A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms
Background Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)‐dependent...
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| Veröffentlicht in: | Journal of clinical laboratory analysis 2018-09, Vol.32 (7), p.e22440-n/a |
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| container_title | Journal of clinical laboratory analysis |
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| creator | Alavian, Seyed Ehsan Sharafi, Heidar Shirmast, Paniz Alavian, Seyed Moayed Behnava, Bita Pouryasin, Mohammad Keshvari, Maryam Pouryasin, Ali |
| description | Background
Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)‐dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV‐infected patients.
Methods
In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR‐RFLP technique and sequencing technique were performed on these samples. To validate the PCR‐RFLP method, the PCR‐RFLP genotyping results should be 100% concordant with the PCR‐sequencing results.
Results
The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR‐RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR‐RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively.
Conclusion
We developed and validated a rapid and inexpensive PCR‐RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms. |
| doi_str_mv | 10.1002/jcla.22440 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6816863</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2108823307</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4480-615fd69055993c88126782e04fbf508659930aa39d68393eb178eeab3cfdac5b3</originalsourceid><addsrcrecordid>eNp9kd1KwzAYhoMobv6ceAES8Ezo_JK0aXoijOF0MnCI4mFI22TraJuabMrOvASv0Suxczr0xKOQfA9PPt4XoRMCPQJAL-ZZqXqUhiHsoC6BRARU0GgXdUGIOBBAWAcdeD8HAJEQvo86NOEcYk676KmPjcqKUuPJ4P7j7f1-OJ7gSi9mNsfGOjzVtV2smqKeYmvw6GHSx84TQmMWhVjVeXuLaQwECG5suaqsa2aFr_wR2jOq9Pr4-zxEj8Orh8FNML67Hg364yALQwEBJ5HJeQJRlCQsE4JQHguqITSpiUDw9TMoxZKcC5YwnZJYaK1SlplcZVHKDtHlxtss00rnma4XTpWycUWl3EpaVci_k7qYyal9kVwQLjhrBWffAmefl9ov5NwuXd3uLClpA6SMQdxS5xsqc9Z7p832BwJyXYJclyC_Smjh0987bdGf1FuAbIDXNvjVPyp5Oxj3N9JPvaCPvQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2108823307</pqid></control><display><type>article</type><title>A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms</title><source>MEDLINE</source><source>Wiley Online Library Journals Frontfile Complete</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><creator>Alavian, Seyed Ehsan ; Sharafi, Heidar ; Shirmast, Paniz ; Alavian, Seyed Moayed ; Behnava, Bita ; Pouryasin, Mohammad ; Keshvari, Maryam ; Pouryasin, Ali</creator><creatorcontrib>Alavian, Seyed Ehsan ; Sharafi, Heidar ; Shirmast, Paniz ; Alavian, Seyed Moayed ; Behnava, Bita ; Pouryasin, Mohammad ; Keshvari, Maryam ; Pouryasin, Ali</creatorcontrib><description>Background
Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)‐dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV‐infected patients.
Methods
In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR‐RFLP technique and sequencing technique were performed on these samples. To validate the PCR‐RFLP method, the PCR‐RFLP genotyping results should be 100% concordant with the PCR‐sequencing results.
Results
The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR‐RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR‐RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively.
