Improvement of short tandem repeat analysis of samples highly contaminated by humic acid
Abstract We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capac...
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| Veröffentlicht in: | Journal of forensic and legal medicine 2013-10, Vol.20 (7), p.922-928 |
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| container_title | Journal of forensic and legal medicine |
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| creator | Seo, Seung Bum, PhD Jin, Hong Xuan, MD Lee, Hye Young, BS Ge, Jianye, PhD King, Jonathan L., MS Lyoo, Sung Hee, BS Shin, Dong Hoon, MD, PhD Lee, Soong Deok, MD, PhD |
| description | Abstract We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples. |
| doi_str_mv | 10.1016/j.jflm.2013.08.001 |
| format | Article |
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DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.</description><identifier>ISSN: 1752-928X</identifier><identifier>EISSN: 1878-7487</identifier><identifier>DOI: 10.1016/j.jflm.2013.08.001</identifier><identifier>PMID: 24112347</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Acids ; Deoxyribonucleic acid ; DNA ; DNA - isolation & purification ; DNA Contamination ; DNA Fingerprinting - instrumentation ; DNA Fingerprinting - methods ; DNA recovery ; Forensic DNA typing ; Forensic medicine ; Humans ; Humic acid ; Humic Substances ; Inhibitor ; Microsatellite Repeats ; Molecular biology ; Pathology ; Polymerase Chain Reaction ; Short tandem repeat ; Soils</subject><ispartof>Journal of forensic and legal medicine, 2013-10, Vol.20 (7), p.922-928</ispartof><rights>Elsevier Ltd and Faculty of Forensic and Legal Medicine</rights><rights>2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine</rights><rights>Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.</rights><rights>Copyright Churchill Livingstone Inc., Medical Publishers Oct 2013</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c439t-328ea496fc902fde039042d03338292d8ea4af369edbdca78b3ca1cd3acdcaac3</citedby><cites>FETCH-LOGICAL-c439t-328ea496fc902fde039042d03338292d8ea4af369edbdca78b3ca1cd3acdcaac3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.jflm.2013.08.001$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3549,27923,27924,45994</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24112347$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Seo, Seung Bum, PhD</creatorcontrib><creatorcontrib>Jin, Hong Xuan, MD</creatorcontrib><creatorcontrib>Lee, Hye Young, BS</creatorcontrib><creatorcontrib>Ge, Jianye, PhD</creatorcontrib><creatorcontrib>King, Jonathan L., MS</creatorcontrib><creatorcontrib>Lyoo, Sung Hee, BS</creatorcontrib><creatorcontrib>Shin, Dong Hoon, MD, PhD</creatorcontrib><creatorcontrib>Lee, Soong Deok, MD, PhD</creatorcontrib><title>Improvement of short tandem repeat analysis of samples highly contaminated by humic acid</title><title>Journal of forensic and legal medicine</title><addtitle>J Forensic Leg Med</addtitle><description>Abstract We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.</description><subject>Acids</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - isolation & purification</subject><subject>DNA Contamination</subject><subject>DNA Fingerprinting - instrumentation</subject><subject>DNA Fingerprinting - methods</subject><subject>DNA recovery</subject><subject>Forensic DNA typing</subject><subject>Forensic medicine</subject><subject>Humans</subject><subject>Humic acid</subject><subject>Humic Substances</subject><subject>Inhibitor</subject><subject>Microsatellite Repeats</subject><subject>Molecular biology</subject><subject>Pathology</subject><subject>Polymerase Chain Reaction</subject><subject>Short tandem