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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...specific to the target regions are designed such that they anneal to the template upstream and downstream from the ROI. Once amplified, the target(s) can be barcoded if needed, and/or size-selected via gel, then sequenced on either ONT or PacBio instruments (Fig. 1). Long amplicons are quite beneficial...
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Methods: Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
- Mathias Stiller,
- Michael Knapp,
- Udo Stenzel,
- Michael Hofreiter,
- and Matthias Meyer
Genome Res. October 2009 19: 1843-1848; Published in Advance July 27, 2009, doi:10.1101/gr.095760.109
..., Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, et al. 2009. Solution hybrid selection with ultra-long oligonucleotides formassively parallel targeted sequencing. Nat Biotechnol 27: 182–189. Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, De...
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METHODS: A Genetic Strategy to Eliminate Self-Activator Baits Prior to High-Throughput Yeast Two-Hybrid Screens
- Albertha J.M. Walhout and
- Marc Vidal
Genome Res. November 1, 1999 9: 1128-1134; doi:10.1101/gr.9.11.1128
...of a sequence-specific DNA-binding domain, such as DB, the fusion protein is not tethered to the reporter genes and therefore does not activate transcription. To demonstrate that forward two-hybrid selections can be applied after self-activator preclearing, ∼1000 MAT α AD-Y transformants were pooled, plated...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable Cp...
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Methods: DNA Enrichment by Allele-Specific Hybridization (DEASH): A Novel Method for Haplotyping and for Detecting Low-Frequency Base Substitutional Variants and Recombinant DNA Molecules
- Alec J. Jeffreys and
- Celia A. May
Genome Res. October 2003 13: 2316-2324; doi:10.1101/gr.1214603
...detection to variants present at a frequency of at least 10-4-10-5 per cell. We nowdescribe an alternative approach that recovers genomic DNA molecules containing a known single-nucleotide variant by hybridization selection using a biotinylated allele-specific oligonucleotide, followed by hybrid capture...
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RESEARCH: A Radiation Hybrid Map of Human Chromosome 5 with Integration of Cytogenetic, Genetic, and Transcript Maps
- John D. McPherson,
- Barbara Apostol,
- Caryn B. Wagner-McPherson,
- Simin Hakim,
- Richard G. Del Mastro,
- Naeema Aziz,
- Elizabeth Baer,
- Genalyn Gonzales,
- Mary Carol Krane,
- Rachelle Markovich,
- Peter Masny,
- Miguel Ortega,
- John Vu,
- Marco Vujicic,
- Deanna M. Church,
- Allan Segal,
- Deborah L. Grady,
- Robert K. Moyzis,
- M. Anne Spence,
- Michael Lovett,
- and John J. Wasmuth
Genome Res. September 1, 1997 7: 897-909; doi:10.1101/gr.7.9.897
...of the irradiated cell line to a recipient cell line. Although a specific gene in the starting cell line may be used to facilitate hybrid selection, the majority of the radiation-reduced fragments are transferred nonselectively. Statistical analysis of the frequency of coretention of markers in the resulting...

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