Conclusion
We developed and validated a rapid and inexpensive PCR‐RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms.</description><identifier>ISSN: 0887-8013</identifier><identifier>EISSN: 1098-2825</identifier><identifier>DOI: 10.1002/jcla.22440</identifier><identifier>PMID: 29660762</identifier><language>eng</language><publisher>United States: John Wiley & Sons, Inc</publisher><subject>Antiviral Agents - therapeutic use ; Chronic infection ; Cohort Studies ; Female ; Gene polymorphism ; Genotyping ; Genotyping Techniques - methods ; Hepatitis ; Hepatitis C ; hepatitis C virus ; Hepatitis C, Chronic - drug therapy ; Hepatitis C, Chronic - epidemiology ; Hepatitis C, Chronic - genetics ; Humans ; inosine triphosphate pyrophosphatase gene ; Interferon ; Iran - epidemiology ; ITPA gene ; Male ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Polymorphism ; Polymorphism, Restriction Fragment Length - genetics ; Polymorphism, Single Nucleotide - genetics ; Pyrophosphatase ; Pyrophosphatases - genetics ; Restriction fragment length polymorphism ; Ribavirin ; Ribavirin - therapeutic use ; sequencing ; single nucleotide polymorphisms ; Single-nucleotide polymorphism</subject><ispartof>Journal of clinical laboratory analysis, 2018-09, Vol.32 (7), p.e22440-n/a</ispartof><rights>2018 Wiley Periodicals, Inc.</rights><rights>Copyright © 2018 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4480-615fd69055993c88126782e04fbf508659930aa39d68393eb178eeab3cfdac5b3</citedby><cites>FETCH-LOGICAL-c4480-615fd69055993c88126782e04fbf508659930aa39d68393eb178eeab3cfdac5b3</cites><orcidid>0000-0002-8882-0825</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816863/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6816863/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1411,27901,27902,45550,45551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29660762$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alavian, Seyed Ehsan</creatorcontrib><creatorcontrib>Sharafi, Heidar</creatorcontrib><creatorcontrib>Shirmast, Paniz</creatorcontrib><creatorcontrib>Alavian, Seyed Moayed</creatorcontrib><creatorcontrib>Behnava, Bita</creatorcontrib><creatorcontrib>Pouryasin, Mohammad</creatorcontrib><creatorcontrib>Keshvari, Maryam</creatorcontrib><creatorcontrib>Pouryasin, Ali</creatorcontrib><title>A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms</title><title>Journal of clinical laboratory analysis</title><addtitle>J Clin Lab Anal</addtitle><description>Background
Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)‐dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV‐infected patients.
Methods
In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR‐RFLP technique and sequencing technique were performed on these samples. To validate the PCR‐RFLP method, the PCR‐RFLP genotyping results should be 100% concordant with the PCR‐sequencing results.
Results
The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR‐RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR‐RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively.
Conclusion
We developed and validated a rapid and inexpensive PCR‐RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms.</description><subject>Antiviral Agents - therapeutic use</subject><subject>Chronic infection</subject><subject>Cohort Studies</subject><subject>Female</subject><subject>Gene polymorphism</subject><subject>Genotyping</subject><subject>Genotyping Techniques - methods</subject><subject>Hepatitis</subject><subject>Hepatitis C</subject><subject>hepatitis C virus</subject><subject>Hepatitis C, Chronic - drug therapy</subject><subject>Hepatitis C, Chronic - epidemiology</subject><subject>Hepatitis C, Chronic - genetics</subject><subject>Humans</subject><subject>inosine triphosphate pyrophosphatase gene</subject><subject>Interferon</subject><subject>Iran - epidemiology</subject><subject>ITPA gene</subject><subject>Male</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism</subject><subject>Polymorphism, Restriction Fragment Length - genetics</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Pyrophosphatase</subject><subject>Pyrophosphatases - genetics</subject><subject>Restriction fragment length polymorphism</subject><subject>Ribavirin</subject><subject>Ribavirin - therapeutic use</subject><subject>sequencing</subject><subject>single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><issn>0887-8013</issn><issn>1098-2825</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kd1KwzAYhoMobv6ceAES8Ezo_JK0aXoijOF0MnCI4mFI22TraJuabMrOvASv0Suxczr0xKOQfA9PPt4XoRMCPQJAL-ZZqXqUhiHsoC6BRARU0GgXdUGIOBBAWAcdeD8HAJEQvo86NOEcYk676KmPjcqKUuPJ4P7j7f1-OJ7gSi9mNsfGOjzVtV2smqKeYmvw6GHSx84TQmMWhVjVeXuLaQwECG5suaqsa2aFr_wR2jOq9Pr4-zxEj8Orh8FNML67Hg364yALQwEBJ5HJeQJRlCQsE4JQHguqITSpiUDw9TMoxZKcC5YwnZJYaK1SlplcZVHKDtHlxtss00rnma4XTpWycUWl3EpaVci_k7qYyal9kVwQLjhrBWffAmefl9ov5NwuXd3uLClpA6SMQdxS5xsqc9Z7p832BwJyXYJclyC_Smjh0987bdGf1FuAbIDXNvjVPyp5Oxj3N9JPvaCPvQ</recordid><startdate>201809</startdate><enddate>201809</enddate><creator>Alavian, Seyed Ehsan</creator><creator>Sharafi, Heidar</creator><creator>Shirmast, Paniz</creator><creator>Alavian, Seyed Moayed</creator><creator>Behnava, Bita</creator><creator>Pouryasin, Mohammad</creator><creator>Keshvari, Maryam</creator><creator>Pouryasin, Ali</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons 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>7U9</scope><scope>H94</scope><scope>K9.