24463578</pmid><doi>10.1038/srep03850</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 101/58 38/47 38/77 631/114 692/699/75/29 9/74 Adult Algorithms Bioinformatics Brugada Syndrome - genetics Cardiac arrhythmia Coronary artery disease DNA sequencing Female Genetic Predisposition to Disease Heart diseases Humanities and Social Sciences Humans Male Mass spectroscopy Middle Aged multidisciplinary Mutation NAV1.5 Voltage-Gated Sodium Channel - chemistry NAV1.5 Voltage-Gated Sodium Channel - genetics Patch-Clamp Techniques Protein Structure, Secondary Science Structure-function relationships |
| title | Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome |
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