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LETTER: Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
- Wei Zhang,
- Weihong Qi,
- Thomas J. Albert,
- Alifiya S. Motiwala,
- David Alland,
- Eija K. Hyytia-Trees,
- Efrain M. Ribot,
- Patricia I. Fields,
- Thomas S. Whittam,
- and Bala Swaminathan
Genome Res. June 2006 16: 757-767; Published in Advance April 10, 2006, doi:10.1101/gr.4759706
...(a total of 1,167,948 bp) and 92,721 bp of the large virulence plasmid (pO157) of eleven outbreak-associated STEC O157 strains. We discovered 906 SNPs in 523 chromosomal genes and observed a high level of DNA polymorphisms among the pO157 plasmids. Based on a uniform rate of synonymous substitution...
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METHODS: Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen
- Lucille Beaudet,
- Julie Bédard,
- Billy Breton,
- Roberto J. Mercuri,
- and Marcia L. Budarf
Genome Res. April 1, 2001 11: 600-608; doi:10.1101/gr.1725501
...) Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 10 : 1249 – 1258 . ↵ Bossé R. , Illy C. , Elands J. , Chelsky D. ( 2000 ) Miniaturizing screening: How low can we go today? Drug Discov. Today HTS supplement 1 : 42 – 47 . ↵ Cai H. , White P.S. , Torney D...
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PERSPECTIVE: Emerging technologies in DNA sequencing
- Michael L. Metzker
Genome Res. December 2005 15: 1767-1776; doi:10.1101/gr.3770505
...concentrations of pyrophosphate or ATP and is a major cause of “drop-outs” in DNA sequence data. Single nucleotide addition (SNA) methods such as pyrosequencing use limiting amounts of individual natural dNTPs to cause DNA synthesis to pause, which, unlike the Sanger method, can be resumed with the addition...
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REVIEW: Reading Bits of Genetic Information: Methods for Single-Nucleotide Polymorphism Analysis
- Ulf Landegren,
- Mats Nilsson,
- and Pui-Yan Kwok
Genome Res. August 1, 1998 8: 769-776; doi:10.1101/gr.8.8.769
...oligonucleotides for localized DNA detection. Science 265 : 2085 – 2088 . ↵ Nilsson M. , Krejci K. , Koch J. , Kwiatkowski M. , Gustavsson P. , Landegren U. ( 1997 ) Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13...
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REVIEW: Pyrosequencing Sheds Light on DNA Sequencing
- Mostafa Ronaghi
Genome Res. January 1, 2001 11: 3-11; doi:10.1101/gr.150601
...) Determination of single nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 10 : 1249 – 1258 . ↵ Bains W. , Smith G.C. ( 1988 ) A novel method for nucleic acid sequence determination. J. Theoret. Biol. 135 : 303 – 307 . ↵ Benkovic S.J. , Cameron C.E. ( 1995 ) Kinetic analysis...
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METHODS: Large-Scale Identification of Single-Feature Polymorphisms in Complex Genomes
- Justin O. Borevitz,
- David Liang,
- David Plouffe,
- Hur-Song Chang,
- Tong Zhu,
- Detlef Weigel,
- Charles C. Berry,
- Elizabeth Winzeler,
- and Joanne Chory
Genome Res. March 1, 2003 13: 513-523; Published in Advance February 12, 2003, doi:10.1101/gr.541303
...number of each gene was investigated to test whether features in genes present at higher copy numbers were more likely to be polymorphic. Copy number was determined by aligning the entire DNA sequence of genes detected by AtGenome1 with a database containing all the genes (see Methods). The number...
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Next-Generation DNA Sequencing/Review: The new paradigm of flow cell sequencing
- Robert A. Holt and
- Steven J.M. Jones
Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107
....” In color space, single nucleotide polymorphisms are identifiable as two adjacent color changes. Sequence errors, however, will introduce a “frame-shift” during translation of the color-space sequence into text (e.g., A, G, C, and T) and, as a result, the inferred DNA sequence will be completely erroneous...
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Methods: Digital Detection of Genetic Mutations Using SPC-Sequencing
- Hameer Ruparel,
- Michael E. Ulz,
- Sobin Kim,
- and Jingyue Ju
Genome Res. February 2004 14: 296-300; doi:10.1101/gr.1344104
.... 1991 . Analysis of genetic markers in forensic DNA samples using the polymerase chain reaction. Anal. Chem. 63 : 2 -15. ↵ Ronaghi, M., Uhlén, M., and Nyrén, P. 1998 . A sequencing method based on real-time pyrophosphate. Science 281 : 363 -365. ↵ Roses, A.D. 2000 . Pharmacogenetics and the practice...
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Method: Calling amplified haplotypes in next generation tumor sequence data
- Ninad Dewal,
- Yang Hu,
- Matthew L. Freedman,
- Thomas LaFramboise,
- and Itsik Pe'er
Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
...alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor “prefers” to have amplified. Next-generation sequencing...
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Methods: Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. November 2008 18: 1844-1850; Published in Advance October 10, 2008, doi:10.1101/gr.078204.108
...of multi-kilobase DNA sequences from oligonucleotides . Nat. Protoc. 1 : 2596 – 2603 . ↵ Ronaghi, M. , Uhlen, M. , Nyren, P. ( 1998 ) A sequencing method based on real-time pyrophosphate . Science 281 : 363 – 365 . ↵ Sjoblom, T. , Jones, S. , Wood, L.D. , Parsons, D.W. , Lin, J. , Barber, T.D. , Mandelker...

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