• Mustjoki, S. & Young, N. S. Somatic mutations in “benign” disease. N. Engl. J. Med. 384, 2039–2052 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vijg, J. & Dong, X. Pathogenic mechanisms of somatic mutation and genome mosaicism in aging. Cell 182, 12–23 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seplyarskiy, V. B. & Sunyaev, S. The origin of human mutation in light of genomic data. Nat. Rev. Genet. 22, 672–686 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Koh, G., Degasperi, A., Zou, X., Momen, S. & Nik-Zainal, S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat. Rev. Cancer 21, 619–637 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Evrony, G. D. et al. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151, 483–496 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Abascal, F. et al. Somatic mutation landscapes at single-molecule resolution. Nature 593, 405–410 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sloan, D. B., Broz, A. K., Sharbrough, J. & Wu, Z. Detecting rare mutations and DNA damage with sequencing-based methods. Trends Biotechnol. 36, 729–740 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baid, G. et al. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nat. Biotechnol. 41, 232–238 (2022).

    PubMed 

    Google Scholar
     

  • Moore, L. et al. The mutational landscape of human somatic and germline cells. Nature 597, 381–386 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Halldorsson, B. V. et al. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 363, eaau1043 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hoang, M. L. et al. Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing. Proc. Natl Acad. Sci. USA 113, 9846–9851 (2016).

  • Xing, D., Tan, L., Chang, C.-H., Li, H. & Xie, X. S. Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands. Proc. Natl Acad. Sci. USA 118, e2013106118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson, P. S. et al. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nat. Genet. 53, 1434–1442 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zou, X. et al. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nat. Cancer 2, 643–657 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanders, M. A. et al. Life without mismatch repair. Preprint at bioRxiv https://doi.org/10.1101/2021.04.14.437578 (2021).

  • Yurchenko, A. A. et al. XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature. Nat. Commun. 11, 5834 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson, P. S. et al. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat. Commun. 13, 3949 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lujan, S. A., Williams, J. S. & Kunkel, T. A. DNA polymerases divide the labor of genome replication. Trends Cell Biol. 26, 640–654 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lujan, S. A. et al. Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome Res. 24, 1751–1764 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shinbrot, E. et al. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 24, 1740–1750 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tomkova, M., Tomek, J., Kriaucionis, S. & Schuster-Böckler, B. Mutational signature distribution varies with DNA replication timing and strand asymmetry. Genome Biol. 19, 129 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haradhvala, N. J. et al. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair. Cell 164, 538–549 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bulock, C. R., Xing, X. & Shcherbakova, P. V. Mismatch repair and DNA polymerase δ proofreading prevent catastrophic accumulation of leading strand errors in cells expressing a cancer-associated DNA polymerase ϵ variant. Nucleic Acids Res. 48, 9124–9134 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shlien, A. et al. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nat. Genet. 47, 257–262 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hodel, K. P. et al. Explosive mutation accumulation triggered by heterozygous human Pol ε proofreading-deficiency is driven by suppression of mismatch repair. eLife 7, e32692 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haradhvala, N. J. et al. Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair. Nat. Commun. 9, 1746 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hodel, K. P. et al. POLE mutation spectra are shaped by the mutant allele identity, its abundance, and mismatch repair status. Mol. Cell 78, 1166–1177 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kunkel, T. A. & Erie, D. A. Eukaryotic mismatch repair in relation to DNA replication. Ann. Rev. Genet. 49, 291–313 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shinmura, K. et al. Defective repair capacity of variant proteins of the DNA glycosylase NTHL1 for 5-hydroxyuracil, an oxidation product of cytosine. Free Radic. Biol. Med. 131, 264–273 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dizdaroglu, M. Oxidatively induced DNA damage and its repair in cancer. Mutat. Res. Rev. Mutat. Res. 763, 212–245 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Madugundu, G. S., Cadet, J. & Wagner, J. R. Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA. Nucleic Acids Res. 42, 7450–7460 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, G., Mosier, S., Gocke, C. D., Lin, M.-T. & Eshleman, J. R. Cytosine deamination is a major cause of baseline noise in next-generation sequencing. Mol. Diagn. Ther. 18, 587–593 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tretyakova, N., Villalta, P. W. & Kotapati, S. Mass spectrometry of structurally modified DNA. Chem. Rev. 113, 2395–2436 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grolleman, J. E. et al. Mutational signature analysis reveals NTHL1 deficiency to cause a multi-tumor phenotype. Cancer Cell 35, 256–266 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Krokan, H. E. & Bjørås, M. Base excision repair. Cold Spring Harb. Perspect. Biol. 5, a012583 (2013).

