Optimized whole-genome amplification strategy for extremely AT-biased template

DNA Research

Volumn 21, Issue 6, 2014, Pages 661-671

  Oyola, Samuel O ^a   Manske, Magnus ^a   Campino, Susana ^a   Claessens, Antoine ^a   Hamilton, William L ^a   Kekre, Mihir ^a   Drury, Eleanor ^a   Mead, Daniel ^a   Gu, Yong ^a   Miles, Alistair ^b,c   MacInnis, Bronwyn ^a,b   Newbold, Chris ^a,b   Berriman, Matthew ^a   Kwiatkowski, Dominic P ^a,b,c  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

AT rich; Malaria; Tetramethylammonium chloride; Whole genome amplification

Indexed keywords

TETRAMETHYLAMMONIUM CHLORIDE; PROTOZOAL DNA;

ARTICLE; AT RICH SEQUENCE; BLOOD SAMPLING; CHIMERA; CONTROLLED STUDY; DNA DETERMINATION; GENE AMPLIFICATION; GENE SEQUENCE; MICROBIAL GENOME; NONHUMAN; PLASMODIUM FALCIPARUM; CHEMISTRY; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; NUCLEIC ACID AMPLIFICATION; PROCEDURES;

PLASMODIUM FALCIPARUM;

DNA, PROTOZOAN; GENOME, PROTOZOAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PLASMODIUM FALCIPARUM;

EID: 84922447484     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsu028     Document Type: Article

References (34)

