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METHODS: Robust and Accurate Single Nucleotide Polymorphism Genotyping by Dynamic Allele-Specific Hybridization (DASH): Design Criteria and Assay Validation
- Jonathan A. Prince,
- Lars Feuk,
- W. Mathias Howell,
- Magnus Jobs,
- Tesfai Emahazion,
- Kaj Blennow,
- and Anthony J. Brookes
Genome Res. January 1, 2001 11: 152-162; doi:10.1101/gr.150201
...is essentially an enhanced form of allele-specific hybridization ( Stoneking et al. 1991 ), transferred from the traditional radioactive/chemiluminescent and membrane-based platform to a convenient microtiter plate format that uses a simple duplex-DNA intercalating dye for signal production and a dynamic low...
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METHODS: A System for Specific, High-throughput Genotyping by Allele-specific Primer Extension on Microarrays
- Tomi Pastinen,
- Mirja Raitio,
- Katarina Lindroos,
- Päivi Tainola,
- Leena Peltonen,
- and Ann-Christine Syvänen
Genome Res. July 1, 2000 10: 1031-1042; doi:10.1101/gr.10.7.1031
...reagents. Less than 1% of the multiplex PCR products are sufficient for the reaction because the RNA polymerase amplifies the template up to 2000-fold ( Eberwine et al. 1992 ) and several labeled nucleotide analogs are incorporated per RNA template in the allele-specific extension reaction. Use of DNA...
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ARTICLE: Quantitation of tropoelastin mRNA and assessment of alternative splicing in human skin fibroblasts by reverse transcriptase-polymerase chain reaction.
- M Holzenberger,
- S A Levi-Minzi,
- C P Herzog,
- S B Deak,
- L Robert,
- and C D Boyd
Genome Res. October 1993 3: 107-114; doi:10.1101/gr.3.2.107
...be independent of sequence-specific variation in rates of reverse transcription or polymerase chain amplification. The quantitative determination of levels of tropoelastin mRNA represented in G-allele-specific PCR-derived BstNI re- striction fragments i presented in Figure 3. Size-separated, radiolabeled DNA...
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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
.... DNA methylation assay scheme. ( A ) Bisulfite conversion of DNA. ( B ) For each CpG site, two pairs of probes were designed to interrogate either the top or bottom strand: an allele-specific oligonucleotide (ASO) and locus-specific oligonucleotide (LSO) probe pair for the methylated state of the Cp...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...the DNA or the protein, further influencing experimental outcomes.Although well-established approaches have been developed to determine DNA binding patterns for a protein of interest, because of a lack of an established, and universally accepted, methodology for identifying direct regulators of a GOI...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...amplification (Chr 7: 124,879,000–48,644,500) was observed 779 bp downstream from the HBV integration site, which is consistent with the breakage-fusion-bridge (BFB) INV model.View larger version: In this window In a new window Figure 4. Inferring SV types based on HBV DNA integration patterns. (A) In sample...
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Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
...components of the contig, supported an accurate contig assembly (Fig. 3A,B).View larger version: In this window In a new window Figure 3. A duplication, inversion of target-derived fragments, and integration of exogenous DNA fragments arose in the deletion clone HepG2 Δt15. (A) The browser view shows Xdrop...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...). Surprised by such a rapid alteration of Pol II and its associated factors by G4 stabilizing ligands, we were curious about the changes in the chromatin states at promoters, including dsDNA melting and chromatin accessibility. Thus, we performed kethoxal-assisted single-stranded DNA sequencing (KAS-seq) (Wu...
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Method: Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
- Joseph B. Hiatt,
- Colin C. Pritchard,
- Stephen J. Salipante,
- Brian J. O'Roak,
- and Jay Shendure
Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112
.... A wide variety of methods have been developed to identify and characterize genetic variation, including, but not limited to allele-specific PCR, mass spectrometry, microarrays, and DNA sequencing. In general, however, these methods are designed to detect heterozygous and homozygous variation and have...
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Research: PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration
- Christopher L. Baker,
- Michael Walker,
- Shimpei Kajita,
- Petko M. Petkov,
- and Kenneth Paigen
Genome Res. May 2014 24: 724-732; Published in Advance March 6, 2014, doi:10.1101/gr.170167.113
...always contains a close match to the consensus motif (Fig. 4; Supplemental Figs. S4, S5). These binding experiments also revealed several properties of PRDM9-DNA interactions. First, competition for PRDM9 binding in vitro is allele-specific. DNAs fromdifferent hotspots activated by the same allele...

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