Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries

BioTechniques

Volumn 55, Issue 2, 2013, Pages 61-67

  Laurie, Matthew T ^a   Bertout, Jessica A ^a   Taylor, Sean D ^a   Burton, Joshua N ^b   Shendure, Jay A ^b   Bielas, Jason H ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Absolute quantification; Droplet digital PCR; Library preparation; Massively parallel sequencing; Next generation sequencing; Quality control; Size determination

Indexed keywords

DNA FRAGMENT; PRIMER DNA; DNA;

ARTICLE; CALIBRATION; CAPILLARY ELECTROPHORESIS; DNA LIBRARY; DNA SEQUENCE; FLUORESCENCE; GEL ELECTROPHORESIS; LIMIT OF QUANTITATION; MEASUREMENT ACCURACY; MEASUREMENT PRECISION; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ULTRAVIOLET SPECTROPHOTOMETRY; CHEMISTRY; GENE LIBRARY; HIGH THROUGHPUT SEQUENCING; HUMAN; POLYMERASE CHAIN REACTION; PROCEDURES; REPRODUCIBILITY; TUMOR CELL LINE;

CELL LINE, TUMOR; DNA, NEOPLASM; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84881486404     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114063     Document Type: Article

References (21)

1. Didelot, X., R. Bowden, D.J. Wilson, T.E. Peto, and D.W. Crook. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13:601-612.
2. Biesecker, L.G., W. Burke, I. Kohane, S.E. Plon, and R. Zimmern. 2012. Next-generation sequencing in the clinic: are we ready? Nat. Rev. Genet. 13:818-824.
3. Martin, J.A. and Z. Wang. 2011. Next-generation transcriptome assembly. Nat. Rev. Genet. 12:671-682.
4. Voelkerding, K.V., S.A. Dames, and J.D. Durtschi. 2009. Next-generation sequencing: from basic research to diagnostics. Clin. Chem. 55:641-658.
5. Su, Z., B. Ning, H. Fang, H. Hong, R. Perkins, W. Tong, and L. Shi. 2011. Next-generation sequencing and its applications in molecular diagnostics. Expert Rev. Mol. Diagn. 11:333-343.
6. Meyerson, M., S. Gabriel, and G. Getz. 2010. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11:685-696.
7. Zhang, J., R. Chiodini, A. Badr, and G. Zhang. 2011. The impact of next-generation sequencing on genomics. J Genet Genomics. 38:95-109.
8. Liu, L., Y. Li, S. Li, N. Hu, Y. He, R. Pong, D. Lin, L. Lu, and M. Law. 2012. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012:251364.
9. Loman, N.J., R.V. Misra, T.J. Dallman, C. Constantinidou, S.E. Gharbia, J. Wain, and M.J. Pallen. 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30:434-439.
10. Glenn, T.C. 2011. Field guide to next-generation DNA sequencers. Molecular ecology resources 11:759-769.
11. Quail, M.A., M. Smith, P. Coupland, T.D. Otto, S.R. Harris, T.R. Connor, A. Bertoni, H.P. Swerdlow, and Y. Gu. 2012. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341.
12. Linnarsson, S. 2010. Recent advances in DNA sequencing methods - general principles of sample preparation. Exp. Cell Res. 316:1339-1343.
13. Meyer, M., A.W. Briggs, T. Maricic, B. Hober, B. Hoffner, J. Krause, A. Weihmann, S. Paabo, and M. Hofreiter. 2008. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res. 36:e5.
14. Buehler, B., H.H. Hogrefe, G. Scott, H. Ravi, C. Pabon-Pena, S. O'Brien, R. Formosa, and S. Happe. 2010. Rapid quantification of DNA libraries for next-generation sequencing. Methods 50:S15-S18.
15. White, R.A., 3rd, P.C. Blainey, H.C. Fan, and S.R. Quake. 2009. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics 10:116.
16. Valasek, M.A. and J.J. Repa. 2005. The power of real-time PCR. Adv. Physiol. Educ. 29:151-159.
17. Yun, J.J., L.E. Heisler, I.I. Hwang, O. Wilkins, S.K. Lau, M. Hyrcza, B. Jayabalasingham, J. Jin, et al. 2006. Genomic DNA functions as a universal external standard in quantitative real-time PCR. Nucleic Acids Res. 34:e85.
18. Hindson, B.J., K.D. Ness, D.A. Masquelier, P. Belgrader, N.J. Heredia, A.J. Makarewicz, I.J. Bright, M.Y. Lucero, et al. 2011. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal. Chem. 83:8604-8610.
19. Hori, M., H. Fukano, and Y. Suzuki. 2007. Uniform amplification of multiple DNAs by emulsion PCR. Biochem. Biophys. Res. Commun. 352:323-328.
20. Xiao, M., A. Phong, K.L. Lum, R.A. Greene, P.R. Buzby, and P.Y. Kwok. 2004. Role of excess inorganic pyrophosphate in primer-extension genotyping assays. Genome Res. 14:1749-1755.
21. Zhang, Y., D. Zhang, W. Li, J. Chen, Y. Peng, and W. Cao. 2003. A novel real-time quantitative PCR method using attached universal template probe. Nucleic Acids Res. 31:e123.