Prion protein gene mutation detection using long-read Nanopore sequencing
Abstract Prion diseases are fatal neurodegenerative conditions that affect humans and animals. Rapid and accurate sequencing of the prion gene PRNP is paramount to human prion disease diagnosis and for animal surveillance programmes. Current methods for PRNP genotyping involve sequencing of small fr...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-12130-7 |
| _version_ | 1811338883495886848 |
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| author | François Kroll Athanasios Dimitriadis Tracy Campbell Lee Darwent John Collinge Simon Mead Emmanuelle Vire |
| author_facet | François Kroll Athanasios Dimitriadis Tracy Campbell Lee Darwent John Collinge Simon Mead Emmanuelle Vire |
| author_sort | François Kroll |
| collection | DOAJ |
| description | Abstract Prion diseases are fatal neurodegenerative conditions that affect humans and animals. Rapid and accurate sequencing of the prion gene PRNP is paramount to human prion disease diagnosis and for animal surveillance programmes. Current methods for PRNP genotyping involve sequencing of small fragments within the protein-coding region. The contribution of variants in the non-coding regions of PRNP including large structural changes is poorly understood. Here, we used long-range PCR and Nanopore sequencing to sequence the full length of PRNP, including its regulatory region, in 25 samples from blood and brain of individuals with inherited or sporadic prion diseases. Nanopore sequencing detected the same variants as identified by Sanger sequencing, including repeat expansions/deletions. Nanopore identified additional single-nucleotide variants in the non-coding regions of PRNP, but no novel structural variants were discovered. Finally, we explored somatic mosaicism of PRNP’s octapeptide repeat region, which is a hypothetical cause of sporadic prion disease. While we found changes consistent with somatic mutations, we demonstrate that they may have been generated by the PCR. Our study illustrates the accuracy of Nanopore sequencing for rapid and field prion disease diagnosis and highlights the need for single-molecule sequencing methods for the detection of somatic mutations. |
| first_indexed | 2024-04-13T18:18:15Z |
| format | Article |
| id | doaj.art-9e9fbd6a422948078a3fa174ad017576 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-13T18:18:15Z |
| publishDate | 2022-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-9e9fbd6a422948078a3fa174ad0175762022-12-22T02:35:37ZengNature PortfolioScientific Reports2045-23222022-05-0112111210.1038/s41598-022-12130-7Prion protein gene mutation detection using long-read Nanopore sequencingFrançois Kroll0Athanasios Dimitriadis1Tracy Campbell2Lee Darwent3John Collinge4Simon Mead5Emmanuelle Vire6MRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLMRC Prion Unit at University College London (UCL), UCL Institute of Prion Diseases, UCLAbstract Prion diseases are fatal neurodegenerative conditions that affect humans and animals. Rapid and accurate sequencing of the prion gene PRNP is paramount to human prion disease diagnosis and for animal surveillance programmes. Current methods for PRNP genotyping involve sequencing of small fragments within the protein-coding region. The contribution of variants in the non-coding regions of PRNP including large structural changes is poorly understood. Here, we used long-range PCR and Nanopore sequencing to sequence the full length of PRNP, including its regulatory region, in 25 samples from blood and brain of individuals with inherited or sporadic prion diseases. Nanopore sequencing detected the same variants as identified by Sanger sequencing, including repeat expansions/deletions. Nanopore identified additional single-nucleotide variants in the non-coding regions of PRNP, but no novel structural variants were discovered. Finally, we explored somatic mosaicism of PRNP’s octapeptide repeat region, which is a hypothetical cause of sporadic prion disease. While we found changes consistent with somatic mutations, we demonstrate that they may have been generated by the PCR. Our study illustrates the accuracy of Nanopore sequencing for rapid and field prion disease diagnosis and highlights the need for single-molecule sequencing methods for the detection of somatic mutations.https://doi.org/10.1038/s41598-022-12130-7 |
| spellingShingle | François Kroll Athanasios Dimitriadis Tracy Campbell Lee Darwent John Collinge Simon Mead Emmanuelle Vire Prion protein gene mutation detection using long-read Nanopore sequencing Scientific Reports |
| title | Prion protein gene mutation detection using long-read Nanopore sequencing |
| title_full | Prion protein gene mutation detection using long-read Nanopore sequencing |
| title_fullStr | Prion protein gene mutation detection using long-read Nanopore sequencing |
| title_full_unstemmed | Prion protein gene mutation detection using long-read Nanopore sequencing |
| title_short | Prion protein gene mutation detection using long-read Nanopore sequencing |
| title_sort | prion protein gene mutation detection using long read nanopore sequencing |
| url | https://doi.org/10.1038/s41598-022-12130-7 |
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