An enhanced single base extension technique for the analysis of complex viral populations.
Many techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. Thi...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2009-10-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0007453&type=printable |
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| author | Dale R Webster Armin G Hekele Adam S Lauring Kael F Fischer Hao Li Raul Andino Joseph L DeRisi |
| author_facet | Dale R Webster Armin G Hekele Adam S Lauring Kael F Fischer Hao Li Raul Andino Joseph L DeRisi |
| author_sort | Dale R Webster |
| collection | DOAJ |
| description | Many techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. The sensitivity of the method was demonstrated by accurate and consistent readouts from a controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotide analog ribavirin on a typical poliovirus population through two rounds of passage. Our results show that this economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomic diversity, our SBE-based technique provides a scalable and cost-effective complement to both traditional and next generation sequencing methodologies. |
| format | Article |
| id | doaj-art-5c93e8bcbc2e449cba173dcda77f14f1 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2009-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-5c93e8bcbc2e449cba173dcda77f14f12025-08-20T02:32:19ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-10-01410e745310.1371/journal.pone.0007453An enhanced single base extension technique for the analysis of complex viral populations.Dale R WebsterArmin G HekeleAdam S LauringKael F FischerHao LiRaul AndinoJoseph L DeRisiMany techniques for the study of complex populations provide either specific information on a small number of variants or general information on the entire population. Here we describe a powerful new technique for elucidating mutation frequencies at each genomic position in a complex population. This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. The sensitivity of the method was demonstrated by accurate and consistent readouts from a controlled population of mutant genotypes. We subsequently deployed the technique to investigate the effects of the nucleotide analog ribavirin on a typical poliovirus population through two rounds of passage. Our results show that this economical platform can be used to investigate dynamic changes occurring at frequencies below 1% within a complex nucleic acid population. Given that many key aspects of the study and treatment of disease are intimately linked to population-level genomic diversity, our SBE-based technique provides a scalable and cost-effective complement to both traditional and next generation sequencing methodologies.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0007453&type=printable |
| spellingShingle | Dale R Webster Armin G Hekele Adam S Lauring Kael F Fischer Hao Li Raul Andino Joseph L DeRisi An enhanced single base extension technique for the analysis of complex viral populations. PLoS ONE |
| title | An enhanced single base extension technique for the analysis of complex viral populations. |
| title_full | An enhanced single base extension technique for the analysis of complex viral populations. |
| title_fullStr | An enhanced single base extension technique for the analysis of complex viral populations. |
| title_full_unstemmed | An enhanced single base extension technique for the analysis of complex viral populations. |
| title_short | An enhanced single base extension technique for the analysis of complex viral populations. |
| title_sort | enhanced single base extension technique for the analysis of complex viral populations |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0007453&type=printable |
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