FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint
Abstract
:1. Introduction
2. Sequencing Platforms
2.1. Ion Torrent
2.2. Illumina
2.3. GeneReader
2.4. Pacific Biosciences
2.5. Oxford Nanopore Technology
3. NGS in Clinical Practice
4. Preanalytical Issue in NGS
4.1. Histologic Specimens
4.2. Cytologic Specimens
5. Analytical Issue in NGS
6. RNA-Based NGS
7. NGS in Epigenetics
8. Interpretation of DNA Sequencing Data
9. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Illumina MiSeq | Illumina HiSeq 2000 | Ion Torrent PGM | PacBio SMRT | Oxford Nanopore MinION | |
---|---|---|---|---|---|
Read Length | Up to 150 bases | Up to 150 bases | ~200 bases | Average 1500 bases | 13–20 kb |
Paired-End | Yes | Yes | Yes | No | No |
Reported Accuracy | Mostly >Q30 | Mostly >Q30 | Mostly Q20 | <Q10 | Mostly Q50 |
Observed Raw Error Rate | 0.80% | 0.26% | 1.71% | 12.86% | 10.50% |
Insert Size | Up to 700 bases | Up to 700 bases | Up to 250 bases | Up to 10 kb | Average of 331 bases |
Run Time | 27 h | 11 days | 2 h | 2 h | 72 h |
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Cappello, F.; Angerilli, V.; Munari, G.; Ceccon, C.; Sabbadin, M.; Pagni, F.; Fusco, N.; Malapelle, U.; Fassan, M. FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J. Pers. Med. 2022, 12, 750. https://doi.org/10.3390/jpm12050750
Cappello F, Angerilli V, Munari G, Ceccon C, Sabbadin M, Pagni F, Fusco N, Malapelle U, Fassan M. FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. Journal of Personalized Medicine. 2022; 12(5):750. https://doi.org/10.3390/jpm12050750
Chicago/Turabian StyleCappello, Filippo, Valentina Angerilli, Giada Munari, Carlotta Ceccon, Marianna Sabbadin, Fabio Pagni, Nicola Fusco, Umberto Malapelle, and Matteo Fassan. 2022. "FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint" Journal of Personalized Medicine 12, no. 5: 750. https://doi.org/10.3390/jpm12050750