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Methods: Analysis of Sequence Variations in Several Human Genes Using Phosphoramidite Bond DNA Fragmentation and Chip-Based MALDI-TOF
- Kevin J. Smylie,
- Charles R. Cantor,
- and Mikhail F. Denissenko
Genome Res. January 2004 14: 134-141; doi:10.1101/gr.1653504
...fragmentation and subsequent MALDI-TOF MS analysis for the high-throughput discovery and measurement of sequence variations in fragments up to 0.5 kb in length in multiple human blood DNA samples. Footnotes [Supplemental material is available online at www.genome.org. The sequence data from...
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Methods: High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12
- Christiane Honisch,
- Anu Raghunathan,
- Charles R. Cantor,
- Bernhard Ø. Palsson,
- and Dirk van den Boom
Genome Res. December 2004 14: 2495-2502; doi:10.1101/gr.2977704
.... Boecker, S., et al. 2004 . High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res. 14 : 126 -133. ↵ Storm, N., Darnhofer-Demar, B., van den Boom, D., and Rodi, C.R. 2003 . MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol. Biol. 212 : 241 -262. ↵ von Wintzingerode, F...
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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
...through different mechanisms with highly variable divergence rates. The SNP loci reported here will provide useful genetic markers for developing high-throughput methods for fine-resolution genotyping of STEC O157. Functional characterization of nucleotide polymorphisms should shed new insights...
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RESOURCE: Large-Scale Validation of Single Nucleotide Polymorphisms in Gene Regions
- Matthew R. Nelson,
- George Marnellos,
- Stefan Kammerer,
- Carolyn R. Hoyal,
- Michael M. Shi,
- Charles R. Cantor,
- and Andreas Braun
Genome Res. August 2004 14: 1664-1668; doi:10.1101/gr.2421604
...of 92 CEPH Caucasians using chip-based MALDI-TOF mass spectrometry with pooled DNA. Of the 204,200 designed assays that were functional, 125,799 SNPs were determined to be polymorphic (minor allele frequency &gt;0.02), of which 101,729 map uniquely to the human . Many of the commonly available Ref...
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Methods: SNP Discovery in Pooled Samples With Mismatch Repair Detection
- Hossein Fakhrai-Rad,
- Jianbiao Zheng,
- Thomas D. Willis,
- Kee Wong,
- Kent Suyenaga,
- Martin Moorhead,
- Jim Eberle,
- Yvonne R. Thorstenson,
- Ted Jones,
- Ronald W. Davis,
- Eugeni Namsaraev,
- and Malek Faham
Genome Res. July 2004 14: 1404-1412; doi:10.1101/gr.2373904
...., Illig, T., Konig, I.R., and Wjst, M. 2002 . Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat. 20 : 57 –64. ↵ Wolford, J.K., Blunt, D., Ballecer, C., and Prochazka, M. 2000 . High-throughput SNP detection by using DNA pooling and denaturing...
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Research: Integrative analysis of the melanoma transcriptome
- Michael F. Berger,
- Joshua Z. Levin,
- Krishna Vijayendran,
- Andrey Sivachenko,
- Xian Adiconis,
- Jared Maguire,
- Laura A. Johnson,
- James Robinson,
- Roel G. Verhaak,
- Carrie Sougnez,
- Robert C. Onofrio,
- Liuda Ziaugra,
- Kristian Cibulskis,
- Elisabeth Laine,
- Jordi Barretina,
- Wendy Winckler,
- David E. Fisher,
- Gad Getz,
- Matthew Meyerson,
- David B. Jaffe,
- Stacey B. Gabriel,
- Eric S. Lander,
- Reinhard Dummer,
- Andreas Gnirke,
- Chad Nusbaum,
- and Levi A. Garraway
Genome Res. April 2010 20: 413-427; Published in Advance February 23, 2010, doi:10.1101/gr.103697.109
...chimeric transcripts, RNA-seq provides sequence-level information for each individual transcript. Whereas several groups have developed methods for targeted high-throughput sequencing of genomic DNA by first capturing genomic regions of interest (typically exons) using molecular inversion probes (Porreca...
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Resource: Accurate detection and genotyping of SNPs utilizing population sequencing data
- Vikas Bansal,
- Olivier Harismendy,
- Ryan Tewhey,
- Sarah S. Murray,
- Nicholas J. Schork,
- Eric J. Topol,
- and Kelly A. Frazer
Genome Res. April 2010 20: 537-545; Published in Advance February 11, 2010, doi:10.1101/gr.100040.109
...to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for single nucleotide polymorphism (SNP) detection...
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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
...November 24, 2003. Received March 18, 2003. Cold Spring Harbor Laboratory Press References ↵ Andersen, P.S., Jespersgaard, C., Vuust, J., Christiansen, M., and Larsen, L.A. 2003 . High-throughput single strand conformation polymorphism mutation detection by automated capillary array electrophoresis...
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LETTER: Identification of the Single Base Change Causing the Callipyge Muscle Hypertrophy Phenotype, the Only Known Example of Polar Overdominance in Mammals
- Brad A. Freking,
- Susan K. Murphy,
- Andrew A. Wylie,
- Simon J. Rhodes,
- John W. Keele,
- Kreg A. Leymaster,
- Randy L. Jirtle,
- and Timothy P.L. Smith
Genome Res. October 1, 2002 12: 1496-1506; Published in Advance September 13, 2002, doi:10.1101/gr.571002
...of alleles for the polymorphism that passed the initial screen in the discovery panel. SNP Genotyping Assays for automated genotype scoring by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) were developed based on the Sequenom (Sequenom) genotyping technology...
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RESOURCE: Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse
- Jennifer L. Moran,
- Andrew D. Bolton,
- Pamela V. Tran,
- Alison Brown,
- Noelle D. Dwyer,
- Danielle K. Manning,
- Bryan C. Bjork,
- Cheng Li,
- Kate Montgomery,
- Sandra M. Siepka,
- Martha Hotz Vitaterna,
- Joseph S. Takahashi,
- Tim Wiltshire,
- David J. Kwiatkowski,
- Raju Kucherlapati,
- and David R. Beier
Genome Res. March 2006 16: 436-440; Published in Advance February 3, 2006, doi:10.1101/gr.4563306
..., with a range of 17–83 Mb. Thus, our SNP panel allows for identification of moderate resolution map position with small numbers of mice in a high-throughput manner. Importantly, the panel is suitable for mapping crosses from many inbred and wild-derived inbred strain combinations. The chromosomal localizations...

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