Next Generation Sequencing in the National Health Service England: A Pipeline that Completely Agrees with Sanger
作者： Kevin Blighe Nick Beauchamp
DOI: 10.4172/1948-5956.1000300
关键词: Gold standard (test) 、 Sanger sequencing 、 DNA sequencing 、 Data mining 、 Patient care 、 National health service 、 Pipeline (software) 、 Diagnostic laboratory 、 Data science 、 Medicine
摘要: As next generation sequencing (NGS) technology has already become a regular fixture in research, it is now time for clinical environments to also reap the benefits of such technology. Indeed, rich promise NGS potential be translated into improved patient care. However, there still doubt about widespread use diagnostics. Before implementation, must consensus on which analytical pipeline use, with follow-up confirmation variants gold standard: Sanger sequencing. Here, we present that complete agreement 341 and being used our diagnostic laboratory National Health Service England screening inherited, pathogenic variants. Details other services can found at http://www.sheffieldchildrens.nhs.uk/our-services/sheffield-diagnostic-genetics-service/. Our broadly follows ‘best practices’ guidelines set by GATK Broad Institute, novel added approach involving randomly selecting subsets reads later merging called from each. This allows falsenegatives eliminated high level confidence. Moreover, modeling reduced depth coverage reveals 30X point false-positives are >99.9% confidence. Our results allude fine balance between read-depth error, believe will increase confidence permit its gradual enrollment laboratories.
hilarispublisher.com参考文章(40)
Richard W Tothill, Maria A Doyle, Cliff Meldrum, Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective The Clinical biochemist. Reviews / Australian Association of Clinical Biochemists. ,vol. 32, pp. 177- 195 ,(2011)
Aaron G. Day-Williams, Eleftheria Zeggini, The effect of next-generation sequencing technology on complex trait research European Journal of Clinical Investigation. ,vol. 41, pp. 561- 567 ,(2011) , 10.1111/J.1365-2362.2010.02437.X
Geraldine A. Auwera, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy‐Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran V. Garimella, David Altshuler, Stacey Gabriel, Mark A. DePristo, From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Current protocols in human genetics. ,vol. 43, ,(2013) , 10.1002/0471250953.BI1110S43
Anton Nekrutenko, James Taylor, None, Next-generation sequencing data interpretation: enhancing reproducibility and accessibility Nature Reviews Genetics. ,vol. 13, pp. 667- 672 ,(2012) , 10.1038/NRG3305
Philip J Stephens, Patrick S Tarpey, Helen Davies, Peter Van Loo, Chris Greenman, David C Wedge, Serena Nik-Zainal, Sancha Martin, Ignacio Varela, Graham R Bignell, Lucy R Yates, Elli Papaemmanuil, David Beare, Adam Butler, Angela Cheverton, John Gamble, Jonathan Hinton, Mingming Jia, Alagu Jayakumar, David Jones, Calli Latimer, King Wai Lau, Stuart McLaren, David J McBride, Andrew Menzies, Laura Mudie, Keiran Raine, Roland Rad, Michael Spencer Chapman, Jon Teague, Douglas Easton, Anita Langerød, Oslo Breast Cancer Consortium (OSBREAC) Karesen Rolf 34 35 Schlichting Ellen 34 Naume Bjorn 35 36 Sauer Torill 35 37 Ottestad Lars 36, Ming Ta Michael Lee, Chen-Yang Shen, Benita Tan Kiat Tee, Bernice Wong Huimin, Annegien Broeks, Ana Cristina Vargas, Gulisa Turashvili, John Martens, Aquila Fatima, Penelope Miron, Suet-Feung Chin, Gilles Thomas, Sandrine Boyault, Odette Mariani, Sunil R Lakhani, Marc van de Vijver, Laura van ‘t Veer, John Foekens, Christine Desmedt, Christos Sotiriou, Andrew Tutt, Carlos Caldas, Jorge S Reis-Filho, Samuel AJR Aparicio, Anne Vincent Salomon, Anne-Lise Børresen-Dale, Andrea L Richardson, Peter J Campbell, P Andrew Futreal, Michael R Stratton, None, The landscape of cancer genes and mutational processes in breast cancer Nature. ,vol. 486, pp. 400- 404 ,(2012) , 10.1038/NATURE11017
Kym M Boycott, Megan R Vanstone, Dennis E Bulman, Alex E MacKenzie, None, Rare-disease genetics in the era of next-generation sequencing: discovery to translation Nature Reviews Genetics. ,vol. 14, pp. 681- 691 ,(2013) , 10.1038/NRG3555
K. Wang, M. Li, H. Hakonarson, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Research. ,vol. 38, ,(2010) , 10.1093/NAR/GKQ603
Shingo Suzuki, Naoaki Ono, Chikara Furusawa, Bei-Wen Ying, Tetsuya Yomo, Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms PLoS ONE. ,vol. 6, pp. e19534- ,(2011) , 10.1371/JOURNAL.PONE.0019534
Helena Kilpinen, Jeffrey C. Barrett, How next-generation sequencing is transforming complex disease genetics. Trends in Genetics. ,vol. 29, pp. 23- 30 ,(2013) , 10.1016/J.TIG.2012.10.001
Kimberly Robasky, Nathan E. Lewis, George M. Church, The role of replicates for error mitigation in next-generation sequencing Nature Reviews Genetics. ,vol. 15, pp. 56- 62 ,(2014) , 10.1038/NRG3655