Subduing the influence of PCR inhibitors on amplifying aged, degraded, and low copy number DNA: PCR enhancer cocktail-p and rescue PCR
PCR inhibitors are a formidable problem to the study of aged, degraded, and/or low copy number DNA. As a result, there is a need to find alternate methods that ameliorate the efficacy of PCR. In this study, we attempted to use genetic methods to identify the species of salmonid (Oncorhynchus spp.) r...
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| description | PCR inhibitors are a formidable problem to the study of aged, degraded, and/or low copy number DNA. As a result, there is a need to find alternate methods that ameliorate the efficacy of PCR. In this study, we attempted to use genetic methods to identify the species of salmonid (Oncorhynchus spp.) remains recovered from archaeological sites along the Feather River located in northern California, United States. In the process of doing so, we compared the efficacy of a PCR enhancer cocktail called "PEC-P" and a reagent rich PCR recipe called "rescue PCR" over standard PCR. Across all treatments (full concentration and 1:10 dilute eluates subjected to standard PCR, PEC-P, and rescue PCR) species identification was possible for 74 of 93 archaeological fish specimens (79.6%). Overall, six of the 93 samples (6.5%) consistently yielded species identification across all treatments. The species of ten specimens (10.8%) were uniquely identified from amplicons produced with either PEC-P or rescue PCR or both. Notably, the species of seven samples (7.5%) were uniquely identified with standard PCR over the alternative treatments. Considering both full concentration and 1:10 dilute eluates (N = 186), standard PCR performed as well as PEC-P (p = 0.1451) and rescue (p = 0.6753). Yet, considering results from full concentration eluates alone (N = 93), PEC-P (60.2%) outperformed both standard PCR (44.1%; p = 0.0277) and rescue PCR (40.9%; p = 0.0046). Stochasticity observed in our study cautions us against choosing a "best" performing method of those explored here and suggests their respective potentials to improve success may be sample dependent. When working with samples compromised by PCR inhibitors, it is useful to have alternative methodologies for subduing the problem. Both PEC-P and rescue PCR represent useful alternative methods for the study of aged, degraded, and/or low copy number DNA samples compromised by PCR inhibitors. |
| doi_str_mv | 10.1371/journal.pone.0234745 |
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As a result, there is a need to find alternate methods that ameliorate the efficacy of PCR. In this study, we attempted to use genetic methods to identify the species of salmonid (Oncorhynchus spp.) remains recovered from archaeological sites along the Feather River located in northern California, United States. In the process of doing so, we compared the efficacy of a PCR enhancer cocktail called "PEC-P" and a reagent rich PCR recipe called "rescue PCR" over standard PCR. Across all treatments (full concentration and 1:10 dilute eluates subjected to standard PCR, PEC-P, and rescue PCR) species identification was possible for 74 of 93 archaeological fish specimens (79.6%). Overall, six of the 93 samples (6.5%) consistently yielded species identification across all treatments. The species of ten specimens (10.8%) were uniquely identified from amplicons produced with either PEC-P or rescue PCR or both. Notably, the species of seven samples (7.5%) were uniquely identified with standard PCR over the alternative treatments. Considering both full concentration and 1:10 dilute eluates (N = 186), standard PCR performed as well as PEC-P (p = 0.1451) and rescue (p = 0.6753). Yet, considering results from full concentration eluates alone (N = 93), PEC-P (60.2%) outperformed both standard PCR (44.1%; p = 0.0277) and rescue PCR (40.9%; p = 0.0046). Stochasticity observed in our study cautions us against choosing a "best" performing method of those explored here and suggests their respective potentials to improve success may be sample dependent. When working with samples compromised by PCR inhibitors, it is useful to have alternative methodologies for subduing the problem. 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rescue PCR</atitle><jtitle>PloS one</jtitle><date>2020-06-16</date><risdate>2020</risdate><volume>15</volume><issue>6</issue><spage>e0234745</spage><epage>e0234745</epage><pages>e0234745-e0234745</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>PCR inhibitors are a formidable problem to the study of aged, degraded, and/or low copy number DNA. 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Notably, the species of seven samples (7.5%) were uniquely identified with standard PCR over the alternative treatments. Considering both full concentration and 1:10 dilute eluates (N = 186), standard PCR performed as well as PEC-P (p = 0.1451) and rescue (p = 0.6753). Yet, considering results from full concentration eluates alone (N = 93), PEC-P (60.2%) outperformed both standard PCR (44.1%; p = 0.0277) and rescue PCR (40.9%; p = 0.0046). Stochasticity observed in our study cautions us against choosing a "best" performing method of those explored here and suggests their respective potentials to improve success may be sample dependent. When working with samples compromised by PCR inhibitors, it is useful to have alternative methodologies for subduing the problem. Both PEC-P and rescue PCR represent useful alternative methods for the study of aged, degraded, and/or low copy number DNA samples compromised by PCR inhibitors.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>32544213</pmid><doi>10.1371/journal.pone.0234745</doi><tpages>e0234745</tpages><orcidid>https://orcid.org/0000-0003-3945-3392</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Anthropology Archaeological sites Biology and Life Sciences Bones Copy number Copy number variations Degradation Deoxyribonucleic acid Dilution DNA DNA polymerase Earth sciences Fish Gene amplification Genetic research Genetic testing Historic buildings & sites Historic sites Identification methods Inhibitors Laboratories Methods Oncorhynchus Polymerase chain reaction Reagents Research and Analysis Methods Salmon Social Sciences Sodium Species Stochasticity Success Vertebra Vertebrae |
| title | Subduing the influence of PCR inhibitors on amplifying aged, degraded, and low copy number DNA: PCR enhancer cocktail-p and rescue PCR |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-26T18%3A43%3A59IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Subduing%20the%20influence%20of%20PCR%20inhibitors%20on%20amplifying%20aged,%20degraded,%20and%20low%20copy%20number%20DNA:%20PCR%20enhancer%20cocktail-p%20and%20rescue%20PCR&rft.jtitle=PloS%20one&rft.au=Kemp,%20Brian%20M&rft.date=2020-06-16&rft.volume=15&rft.issue=6&rft.spage=e0234745&rft.epage=e0234745&rft.pages=e0234745-e0234745&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0234745&rft_dat=%3Cgale_plos_%3EA626791061%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2413949721&rft_id=info:pmid/32544213&rft_galeid=A626791061&rft_doaj_id=oai_doaj_org_article_da68c6952b86448083e0c307dc9b0302&rfr_iscdi=true |