repeat</subject><subject>Soils</subject><issn>1752-928X</issn><issn>1878-7487</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU9rFTEUxQdRbK1-ARcScONmxps_700CIpSitVBwoUJ3IS-548uYzDyTmcJ8ezN9rUIXrnLD_Z0D59yqek2hoUC37_um70JsGFDegGwA6JPqlMpW1q2Q7dMytxtWKyZvTqoXOfcAG8HazfPqhAlKGRftaXVzFQ9pvMWIw0TGjuT9mCYymcFhJAkPaCZiBhOW7PPd3sRDwEz2_uc-LMSOw2SiH8yEjuwWsp-jt8RY715WzzoTMr66f8-qH58_fb_4Ul9_vby6OL-ureBqqjmTaITadlYB6xwCVyCYA865ZIq5dWs6vlXods6aVu64NdQ6bmz5GsvPqndH3xLj94x50tFniyGYAcc5ayoEF0CBs4K-fYT245xKuDuKclAtV4ViR8qmMeeEnT4kH01aNAW99q57vfau1941SF16L6I399bzLqL7K3kougAfjgCWLm49Jp2tx8Gi8wntpN3o_-__8ZHcBj94a8IvXDD_y6Ez06C_rZdfD19CAaNc8j_21KnG</recordid><startdate>20131001</startdate><enddate>20131001</enddate><creator>Seo, Seung Bum, PhD</creator><creator>Jin, Hong Xuan, MD</creator><creator>Lee, Hye Young, BS</creator><creator>Ge, Jianye, PhD</creator><creator>King, Jonathan L., MS</creator><creator>Lyoo, Sung Hee, BS</creator><creator>Shin, Dong Hoon, MD, PhD</creator><creator>Lee, Soong Deok, MD, PhD</creator><general>Elsevier Ltd</general><general>Churchill Livingstone Inc., Medical Publishers</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>7X8</scope></search><sort><creationdate>20131001</creationdate><title>Improvement of short tandem repeat analysis of samples highly contaminated by humic acid</title><author>Seo, Seung Bum, PhD ; Jin, Hong Xuan, MD ; Lee, Hye Young, BS ; Ge, Jianye, PhD ; King, Jonathan L., MS ; Lyoo, Sung Hee, BS ; Shin, Dong Hoon, MD, PhD ; Lee, Soong Deok, MD, PhD</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c439t-328ea496fc902fde039042d03338292d8ea4af369edbdca78b3ca1cd3acdcaac3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Acids</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - isolation & purification</topic><topic>DNA Contamination</topic><topic>DNA Fingerprinting - instrumentation</topic><topic>DNA Fingerprinting - methods</topic><topic>DNA recovery</topic><topic>Forensic DNA typing</topic><topic>Forensic medicine</topic><topic>Humans</topic><topic>Humic acid</topic><topic>Humic Substances</topic><topic>Inhibitor</topic><topic>Microsatellite Repeats</topic><topic>Molecular biology</topic><topic>Pathology</topic><topic>Polymerase Chain Reaction</topic><topic>Short tandem repeat</topic><topic>Soils</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Seo, Seung Bum, PhD</creatorcontrib><creatorcontrib>Jin, Hong Xuan, MD</creatorcontrib><creatorcontrib>Lee, Hye Young, BS</creatorcontrib><creatorcontrib>Ge, Jianye, PhD</creatorcontrib><creatorcontrib>King, Jonathan L., MS</creatorcontrib><creatorcontrib>Lyoo, Sung Hee, BS</creatorcontrib><creatorcontrib>Shin, Dong Hoon, MD, PhD</creatorcontrib><creatorcontrib>Lee, Soong Deok, MD, PhD</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of forensic and legal medicine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Seo, Seung Bum, PhD</au><au>Jin, Hong Xuan, MD</au><au>Lee, Hye Young, BS</au><au>Ge, Jianye, PhD</au><au>King, Jonathan L., MS</au><au>Lyoo, Sung Hee, BS</au><au>Shin, Dong Hoon, MD, PhD</au><au>Lee, Soong Deok, MD, PhD</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improvement of short tandem repeat analysis of samples highly contaminated by humic acid</atitle><jtitle>Journal of forensic and legal medicine</jtitle><addtitle>J Forensic Leg Med</addtitle><date>2013-10-01</date><risdate>2013</risdate><volume>20</volume><issue>7</issue><spage>922</spage><epage>928</epage><pages>922-928</pages><issn>1752-928X</issn><eissn>1878-7487</eissn><abstract>Abstract We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>24112347</pmid><doi>10.1016/j.jflm.2013.08.001</doi><tpages>7</tpages></addata></record> |
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| source | MEDLINE; ScienceDirect Journals (5 years ago - present) |
| subjects | Acids Deoxyribonucleic acid DNA DNA - isolation & purification DNA Contamination DNA Fingerprinting - instrumentation DNA Fingerprinting - methods DNA recovery Forensic DNA typing Forensic medicine Humans Humic acid Humic Substances Inhibitor Microsatellite Repeats Molecular biology Pathology Polymerase Chain Reaction Short tandem repeat Soils |
| title | Improvement of short tandem repeat analysis of samples highly contaminated by humic acid |
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