NanoString Technology for Human Papillomavirus Typing
High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter<sup>®</sup> platform for detection and digital readout of 48 HPV types...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-01-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/2/188 |
| _version_ | 1827597530534248448 |
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| author | Mangalathu S. Rajeevan Sonya Patel Tengguo Li Elizabeth R. Unger |
| author_facet | Mangalathu S. Rajeevan Sonya Patel Tengguo Li Elizabeth R. Unger |
| author_sort | Mangalathu S. Rajeevan |
| collection | DOAJ |
| description | High-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter<sup>®</sup> platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 HPV types and the globin gene. We tested residual DNA extracts from epidemiologic specimens and defined samples (HPV plasmids at 10 to 10<sup>4</sup> copies/reaction) directly (No-PCR) as well as after L1 consensus PCR of 45 (PCR-45) or 15 cycles (PCR-15). Assay and interpretation followed NS recommendations. We evaluated analytic performance by comparing NanoString results for types included in prior assays: Roche Linear Array (LA) or HPV TypeSeq assay. No-PCR results on 40 samples showed good type-specific agreement with LA (k = 0.621) but sensitivity was 65% with lower limit of detection (LOD) at 10<sup>4</sup> plasmid copies. PCR-45 results showed almost perfect type-specific agreement with LA (k = 0.862), 82% sensitivity and LOD at 10 copies. PCR-15 results on 75 samples showed substantial type-specific agreement with LA (k = 0.796, 92% sensitivity) and TypeSeq (k = 0.777, 87% sensitivity), and LOD at 10 copies of plasmids. This proof-of-principle study demonstrates the efficacy of the NS platform with HPV CodeSet for type-specific detection using a low number of PCR cycles (PCR-15). Studies are in progress to evaluate assay reproducibility and analytic validation with a larger number of samples. |
| first_indexed | 2024-03-09T03:33:43Z |
| format | Article |
| id | doaj.art-9e8c1d6f6f8940beb5c5bc08729813f1 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T03:33:43Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-9e8c1d6f6f8940beb5c5bc08729813f12023-12-03T14:52:06ZengMDPI AGViruses1999-49152021-01-0113218810.3390/v13020188NanoString Technology for Human Papillomavirus TypingMangalathu S. Rajeevan0Sonya Patel1Tengguo Li2Elizabeth R. Unger3Centers for Disease Control and Prevention, Division of High-Consequence Pathogens & Pathology, 1600 Clifton Road, Atlanta, GA 30329, USACenters for Disease Control and Prevention, Division of High-Consequence Pathogens & Pathology, 1600 Clifton Road, Atlanta, GA 30329, USACenters for Disease Control and Prevention, Division of High-Consequence Pathogens & Pathology, 1600 Clifton Road, Atlanta, GA 30329, USACenters for Disease Control and Prevention, Division of High-Consequence Pathogens & Pathology, 1600 Clifton Road, Atlanta, GA 30329, USAHigh-throughput HPV typing assays with increased automation, faster turnaround and type-specific digital readout would facilitate studies monitoring the impact of HPV vaccination. We evaluated the NanoString nCounter<sup>®</sup> platform for detection and digital readout of 48 HPV types in a single reaction. NanoString (NS) used proprietary software to design CodeSets: type-specific probe pairs targeting 48 HPV types and the globin gene. We tested residual DNA extracts from epidemiologic specimens and defined samples (HPV plasmids at 10 to 10<sup>4</sup> copies/reaction) directly (No-PCR) as well as after L1 consensus PCR of 45 (PCR-45) or 15 cycles (PCR-15). Assay and interpretation followed NS recommendations. We evaluated analytic performance by comparing NanoString results for types included in prior assays: Roche Linear Array (LA) or HPV TypeSeq assay. No-PCR results on 40 samples showed good type-specific agreement with LA (k = 0.621) but sensitivity was 65% with lower limit of detection (LOD) at 10<sup>4</sup> plasmid copies. PCR-45 results showed almost perfect type-specific agreement with LA (k = 0.862), 82% sensitivity and LOD at 10 copies. PCR-15 results on 75 samples showed substantial type-specific agreement with LA (k = 0.796, 92% sensitivity) and TypeSeq (k = 0.777, 87% sensitivity), and LOD at 10 copies of plasmids. This proof-of-principle study demonstrates the efficacy of the NS platform with HPV CodeSet for type-specific detection using a low number of PCR cycles (PCR-15). Studies are in progress to evaluate assay reproducibility and analytic validation with a larger number of samples.https://www.mdpi.com/1999-4915/13/2/188NanoStringHPV detectionLinear ArrayTypeSeqPCR cycles |
| spellingShingle | Mangalathu S. Rajeevan Sonya Patel Tengguo Li Elizabeth R. Unger NanoString Technology for Human Papillomavirus Typing Viruses NanoString HPV detection Linear Array TypeSeq PCR cycles |
| title | NanoString Technology for Human Papillomavirus Typing |
| title_full | NanoString Technology for Human Papillomavirus Typing |
| title_fullStr | NanoString Technology for Human Papillomavirus Typing |
| title_full_unstemmed | NanoString Technology for Human Papillomavirus Typing |
| title_short | NanoString Technology for Human Papillomavirus Typing |
| title_sort | nanostring technology for human papillomavirus typing |
| topic | NanoString HPV detection Linear Array TypeSeq PCR cycles |
| url | https://www.mdpi.com/1999-4915/13/2/188 |
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