A Scalable, Fully Automated Process for Construction of Sequence-ready Barcoded Libraries for 454

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2010 Feb 9

PMID 20137071

Citations 60

Authors

Niall J Lennon

Robert E Lintner

Scott Anderson

Pablo Alvarez

Andrew Barry

William Brockman

Riza Daza

Rachel L Erlich

Georgia Giannoukos

Lisa Green

Andrew Hollinger

Cindi A Hoover

David B Jaffe

Frank Juhn

Danielle McCarthy

Danielle Perrin

Karen Ponchner

Taryn L Powers

Kamran Rizzolo

Dana Robbins

Elizabeth Ryan

Carsten Russ

Todd Sparrow

John Stalker

Scott Steelman

Michael Weiand

Andrew Zimmer

Matthew R Henn

Chad Nusbaum

Robert Nicol

Affiliations

Soon will be listed here.

Abstract

We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.

Citing Articles

Genomic characterization of the species complex, a prominent member of the human skin microbiome.

Ahmed N, Joglekar P, Deming C, Lemon K, Kong H, Segre J mSystems. 2023; 8(6):e0063223.

PMID: 38126779 PMC: 10790575. DOI: 10.1128/msystems.00632-23.

Enabling automated and reproducible spatially resolved transcriptomics at scale.

Stenbeck L, Taborsak-Lines F, Giacomello S Heliyon. 2022; 8(6):e09651.

PMID: 35756107 PMC: 9213715. DOI: 10.1016/j.heliyon.2022.e09651.

Diverging landscape impacts on macronutrient status despite overlapping diets in managed () and native () bees.

Mogren C, Benitez M, McCarter K, Boyer F, Lundgren J Conserv Physiol. 2020; 8(1):coaa109.

PMID: 33365131 PMC: 7745716. DOI: 10.1093/conphys/coaa109.

Experimental factors are associated with fetal fraction in size selection noninvasive prenatal testing.

Qiao L, Mao J, Liu M, Liu Y, Song X, Tang H Am J Transl Res. 2019; 11(10):6370-6381.

PMID: 31737189 PMC: 6834515.

Resistin-like Molecule α Provides Vitamin-A-Dependent Antimicrobial Protection in the Skin.

Harris T, Gattu S, Propheter D, Kuang Z, Bel S, Ruhn K Cell Host Microbe. 2019; 25(6):777-788.e8.

PMID: 31101494 PMC: 6628910. DOI: 10.1016/j.chom.2019.04.004.

References

OBrien Jr W . Ultrasound-biophysics mechanisms. Prog Biophys Mol Biol. 2006; 93(1-3):212-55. PMC: 1995002. DOI: 10.1016/j.pbiomolbio.2006.07.010. View

Mardis E . Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008; 9:387-402. DOI: 10.1146/annurev.genom.9.081307.164359. View

Hamady M, Walker J, Harris J, Gold N, Knight R . Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008; 5(3):235-7. PMC: 3439997. DOI: 10.1038/nmeth.1184. View

Binladen J, Gilbert M, Bollback J, Panitz F, Bendixen C, Nielsen R . The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One. 2007; 2(2):e197. PMC: 1797623. DOI: 10.1371/journal.pone.0000197. View

Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L . Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437(7057):376-80. PMC: 1464427. DOI: 10.1038/nature03959. View

HAWKINS T, Roy A, Santillan C . DNA purification and isolation using a solid-phase. Nucleic Acids Res. 1994; 22(21):4543-4. PMC: 308491. DOI: 10.1093/nar/22.21.4543. View

Frank D . BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics. 2009; 10:362. PMC: 2777893. DOI: 10.1186/1471-2105-10-362. View

Rutledge R, 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. PMC: 2397388. DOI: 10.1186/1472-6750-8-47. View

Ooi S, Shoemaker D, Boeke J . A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science. 2001; 294(5551):2552-6. DOI: 10.1126/science.1065672. View

10.

Kaiser J . DNA sequencing. A plan to capture human diversity in 1000 genomes. Science. 2008; 319(5862):395. DOI: 10.1126/science.319.5862.395. View

11.

Quail M, Kozarewa I, Smith F, Scally A, Stephens P, Durbin R . A large genome center's improvements to the Illumina sequencing system. Nat Methods. 2008; 5(12):1005-10. PMC: 2610436. DOI: 10.1038/nmeth.1270. View

12.

Giaever G, Chu A, Ni L, Connelly C, Riles L, Veronneau S . Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002; 418(6896):387-91. DOI: 10.1038/nature00935. View

13.

Yassour M, Kaplan T, Fraser H, Levin J, Pfiffner J, Adiconis X . Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009; 106(9):3264-9. PMC: 2638735. DOI: 10.1073/pnas.0812841106. View

14.

. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455(7216):1061-8. PMC: 2671642. DOI: 10.1038/nature07385. View

15.

Kozarewa I, Ning Z, Quail M, Sanders M, Berriman M, Turner D . Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods. 2009; 6(4):291-5. PMC: 2664327. DOI: 10.1038/nmeth.1311. View

16.

He M, Petoukhov S, Ricci P . Genetic code, hamming distance and stochastic matrices. Bull Math Biol. 2004; 66(5):1405-21. DOI: 10.1016/j.bulm.2004.01.002. View

17.

Meyer M, Briggs A, Maricic T, Hober B, Hoffner B, Krause J . From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res. 2007; 36(1):e5. PMC: 2248761. DOI: 10.1093/nar/gkm1095. View

18.

Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M . A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 2007; 35(19):e130. PMC: 2095802. DOI: 10.1093/nar/gkm760. View

19.

Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss J . The NIH Human Microbiome Project. Genome Res. 2009; 19(12):2317-23. PMC: 2792171. DOI: 10.1101/gr.096651.109. View

20.

Wang X, Sun Q, McGrath S, Mardis E, Soloway P, Clark A . Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One. 2008; 3(12):e3839. PMC: 2585789. DOI: 10.1371/journal.pone.0003839. View