</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8882-0825</orcidid></search><sort><creationdate>201809</creationdate><title>A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms</title><author>Alavian, Seyed Ehsan ; Sharafi, Heidar ; Shirmast, Paniz ; Alavian, Seyed Moayed ; Behnava, Bita ; Pouryasin, Mohammad ; Keshvari, Maryam ; Pouryasin, Ali</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4480-615fd69055993c88126782e04fbf508659930aa39d68393eb178eeab3cfdac5b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Antiviral Agents - therapeutic use</topic><topic>Chronic infection</topic><topic>Cohort Studies</topic><topic>Female</topic><topic>Gene polymorphism</topic><topic>Genotyping</topic><topic>Genotyping Techniques - methods</topic><topic>Hepatitis</topic><topic>Hepatitis C</topic><topic>hepatitis C virus</topic><topic>Hepatitis C, Chronic - drug therapy</topic><topic>Hepatitis C, Chronic - epidemiology</topic><topic>Hepatitis C, Chronic - genetics</topic><topic>Humans</topic><topic>inosine triphosphate pyrophosphatase gene</topic><topic>Interferon</topic><topic>Iran - epidemiology</topic><topic>ITPA gene</topic><topic>Male</topic><topic>Polymerase chain reaction</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism</topic><topic>Polymorphism, Restriction Fragment Length - genetics</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Pyrophosphatase</topic><topic>Pyrophosphatases - genetics</topic><topic>Restriction fragment length polymorphism</topic><topic>Ribavirin</topic><topic>Ribavirin - therapeutic use</topic><topic>sequencing</topic><topic>single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alavian, Seyed Ehsan</creatorcontrib><creatorcontrib>Sharafi, Heidar</creatorcontrib><creatorcontrib>Shirmast, Paniz</creatorcontrib><creatorcontrib>Alavian, Seyed Moayed</creatorcontrib><creatorcontrib>Behnava, Bita</creatorcontrib><creatorcontrib>Pouryasin, Mohammad</creatorcontrib><creatorcontrib>Keshvari, Maryam</creatorcontrib><creatorcontrib>Pouryasin, Ali</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>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of clinical laboratory analysis</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alavian, Seyed Ehsan</au><au>Sharafi, Heidar</au><au>Shirmast, Paniz</au><au>Alavian, Seyed Moayed</au><au>Behnava, Bita</au><au>Pouryasin, Mohammad</au><au>Keshvari, Maryam</au><au>Pouryasin, Ali</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms</atitle><jtitle>Journal of clinical laboratory analysis</jtitle><addtitle>J Clin Lab Anal</addtitle><date>2018-09</date><risdate>2018</risdate><volume>32</volume><issue>7</issue><spage>e22440</spage><epage>n/a</epage><pages>e22440-n/a</pages><issn>0887-8013</issn><eissn>1098-2825</eissn><abstract>Background
Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)‐dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV‐infected patients.
Methods
In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR‐RFLP technique and sequencing technique were performed on these samples. To validate the PCR‐RFLP method, the PCR‐RFLP genotyping results should be 100% concordant with the PCR‐sequencing results.
Results
The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR‐RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR‐RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively.
Conclusion
We developed and validated a rapid and inexpensive PCR‐RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms.</abstract><cop>United States</cop><pub>John Wiley & Sons, Inc</pub><pmid>29660762</pmid><doi>10.1002/jcla.22440</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-8882-0825</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Antiviral Agents - therapeutic use Chronic infection Cohort Studies Female Gene polymorphism Genotyping Genotyping Techniques - methods Hepatitis Hepatitis C hepatitis C virus Hepatitis C, Chronic - drug therapy Hepatitis C, Chronic - epidemiology Hepatitis C, Chronic - genetics Humans inosine triphosphate pyrophosphatase gene Interferon Iran - epidemiology ITPA gene Male Polymerase chain reaction Polymerase Chain Reaction - methods Polymorphism Polymorphism, Restriction Fragment Length - genetics Polymorphism, Single Nucleotide - genetics Pyrophosphatase Pyrophosphatases - genetics Restriction fragment length polymorphism Ribavirin Ribavirin - therapeutic use sequencing single nucleotide polymorphisms Single-nucleotide polymorphism |
| title | A facile PCR‐RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms |
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