1. Manske, M., Miotto, O., Campino, S., et al. 2012, Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing, Nature, 487, 375-9.
2. Miotto, O., Almagro-Garcia, J., Manske, M., et al. 2013, Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia, Nat. Genet., 45, 648-55.
3. Lasken, R.S. and Egholm, M.2003, Whole genome ampli-fication:abundantsuppliesofDNAfromprecious samples or clinical specimens, Trends Biotechnol., 21, 531-5.
4. Coombs, N.J., Gough, A.C. and Primrose, J.N. 1999, Optimisation of DNA and RNA extraction from archival formalin-fixed tissue, Nucleic Acids Res., 27, e12.
5. Farnert, A., Arez, A.P., Correia, A.T., Bjorkman, A., Snounou, G. and do Rosario, V. 1999, Sampling and storage of blood and the detection of malaria parasites by polymerase chain reaction, Trans. R. Soc. Trop. Med. Hyg., 93, 50-3.
6. Jackson, J., Laikre, L., Baker, C.S. and Kendall, K. 2012, Guidelines for collecting and maintaining archives for genetic monitoring, Conservation Genet. Resour., 4, 527-36.
7. Shi, S.R., Cote, R.J., Wu, L., et al. 2002, DNA extraction from archival formalin-fixed, paraffin-embedded tissuesections basedonthe antigen retrieval principle: heating under the influence of pH, J. Histochem. Cytochem., 50, 1005-11.
8. Bereczky, S., Martensson, A., Gil, J.P. and Farnert, A. 2005, Short report: rapid DNA extraction from archive blood spots on filter paper for genotyping of Plasmodium falcip-arum, Am. J. Trop. Med. Hyg., 72, 249-51.
9. Hwang, J., Jaroensuk, J., Leimanis, M.L., et al. 2012, Long-term storage limits PCR-based analyses of malaria parasites in archival dried blood spots, Malar. J., 11, 339.
10. Kain, K.C. and Lanar, D.E. 1991, Determinationofgenetic variationwithinPlasmodiumfalciparumbyusingenzyma-ticallyamplifiedDNAfromfilterpaperdisks impregnated with whole blood, J. Clin. Microbiol., 29, 1171-4.
11. Spits, C., Le Caignec, C., De Rycke, M., et al. 2006, Whole-genomemultiple displacement amplificationfrom single cells, Nat. Protoc., 1, 1965-70.
12. Dean, F.B., Hosono, S., Fang, L., et al. 2002, Comprehensive human genome amplification using multiple displace-mentamplification, Proc.Natl. Acad. Sci. USA, 99, 5261-6.
13. Dean, F.B., Nelson, J.R., Giesler, T.L. and Lasken, R.S. 2001, Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification, Genome Res., 11, 1095-9.
14. Telenius, H., Carter, N.P., Bebb, C.E., Nordenskjold, M., Ponder, B.A. and Tunnacliffe, A. 1992, Degenerate oligo-nucleotide-primed PCR: general amplification of target DNAbyasingledegenerateprimer, Genomics, 13, 718-25.
15. Zhang, L., Cui, X., Schmitt, K., Hubert, R., Navidi, W. and Arnheim, N. 1992, Whole genome amplification from a single cell: implications for genetic analysis, Proc. Natl. Acad. Sci. USA, 89, 5847-51.
16. Lasken, R.S. 2009, Genomic DNA amplification by the multiple displacement amplification (MDA) method, Biochem. Soc. Trans., 37, 450-3.
17. Morin, J.A., Cao, F.J., Lazaro, J.M., et al. 2012, Active DNA unwinding dynamics during processive DNA replication, Proc. Natl. Acad. Sci. USA, 109, 8115-20.
18. Zhang, D.Y., Brandwein, M., Hsuih, T. and Li, H.B. 2001, Ramificationamplification:anovelisothermalDNA amplification method, Mol. Diagn., 6, 141-50.
19. Pinard, R., de Winter, A., Sarkis, G.J., et al. 2006, Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing, BMC Genomics, 7, 216.
20. Pugh, T.J., Delaney, A.D., Farnoud, N., et al. 2008, Impactof whole genome amplificationonanalysisofcopy number variants, Nucleic Acids Res., 36, e80.
21. Kozarewa, I., Ning, Z., Quail, M.A., Sanders, M.J., Berriman, M. and Turner, D.J. 2009, Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (GC)-biased genomes, Nat. Methods, 6, 291-5.
22. Oyola, S.O., Otto, T.D., Gu, Y., et al. 2012, Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes, BMC Genomics, 13, 1.
23. Hayton, K., Gaur, D., Liu, A., et al. 2008, Erythrocyte binding protein PfRH5 polymorphisms determine species-specificpathwaysofPlasmodium falciparum invasion, Cell Host Microbe, 4, 40-51.
24. Han, T., Chang, C.-W., Kwekel, J., et al. 2012, Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development, BMC Genomics, 13, 217.
25. Spits, C., Le Caignec, C., De Rycke, M., et al. 2006, Optimization and evaluation of single-cell whole-genome multiple displacement amplification, Hum. Mutat., 27, 496-503.
26. Benson, G. 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res., 27, 573-80.
27. Lasken, R. and Stockwell, T. 2007, Mechanism of chimera formation during the multiple displacement amplification reaction, BMC Biotechnol., 7, 19.
28. McKenna, A., Hanna, M., Banks, E., et al. 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297-303.
29. Zong, C., Lu, S., Chapman, A.R. and Xie, X.S. 2012, Genome-wide detection of single-nucleotide and copy-number variations of a single human cell, Science, 338, 1622-6.
30. Schneider, P., Balogh, K., Naveran, N., et al. 2004, Whole genome amplification-the solution for a common probleminforensiccasework?Int.Congr.Ser., 12, 61, 24-6.
31. Nair, S., Nkhoma, S.C., Serre, D., et al. 2014, Single-cell genomics for dissection of complex malaria infections, Genome Res., 24, 1028-38.
32. Oyola, S.O., Gu, Y., Manske, M., et al. 2013, Efficient depletion of host DNA contamination in malaria clinical sequencing, J. Clin. Microbiol., 51, 745-51.
33. Feehery, G.R., Yigit, E., Oyola, S.O., et al. 2013, A method for selectively enriching microbial DNA from contaminating vertebrate host DNA, PLoS ONE, 8, e76096.
34. Venkatesan, M., Amaratunga, C., Campino, S., et al. 2012, Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples, Malar. J., 11, 41.