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Methods: DNA amplification method tolerant to sample degradation
- Gang Wang,
- Elizabeth Maher,
- Cameron Brennan,
- Lynda Chin,
- Christopher Leo,
- Manjit Kaur,
- Penny Zhu,
- Martha Rook,
- Jia Liu Wolfe,
- and G. Mike Makrigiorgos
Genome Res. November 2004 14: 2357-2366; doi:10.1101/gr.2813404
...: A Practical Approach . Oxford University Press, Oxford, UK. ↵ 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 -1099. ↵ Dean, F.B., Hosono, S., Fang...
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Method: Transcript amplification from single bacterium for transcriptome analysis
- Yun Kang,
- Michael H. Norris,
- Jan Zarzycki-Siek,
- William C. Nierman,
- Stuart P. Donachie,
- and Tung T. Hoang
Genome Res. June 2011 21: 925-935; Published in Advance May 2, 2011, doi:10.1101/gr.116103.110
...). Abbreviations are as follows: aa-dUTP indicates 5-(3-aminoallyl)-29-deoxyuridine-59-triphosphate; dNTP, deoxyribonucleotide triphosphate; DpnI, restriction endonuclease from Diplococcus pneumoniae; EDTA, ethylenediaminetetraacetic acid;u29 polymerase, DNA polymerase from a Bacillus subtilis phage Phi29; M, 1 kb...
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METHODS: Unbiased Whole-Genome Amplification Directly From Clinical Samples
- Seiyu Hosono,
- A. Fawad Faruqi,
- Frank B. Dean,
- Yuefen Du,
- Zhenyu Sun,
- Xiaohong Wu,
- Jing Du,
- Stephen F. Kingsmore,
- Michael Egholm,
- and Roger S. Lasken
Genome Res. May 1, 2003 13: 954-964; Published in Advance April 14, 2003, doi:10.1101/gr.816903
....J. , Bottomley W. , et al. ( 2002 ) Mutations of the BRAF gene in human cancer. Nature 417 : 949 – 954 . ↵ Dean F.B. , Nelson J.R. , Giesler T.L. , Lasken R.S. ( 2001 ) Rapid amplification of plasmid and phage DNA using φ29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11 : 1095...
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Methods: Two Methods of Whole-Genome Amplification Enable Accurate Genotyping Across a 2320-SNP Linkage Panel
- David L. Barker,
- Mark S.T. Hansen,
- A. Fawad Faruqi,
- Diane Giannola,
- Orlando R. Irsula,
- Roger S. Lasken,
- Martin Latterich,
- Vladimir Makarov,
- Arnold Oliphant,
- Jonathon H. Pinter,
- Richard Shen,
- Irina Sleptsova,
- William Ziehler,
- and Eric Lai
Genome Res. May 2004 14: 901-907; doi:10.1101/gr.1949704
...oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc. Natl. Acad. Sci. 93 : 14676 -14679. ↵ 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...
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Method: Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
- Michael S. Fitzsimons,
- Mark Novotny,
- Chien-Chi Lo,
- Armand E.K. Dichosa,
- Joyclyn L. Yee-Greenbaum,
- Jeremy P. Snook,
- Wei Gu,
- Olga Chertkov,
- Karen W. Davenport,
- Kim McMurry,
- Krista G. Reitenga,
- Ashlynn R. Daughton,
- Jian He,
- Shannon L. Johnson,
- Cheryl D. Gleasner,
- Patti L. Wills,
- Beverly Parson-Quintana,
- Patrick S. Chain,
- John C. Detter,
- Roger S. Lasken,
- and Cliff S. Han
Genome Res. May 2013 23: 878-888; Published in Advance March 14, 2013, doi:10.1101/gr.142208.112
.... This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique...
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Method: Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
- Jeffrey S. McLean,
- Mary-Jane Lombardo,
- Michael G. Ziegler,
- Mark Novotny,
- Joyclyn Yee-Greenbaum,
- Jonathan H. Badger,
- Glenn Tesler,
- Sergey Nurk,
- Valery Lesin,
- Daniel Brami,
- Adam P. Hall,
- Anna Edlund,
- Lisa Z. Allen,
- Scott Durkin,
- Sharon Reed,
- Francesca Torriani,
- Kenneth H. Nealson,
- Pavel A. Pevzner,
- Robert Friedman,
- J. Craig Venter,
- and Roger S. Lasken
Genome Res. May 2013 23: 867-877; Published in Advance April 5, 2013, doi:10.1101/gr.150433.112
...in parallel with each sort of single cells to determine the relative amount and identity of contaminating bacterial DNA in the MDA reagents; this is a necessary standard practice in single-cell genomics due to the highly processive strand displacement activity of the phi29 DNA polymerase and the near...
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Method: Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
- Helena M.B. Seth-Smith,
- Simon R. Harris,
- Rachel J. Skilton,
- Frans M. Radebe,
- Daniel Golparian,
- Elena Shipitsyna,
- Pham Thanh Duy,
- Paul Scott,
- Lesley T. Cutcliffe,
- Colette O’Neill,
- Surendra Parmar,
- Rachel Pitt,
- Stephen Baker,
- Catherine A. Ison,
- Peter Marsh,
- Hamid Jalal,
- David A. Lewis,
- Magnus Unemo,
- Ian N. Clarke,
- Julian Parkhill,
- and Nicholas R. Thomson
Genome Res. May 2013 23: 855-866; Published in Advance March 22, 2013, doi:10.1101/gr.150037.112
...Ridgway and Taylor-Robinson 1991). This implies that the growth of strains itself may impose a selective bias on the strains whose s we are able to sequence. It is clear that a rapid, simple, culture-independent technique for generating DNA for whole- sequencing is required. Whole- amplification (WGA...
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Method: Sequencing of isolated sperm cells for direct haplotyping of a human genome
- Ewen F. Kirkness,
- Rashel V. Grindberg,
- Joyclyn Yee-Greenbaum,
- Christian R. Marshall,
- Stephen W. Scherer,
- Roger S. Lasken,
- and J. Craig Venter
Genome Res. May 2013 23: 826-832; Published in Advance January 2, 2013, doi:10.1101/gr.144600.112
...,Whittaker P, DelgadoM, et al. 2006. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 38: 1166–1172. Dean FB, Nelson JR, Giesler TL, Lasken RS. 2001. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiplyprimed...

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