Searching journal content for articles similar to Lujan et al. 24 (11): 1751.

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  1. 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
    ...by whole- sequencing. Proc Natl Acad Sci 109: E2774–E2783. ↵Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, et al. 2014. Heterogeneous polymerase fidelity and mismatch repair bias variation and composition. Genome Res 24: 1751...
  2. Research: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
    • Bettina Meier,
    • Nadezda V. Volkova,
    • Ye Hong,
    • Pieta Schofield,
    • Peter J. Campbell,
    • Moritz Gerstung,
    • and Anton Gartner
    Genome Res. May 2018 28: 666-675; Published in Advance April 10, 2018, doi:10.1101/gr.226845.117
    ...to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the . DNA mismatch repair (MMR) deficiency leads to hypermutation and is found in different cancer types. Although it is possible to associate mutational signatures extracted from human cancers with possible mutational...
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  3. Research: Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand
    • Maria A. Andrianova,
    • Georgii A. Bazykin,
    • Sergey I. Nikolaev,
    • and Vladimir B. Seplyarskiy
    Genome Res. August 2017 27: 1336-1343; Published in Advance May 16, 2017, doi:10.1101/gr.219915.116
    ..., Kunkel TA. 2012. Mismatch repair balances leading and lagging strand DNA replication fidelity. PLoS Genet 8: e1003016. Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, et al. 2014. Heterogeneous polymerase fidelity and mismatch...
  4. Research: Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
    • Rob W. Ness,
    • Andrew D. Morgan,
    • Radhakrishnan B. Vasanthakrishnan,
    • Nick Colegrave,
    • and Peter D. Keightley
    Genome Res. November 2015 25: 1739-1749; Published in Advance August 10, 2015, doi:10.1101/gr.191494.115
    ...and rate of insertion and deletion mutations? (2) What is the extent of mutation rate variation between individuals within a species? (3) Is there evidence of mutation rate heterogeneity across the and what genomic properties predict the rate of mutation at individual sites? Results We conducted a mutation...
  5. 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...
  6. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...), and predicts themost probable genotype at a locus based on STR motif, length, and base quality. However, RepeatSeq uses the whole-read mapping approach, which introduces a bias toward the STR length in the reference (Gymrek et al. 2012) and thus might obscure the true STR variation spectrum. Such biases can...
  7. 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
    ...-read sequencing on the highest throughput short-read instruments; thus, achieving sufficient coverage to detect low-frequency variants (such as somatic variation) in heterogenous samples remains challenging. Targeted sequencing, on the other hand, provides the depth necessary to detect these low...
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  8. Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
    • Matthias H. Weissensteiner,
    • Marzia A. Cremona,
    • Wilfried M. Guiblet,
    • Nicholas Stoler,
    • Robert S. Harris,
    • Monika Cechova,
    • Kristin A. Eckert,
    • Francesca Chiaromonte,
    • Yi-Fei Huang,
    • and Kateryna D. Makova
    Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
    ...-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif...
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  9. 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
    ...; however, they require custom pegRNA sequences, have potential biases in the reverse transcriptase step owing to sequence-specific targets and mismatches between the primer binding sequence and the off-target, and do not directly detect nicking events, which may be the most common form of off...
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  10. Method: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
    • Christopher Jen-Yue Wei and
    • Kun Zhang
    Genome Res. April 2020 30: 602-610; Published in Advance March 3, 2020, doi:10.1101/gr.255851.119
    ...as polymerase slippage (Ellegren 2004). Estimates of microsatellite mutation rates range from 10−3 mutations per locus per cell division in mismatch repair-deficient cells, such as in some cancers, to 10−5 mutations per locus per cell division in microsatellite-stable cell types (Sun et al. 2012...
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