  • Stringer, J. M., Winship, A., Liew, S. H. & Hutt, K. The capacity of oocytes for DNA repair. Cell. Mol. Life Sci. 75, 2777–2792 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Guo, Q. et al. The mutational signatures of formalin fixation on the human genome. Nat. Commun. 13, 4487 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clark, T. A., Spittle, K. E., Turner, S. W. & Korlach, J. Direct detection and sequencing of damaged DNA bases. Genome Integr. 2, 10 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Petljak, M. et al. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature 607, 799–807 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanchez-Contreras, M. et al. A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA. Nucleic Acids Res. 49, 11103–11118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ju, Y. S. et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 3, e02935 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kauppila, J. H. K. & Stewart, J. B. Mitochondrial DNA: radically free of free-radical driven mutations. Biochim. Biophys. Acta 1847, 1354–1361 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kennedy, S. R., Salk, J. J., Schmitt, M. W. & Loeb, L. A. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet. 9, e1003794 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yuan, Y. et al. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat. Genet. 52, 342–352 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fontana, G. A. & Gahlon, H. L. Mechanisms of replication and repair in mitochondrial DNA deletion formation. Nucleic Acids Res. 48, 11244–11258 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lodato, M. A. et al. Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 359, 555–559 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Matsuda, T., Matsuda, S. & Yamada, M. Mutation assay using single-molecule real-time (SMRTTM) sequencing technology. Genes Environ. 37, 15 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hestand, M. S., Houdt, J. V., Cristofoli, F. & Vermeesch, J. R. Polymerase specific error rates and profiles identified by single molecule sequencing. Mutat. Res. 784–785, 39–45 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Agarwal, A., Gupta, S. & Sharma, R. in Andrological Evaluation of Male Infertility: A Laboratory Guide (eds Agarwal, A. et al.) 101–107 (Springer, 2016).

  • Buisson, R. et al. Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. Science 364, eaaw2872 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, H., de Gannes, M. K., Luchetti, G. & Pilsner, J. R. Rapid method for the isolation of mammalian sperm DNA. BioTechniques 58, 293–300 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jenkins, T. G., Liu, L., Aston, K. I. & Carrell, D. T. Pre-screening method for somatic cell contamination in human sperm epigenetic studies. Syst. Biol. Reprod. Med. 64, 146–155 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heng, L. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).

  • Van der Auwera, G. A. & O’Connor, B. D. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. (O’Reilly Media, 2020).

  • Poplin, R. et al. A universal SNP and small-indel variant caller using deep neural networks. Nat. Biotechnol. 36, 983–987 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • R Core Team. R: A Language and Environment for Statistical Computing (2021).

  • Martin, M., Hervé, P., Valerie, O. & Nathaniel, H. Rsamtools: binary alignment (BAM), FASTA, variant call (BCF), and tabix (2020).

  • Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Knaus, B. J. & Grünwald, N. J. vcfr: a package to manipulate and visualize variant call format data in R. Mol. Ecol. Resour. 17, 44–53 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wickham, H. The split-apply-combine strategy for data analysis. J. Stat. Softw. 40, 1–29 (2011).

    Article 

    Google Scholar
     

  • Jianfeng, L. configr: an implementation of parsing and writing configuration file (2020).

  • Ching, T. qs: quick serialization of R objects https://CRAN.R-project.org/package=qs (2021).

  • Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 10, 33 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Milton, S. & Wickham, H. magrittr: a forward-pipe operator for R (2020).

  • Wickham, H., Hester, J. & Bryan, J. readr: read rectangular text data (2022).

  • Wickham, H., François, R., Henry, L. & Müller, K. dplyr: a grammar of data manipulation (2021).

  • Lee, S., Cook, D. & Lawrence, M. plyranges: a grammar of genomic data transformation. Genome Biol. 20, 4 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wickham, H. stringr: simple, consistent wrappers for common string operations (2019).

  • Eddelbuettel, D. digest: create compact hash digests of R objects (2021).

  • Lawrence, M., Gentleman, R. & Carey, V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25, 1841–1842 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kuhn, R. M., Haussler, D. & Kent, W. J. The UCSC genome browser and associated tools. Brief. Bioinform. 14, 144–161 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zerbino, D. R., Johnson, N., Juettemann, T., Wilder, S. P. & Flicek, P. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics 30, 1008–1009 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kokot, M., Długosz, M. & Deorowicz, S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33, 2759–2761 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hunt, M. et al. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14, R47 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ponstingl, H. & Ning, Z. SMALT – a new mapper for DNA sequencing reads [poster]. F1000Posters 1, 313 (2010).

  • Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. & Karolchik, D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 2204–2207 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vollger, M. R. et al. Segmental duplications and their variation in a complete human genome. Science 376, eabj6965 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0 (2015).

  • Karimzadeh, M., Ernst, C., Kundaje, A. & Hoffman, M. M. Umap and Bismap: quantifying genome and methylome mappability. Nucleic Acids Res. 46, e120 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).

  • Liao, W.-W. et al. A draft human pangenome reference. Nature 617, 312–324 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jónsson, H. et al. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature 549, 519 (2017).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Zhu, C.-H. et al. Investigation of the mechanisms leading to human sperm DNA damage based on transcriptome analysis by RNA-seq techniques. Reprod. BioMed. Online 46, 11–19 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gori, K. & Baez-Ortega, A. sigfit: flexible Bayesian inference of mutational signatures. Preprint at bioRxiv https://doi.org/10.1101/372896 (2020).

  • Cagan, A. et al. Somatic mutation rates scale with lifespan across mammals. Nature 604, 517–524 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hansen, R. S. et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139–144 (2010).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Seplyarskiy, V. B. et al. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res. 26, 174–182 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461–465 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wagih, O. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33, 3645–3647 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Freudenthal, B. D., Beard, W. A., Shock, D. D. & Wilson, S. H. Observing a DNA polymerase choose right from wrong. Cell 154, 157–168 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Verderio, P. et al. External quality assurance programs for processing methods provide evidence on impact of preanalytical variables. New Biotechnol. 72, 29–37 (2022).

    Article 
    CAS 

    Google Scholar
     



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