Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues
Testing for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pa...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2014-04-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/334.pdf |
| _version_ | 1827606482057691136 |
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| author | Jesse J. Waggoner Benjamin A. Pinsky |
| author_facet | Jesse J. Waggoner Benjamin A. Pinsky |
| author_sort | Jesse J. Waggoner |
| collection | DOAJ |
| description | Testing for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pathogen Complex 400 protocols on the QIAsymphony Sample Processing (SP) system were compared using bronchoalveolar lavage fluid (BAL), tissue samples, and urine. The QIAsymphonyAssay Set-up (AS) system was used to assemble reactions using artus CMV PCR reagents and amplification was carried out on the Rotor-Gene Q. Samples from 93 patients previously tested for CMV DNA and negative samples spiked with CMV AD-169 were used to evaluate assay performance. The Pathogen Complex 400 protocol yielded the following results: BAL, sensitivity 100% (33/33), specificity 87% (20/23); tissue, sensitivity 100% (25/25), specificity 100% (20/20); urine, sensitivity 100% (21/21), specificity 100% (20/20). Cell-free 1000 extraction gave comparable results for BAL and tissue, however, for urine, the sensitivity was 86% (18/21) and specimen quantitation was inaccurate. Comparative studies of different extraction protocols and DNA detection methods in body fluids and tissues are needed, as assays optimized for blood or plasma will not necessarily perform well on other specimen types. |
| first_indexed | 2024-03-09T06:37:51Z |
| format | Article |
| id | doaj.art-14c21a08f70f4653aac015c86822874d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:37:51Z |
| publishDate | 2014-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-14c21a08f70f4653aac015c86822874d2023-12-03T10:54:59ZengPeerJ Inc.PeerJ2167-83592014-04-012e33410.7717/peerj.334334Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissuesJesse J. Waggoner0Benjamin A. Pinsky1Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USADepartment of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USATesting for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pathogen Complex 400 protocols on the QIAsymphony Sample Processing (SP) system were compared using bronchoalveolar lavage fluid (BAL), tissue samples, and urine. The QIAsymphonyAssay Set-up (AS) system was used to assemble reactions using artus CMV PCR reagents and amplification was carried out on the Rotor-Gene Q. Samples from 93 patients previously tested for CMV DNA and negative samples spiked with CMV AD-169 were used to evaluate assay performance. The Pathogen Complex 400 protocol yielded the following results: BAL, sensitivity 100% (33/33), specificity 87% (20/23); tissue, sensitivity 100% (25/25), specificity 100% (20/20); urine, sensitivity 100% (21/21), specificity 100% (20/20). Cell-free 1000 extraction gave comparable results for BAL and tissue, however, for urine, the sensitivity was 86% (18/21) and specimen quantitation was inaccurate. Comparative studies of different extraction protocols and DNA detection methods in body fluids and tissues are needed, as assays optimized for blood or plasma will not necessarily perform well on other specimen types.https://peerj.com/articles/334.pdfCytomegalovirusLaboratory medicineClinical virology |
| spellingShingle | Jesse J. Waggoner Benjamin A. Pinsky Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues PeerJ Cytomegalovirus Laboratory medicine Clinical virology |
| title | Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues |
| title_full | Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues |
| title_fullStr | Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues |
| title_full_unstemmed | Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues |
| title_short | Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues |
| title_sort | comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus dna in fluids and tissues |
| topic | Cytomegalovirus Laboratory medicine Clinical virology |
| url | https://peerj.com/articles/334.pdf |
| work_keys_str_mv | AT jessejwaggoner comparisonofautomatednucleicacidextractionmethodsforthedetectionofcytomegalovirusdnainfluidsandtissues AT benjaminapinsky comparisonofautomatednucleicacidextractionmethodsforthedetectionofcytomegalovirusdnainfluidsandtissues |