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METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
- Robert G. Blazej,
- Brian M. Paegel,
- and Richard A. Mathies
Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
...is an internally controlled method for polymorphism discovery, multiplexed allele frequency determination, and genotyping. The compact (16,569 bp) and well-characterized human mitochondrial was selected as a test system for PRS development. Two mitochondrial s from unrelated Centre d'Etude Polymorphisme Humane...
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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
...to a different temperature (PTC-200; MJ Research). For the seven AlphaScreen ASH assays, the optimal hybridization temperature was found to be between 53°C and 63°C, primarily depending on the Tm of the allele-specific probe. The results obtained for the ASH genotyping of 21 Centre d'Etude du Polymorphisme...
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Methods: Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy
- Edward F. Attiyeh,
- Sharon J. Diskin,
- Marc A. Attiyeh,
- Yaël P. Mossé,
- Cuiping Hou,
- Eric M. Jackson,
- Cecilia Kim,
- Joseph Glessner,
- Hakon Hakonarson,
- Jaclyn A. Biegel,
- and John M. Maris
Genome Res. February 2009 19: 276-283; Published in Advance January 13, 2009, doi:10.1101/gr.075671.107
..., L. , Hangaishi, A. , Kurokawa, M. , Chiba, S. , Bailey, D.K. , Kennedy, G.C. , et al. ( 2005 ) A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays . Cancer Res. 65 : 6071 – 6079 . ↵ Olshen, A.B. , Venkatraman, E.S. , Lucito...
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Methods: Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
- Christopher W. Wong,
- Thomas J. Albert,
- Vinsensius B. Vega,
- Jason E. Norton,
- David J. Cutler,
- Todd A. Richmond,
- Lawrence W. Stanton,
- Edison T. Liu,
- and Lance D. Miller
Genome Res. March 2004 14: 398-405; doi:10.1101/gr.2141004
...-CoV isolates. As the array synthesis process is maskless, it is highly flexible, allowing any new sequence variation to be rapidly included on redesigned arrays within 2 d of discovery without additional manufacturing costs. To validate this sequencing platform, we resequenced the complete SARS-CoV s from Vero...
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Methods: Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
- Hajime Matsuzaki,
- Halina Loi,
- Shoulian Dong,
- Ya-Yu Tsai,
- Joy Fang,
- Jane Law,
- Xiaojun Di,
- Wei-Min Liu,
- Geoffrey Yang,
- Guoying Liu,
- Jing Huang,
- Giulia C. Kennedy,
- Thomas B. Ryder,
- Gregory A. Marcus,
- P. Sean Walsh,
- Mark D. Shriver,
- Jennifer M. Puck,
- Keith W. Jones,
- and Rui Mei
Genome Res. March 2004 14: 414-425; doi:10.1101/gr.2014904
...from the Centre d'Etude du Polymorphisme Humain (CEPH) or the National Institute of General Medical Sciences (NIGMS) repositories. The majority of the trio genotyping data was used for SNP selection; however, five trios were reserved as a validation data set. There were 61 inheritance errors out of 167...
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Resource: Genome-wide discovery of human splicing branchpoints
- Tim R. Mercer,
- Michael B. Clark,
- Stacey B. Andersen,
- Marion E. Brunck,
- Wilfried Haerty,
- Joanna Crawford,
- Ryan J. Taft,
- Lars K. Nielsen,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
...junction, we have used two complementary approaches: purification of lariats by exoribonuclease digestion of linear RNAs; and capture of the branchpoint junction with oligonucleotide probes for targeted RNA sequencing. The sequencing and alignment of these approaches enables the first -wide discovery...
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METHODS: A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension
- Jingwen Chen,
- Marie A. Iannone,
- May-Sung Li,
- J. David Taylor,
- Philip Rivers,
- Anita J. Nelsen,
- Kimberly A. Slentz-Kesler,
- Allen Roses,
- and Michael P. Weiner
Genome Res. April 1, 2000 10: 549-557; doi:10.1101/gr.10.4.549
...: 234 – 243 . ↵ Lai E. , Riley J. , Purvis I. , Roses A. ( 1998 ) A 4-MB high-density single nucleotide polymorphism-based map around human APOE. Genomics 54 : 31 – 38 . ↵ Landegren U. , Kaiser R. , Sanders J. , Hood L. ( 1988 ) A ligase-mediated gene detection technique. Science 241 : 1077 – 1080...
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Method: Haplotype-based profiling of subtle allelic imbalance with SNP arrays
- Selina Vattathil and
- Paul Scheet
Genome Res. January 2013 23: 152-158; Published in Advance October 1, 2012, doi:10.1101/gr.141374.112
...-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2: e41. doi: 10.1371/journal.pcbi.0020041. Chen H, Xing H, Zhang N. 2011. Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays. PLoS Comput Biol 7: e1001060. doi: 10.1371/journal...
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Methods: A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome
- Hui-Yun Wang,
- Minjie Luo,
- Irina V. Tereshchenko,
- Danielle M. Frikker,
- Xiangfeng Cui,
- James Y. Li,
- Guohong Hu,
- Yi Chu,
- Marco A. Azaro,
- Yong Lin,
- Li Shen,
- Qifeng Yang,
- Manousos E. Kambouris,
- Richeng Gao,
- Weichung Shih,
- and Honghua Li
Genome Res. February 2005 15: 276-283; doi:10.1101/gr.2885205
.... Genetic analysis is one of the most powerful tools for this purpose. The recent discovery of millions of single nucleotide polymorphisms (SNPs) has provided a rich resource for such analysis. dbSNP Build 121 of the SNP database maintained by the National Center for Biotechnology Information (NCBI...
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Methods: Decoding Randomly Ordered DNA Arrays
- Kevin L. Gunderson,
- Semyon Kruglyak,
- Michael S. Graige,
- Francisco Garcia,
- Bahram G. Kermani,
- Chanfeng Zhao,
- Diping Che,
- Todd Dickinson,
- Eliza Wickham,
- Jim Bierle,
- Dennis Doucet,
- Monika Milewski,
- Robert Yang,
- Chris Siegmund,
- Juergen Haas,
- Lixin Zhou,
- Arnold Oliphant,
- Jian-Bing Fan,
- Steven Barnard,
- and Mark S. Chee
Genome Res. May 2004 14: 870-877; Published in Advance April 12, 2004, doi:10.1101/gr.2255804
...single nucleotide polymorphism genotyping and gene expression profiling. The algorithm requires only a few labels and several sequential hybridizations to identify thousands of different DNA sequences with great accuracy. We have decoded tens of thousands of arrays, each with 1520 sequences represented...

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