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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...-cell DNA sequencing and forensics, the amount of DNA available is low and requires amplification (Butler 2006; Evrony et al. 2015). Although high-depth whole- sequencing (WGS) of PCR-amplified libraries could achieve large-scale, high-fidelity profiling of microsatellites, this is not feasible to scale...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...-stranded DNA (dsDNA) with a single-cycle polymerase chain reaction (PCR) reaction consisting of 10 µL of washed Dynabead-bound sample, 12 µL of 2X Q5 high-fidelity DNA polymerase (NEB), and 2 µL of P5_primer_short (Supplemental Table S4). Samples are incubated for 2 min at 98°C followed by 5 min at 65°C...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...) can be determined through digital droplet polymerase chain reaction (ddPCR) or targeted sequencing (panels) (Diaz and Bardelli 2014; Wan et al. 2017; Corcoran and Chabner 2018; Lustberg et al. 2018; Bronkhorst et al. 2019a; Husain et al. 2022). However, tumor detection from small sample volumes (∼10 m...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
..., Seattle, Washington 98195, USA ↵8 These authors contributed equally to this work. Corresponding authors: absterga@uw.edu, mvollger@uw.eduAbstractLong-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single...
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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: DNA mismatch repair preferentially protects genes from mutation
- Eric J. Belfield,
- Zhong Jie Ding,
- Fiona J.C. Jamieson,
- Anne M. Visscher,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2018 28: 66-74; Published in Advance December 12, 2017, doi:10.1101/gr.219303.116
...the .Most spontaneous mutations likely arise from errors of DNA replication (Kunz et al. 1998; Stuart et al. 2000). Eukaryotic organisms have evolved sequential processes for enhancing the accurate replication of the and for repairing DNA replication errors. First, most DNA-replicating DNA polymerase enzyme...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...Evolutionary expansion of DNA hypomethylation in the mammalian germline Jianghan Qu1, Emily Hodges2, Antoine Molaro3,4, Pascal Gagneux5, Matthew D. Dean1, Gregory J. Hannon3,6,7,8 and Andrew D. Smith1 1Molecular and Computational Biology Section, Division of Biological Sciences, University...
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Research: Error-prone polymerase activity causes multinucleotide mutations in humans
- Kelley Harris and
- Rasmus Nielsen
Genome Res. September 2014 24: 1445-1454; Published in Advance July 30, 2014, doi:10.1101/gr.170696.113
...previously shown to dominate the spectrum of the error-prone polymerase Pol ζ , suggesting that low-fidelity DNA replication by Pol ζ is at least partly responsible for the MNMs that are segregating in the human population. We develop statistical estimates of MNM prevalence that can be used to correct...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...—PacBio relies on a DNA polymerase and measures the fluorescence of modified DNA precursors while they are being incorporated into a nascent chain, whereas ONT measures the electrical conductance as native DNA passes through a membrane pore—one shared component stands out: T4 DNA ligase, which is used to glue...
REVIEW: Applications of the polymerase chain reaction in environmental microbiology.
- A K Bej and
- M H Mahbubani
Genome Res. February 1992 1: 151-159; doi:10.1101/gr.1.3.151
..., M.S. and Hartley. J.L. 1990 . Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reaction. Gene 93 : 125 – 128 . 26. Cariello, N.F., , Swenberg, J.A. , Skopek. T.R. Cariello, N.F., Swenberg, J.A. and Skopek. T.R. 1991 . Fidelity of Thermococcus litoralis DNA...
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