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Letter: Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences
- Elmar Schilling,
- Carol El Chartouni,
- and Michael Rehli
Genome Res. November 2009 19: 2028-2035; Published in Advance August 17, 2009, doi:10.1101/gr.095562.109
..., a representative set of DMR was sequenced in both strains before subsequent analysis by MALDI-TOF MS of bisulfite treated DNA. (For information on sequences and primers see Supplemental Fig. S2 and Supplemental Table S3, respectively.) DNA sequencing indicated that DMR were often associated with strain...
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Methods: High-throughput DNA methylation profiling using universal bead arrays
- Marina Bibikova,
- Zhenwu Lin,
- Lixin Zhou,
- Eugene Chudin,
- Eliza Wickham Garcia,
- Bonnie Wu,
- Dennis Doucet,
- Neal J. Thomas,
- Yunhua Wang,
- Ekkehard Vollmer,
- Torsten Goldmann,
- Carola Seifart,
- Wei Jiang,
- David L. Barker,
- Mark S. Chee,
- Joanna Floros,
- and Jian-Bing Fan
Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
...to bisulfite-converted genomic DNA. An allele-specific primer extension step was then carried out; ASOs were extended only if their 3′-base was complementary to their cognate CpG site in the gDNA template. Allele-specific extension was followed by ligation of the extended ASOs to their corresponding LSOs...
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Methods: A probabilistic approach for SNP discovery in high-throughput human resequencing data
- Rose Hoberman,
- Joana Dias,
- Bing Ge,
- Eef Harmsen,
- Michael Mayhew,
- Dominique J. Verlaan,
- Tony Kwan,
- Ken Dewar,
- Mathieu Blanchette,
- and Tomi Pastinen
Genome Res. September 2009 19: 1542-1552; Published in Advance July 15, 2009, doi:10.1101/gr.092072.109
...be beneficial to generate high-density genotyping data in parallel with full sequence. Alternatively, complete allele dropout can be virtually eliminated by a redundant design of LR-PCR primers. It is highly unlikely that two independent sets of primers would both contain SNPs, and so—assuming complete allele...
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ARTICLE: Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation
- Lili Milani,
- Anders Lundmark,
- Jessica Nordlund,
- Anna Kiialainen,
- Trond Flaegstad,
- Gudmundur Jonmundsson,
- Jukka Kanerva,
- Kjeld Schmiegelow,
- Kevin L. Gunderson,
- Gudmar Lönnerholm,
- and Ann-Christine Syvänen
Genome Res. January 2009 19: 1-11; Published in Advance November 7, 2008, doi:10.1101/gr.083931.108
...cells. For genotyping we used the HumanNS-12 BeadChips which are based on the Infinium I assay, which avoids PCR-amplification for sample treatment and uses robust allele-specific primer extension of biotinylated dNTPs for discrimination of the two SNP alleles ( Gunderson et al. 2005 ). Both alleles...
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Methods: A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
- Jian-Bing Fan,
- Joanne M. Yeakley,
- Marina Bibikova,
- Eugene Chudin,
- Eliza Wickham,
- Jing Chen,
- Dennis Doucet,
- Philippe Rigault,
- Baohong Zhang,
- Richard Shen,
- Celeste McBride,
- Hai-Ri Li,
- Xiang-Dong Fu,
- Arnold Oliphant,
- David L. Barker,
- and Mark S. Chee
Genome Res. May 2004 14: 878-885; doi:10.1101/gr.2167504
...in Figure 1 . First, total RNA is converted to cDNA using biotinylated primers (both oligo-d(T)18 and random hexamers). The biotinylated cDNA is then attached to a streptavidin solid support and assay oligonucleotides are annealed to their target sequences in the cDNA. A pair of oligonucleotides is annealed...
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LETTER: Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery
- Daniel G. Peterson,
- Stefan R. Schulze,
- Erica B. Sciara,
- Scott A. Lee,
- John E. Bowers,
- Alexander Nagel,
- Ning Jiang,
- Deanne C. Tibbitts,
- Susan R. Wessler,
- and Andrew H. Paterson
Genome Res. May 1, 2002 12: 795-807; Published in Advance April 12, 2002, doi:10.1101/gr.226102
...clones (D. Peterson, A. Nagel, S. Wessler, and A. Paterson, unpubl.). The use of ssDNA fractions in cloning would be advantageous in instances where the quantity of genomic DNA is limited. Additionally, fewer base pair mismatches would be expected if primer extension techniques rather than strand...
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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
...utilizedto investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed...
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Methods: High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays
- Graham R. Bignell,
- Jing Huang,
- Joel Greshock,
- Stephen Watt,
- Adam Butler,
- Sofie West,
- Mira Grigorova,
- Keith W. Jones,
- Wen Wei,
- Michael R. Stratton,
- P. Andrew Futreal,
- Barbara Weber,
- Michael H. Shapero,
- and Richard Wooster
Genome Res. February 2004 14: 287-295; doi:10.1101/gr.2012304
...method that uses a small number of oligonucleotide primers, coupled to allele discrimination on synthetic DNA microarrays. The method (whole- sampling assay, or WGSA) uses a simple restriction enzyme digestion, followed by linker-ligation of a common adaptor sequence to every fragment, allowing multiple...
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INSIGHT/OUTLOOK: “Spot-On” SNP Genotyping
- Michael C. Ellis
Genome Res. July 1, 2000 10: 895-897; doi:10.1101/gr.10.7.895
...genotyping ( Pastinen et al. 2000 ). Array of Light The genotyping system developed by groups at the National Public Health Institute of Finland and Uppsala University uses allele-specific oligonucleotides on microarrays as templates for primer extension-based genotyping (Figure 1 A). The technique, derived...
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METHODS: Genotyping on a Thermal Gradient DNA Chip
- Tomoharu Kajiyama,
- Yuji Miyahara,
- Larry J. Kricka,
- Peter Wilding,
- David J. Graves,
- Saul Surrey,
- and Paolo Fortina
Genome Res. March 1, 2003 13: 467-475; doi:10.1101/gr.790603
...for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10 : 1031 – 1042 . ↵ Pollak E.S. , Hung H.L. , Godin W. , Overton G.C. , High K.A. ( 1996 ) Functional characterization of the human factor VII 5′-flanking region. J. Biol. Chem. 271 : 1738 – 1747...

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