A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

Genome Biology

Volumn 11, Issue 2, 2010, Pages

  Lennon, Niall J ^a   Lintner, Robert E ^a   Anderson, Scott ^a   Alvarez, Pablo ^b   Barry, Andrew ^a   Brockman, William ^c   Daza, Riza ^a   Erlich, Rachel L ^a   Giannoukos, Georgia ^a   Green, Lisa ^a   Hollinger, Andrew ^a   Hoover, Cindi A ^d   Jaffe, David B ^a   Juhn, Frank ^a   McCarthy, Danielle ^a   Perrin, Danielle ^a   Ponchner, Karen ^a   Powers, Taryn L ^a   Rizzolo, Kamran ^a   Robbins, Dana ^a   Ryan, Elizabeth ^a   Russ, Carsten ^a   Sparrow, Todd ^a   Stalker, John ^a   Steelman, Scott ^a   Weiand, Michael ^a   Zimmer, Andrew ^a   Henn, Matthew R ^a   Nusbaum, Chad ^a   Nicol, Robert ^a   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b AKAMAI TECHNOLOGIES   (United States)

^c GOOGLE INC   (United States)

^d DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MICROSPHERE;

ANALYTICAL ERROR; ARTICLE; AUTOMATION; CONTROLLED STUDY; DNA BARCODING; GENE SEQUENCE; HUMAN; MOLECULAR LIBRARY; PROCESS OPTIMIZATION; ALGORITHM; DNA SEQUENCE; GENE LIBRARY; HIGH THROUGHPUT SCREENING; INFORMATION PROCESSING; METHODOLOGY;

ALGORITHMS; AUTOMATIC DATA PROCESSING; GENE LIBRARY; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICROSPHERES; SEQUENCE ANALYSIS, DNA;

EID: 77953218382     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-2-r15     Document Type: Article

References (25)

1. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
3. Bodenteich A, Chissoe S, Wang YF, Roe BA. Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. Automated DNA Sequencing and Analysis Techniques 1993, 42-50. London, UK: Academic Press, Venter JC.
4. O'Brien WDJ. Ultrasound-biophysics mechanisms. Prog Biophys Mol Biol 2007, 93:212-255. 1995002, 16934858, 10.1016/j.pbiomolbio.2006.07.010.
5. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5:1005-1010. 2610436, 19034268, 10.1038/nmeth.1270.
6. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 2008, 3:e3839. 2585789, 19052635, 10.1371/journal.pone.0003839.
7. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6:291-295. 2664327, 19287394, 10.1038/nmeth.1311.
8. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci USA 2009, 106:3264-3269. 2638735, 19208812, 10.1073/pnas.0812841106.
9. Hawkins TL, O'Connor-Morin T, Roy A, Santillan C. DNA purification and isolation using a solid-phase. Nucleic Acids Res 1994, 22:4543-4544. 308491, 7971285, 10.1093/nar/22.21.4543.
10. Ooi SL, Shoemaker DD, Boeke JD. A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 2001, 294:2552-2556. 10.1126/science.1065672, 11701889.
11. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391. 10.1038/nature00935, 12140549.
12. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 2007, 35:e130. 2095802, 17932070, 10.1093/nar/gkm760.
13. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2007, 2:e197. 1797623, 17299583, 10.1371/journal.pone.0000197.
14. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008, 5:235-237. 10.1038/nmeth.1184, 18264105.
15. Ostergard PJR. Upper bounds for q-ary covering codes. IEEE Trans Information Theory 1991, 37:660-664.
16. Hamming RW. Error detecting and error correcting codes. Bell System Tech J 1950, 29:147-160.
17. He MX, Petoukhov SV, Ricci PE. Genetic code, hamming distance and stochastic matrices. Bull Math Biol 2004, 66:1405-1421. 10.1016/j.bulm.2004.01.002, 15294430.
18. Frank DN. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 2009, 10:362. 2777893, 19874596, 10.1186/1471-2105-10-362.
19. Meyer M, Briggs AW, Maricic T, Höber B, Höffner B, Krause J, Weihmann A, Pääbo S, Hofreiter M. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res 2008, 36:e5. 2248761, 18084031, 10.1093/nar/gkm1095.
20. Rutledge RG, Stewart D. A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR. BMC Biotechnol 2008, 8:47. 2397388, 18466619, 10.1186/1472-6750-8-47.
21. Kaiser J. DNA sequencing: a plan to capture human diversity in 1000 genomes. Science 2008, 319:395-395. 10.1126/science.319.5862.395, 18218868.
22. Thousand Genomes Project. , http://www.1000genomes.org
23. McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Yung WK, Bogler O, Weinstein JN, Berg S, Berger M, Prados M, Muzny D, Morgan M, Scherer S, Sabo A, Nazareth L, Lewis L, Hall O, Zhu Y, Ren Y, Alvi O, Yao J, Hawes A, Jhangiani S, Fowler G, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008, 455:1061-1068. 2671642, 18772890, 10.1038/nature07385.
24. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, et al. NIH HMP Working Group The NIH Human Microbiome Project. Genome Res 2009, 19:2317-2323. 2792171, 19819907, 10.1101/gr.096651.109, NIH HMP Working Group.
25. Automation and Plate-based Protocols. , http://www.broadinstitute.org/ftp/pub/papers/454barcodedlib/