Detecting ultralow-frequency mutations by Duplex Sequencing

Cited by (462)

Items 301–400 of 462

1. De novo rates of a Trypanosoma-resistant mutation in two human populations
   Daniel R. Melamed, R. Shemer, Evgeni Bolotin, M. B. Yakass, Dorit Fink-Barkai, E. Hiadzi, K. Skorecki, Adi Livnat · 2024 · bioRxiv
2. Neutral evolution of rare cancer mutations in the computer and the clinic
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3. Sperm from infertile, oligozoospermic men have elevated mutation rates
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4. TP53 somatic evolution in cervical liquid-based cytology and blood from individuals with and without ovarian cancer and BRCA1 or BRCA2 germline mutations
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5. Application of duplex sequencing to evaluate mutagenicity of aristolochic acid and methapyrilene in Fisher 344 rats.
   S. Sahib, Jian Yan, Tao Chen · 2024 · Food and Chemical Toxicology
6. Exclusion of persistent mutations in splicing factor genes and isocitrate dehydrogenase 2 improves the prognostic power of molecular measurable residual disease assessment in acute myeloid leukemia
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7. Utility of Measurable Residual Disease (MRD) Assessment in Mantle Cell Lymphoma
   Simon Wu, P. Blombery, D. Westerman, C. Tam · 2023 · Current Treatment Options in Oncology
8. Cell-free circulating RAS mutation concentrations significantly impact the survival of metastatic colorectal cancer patients
   A. Muendlein, K. Geiger, Christine F. Heinzle, Stella Gaenger, T. Winder, L. Severgnini, P. Reimann, E. Brandtner, A. Leiherer, H. Drexel et al. · 2023 · Journal of Cancer Research and Clinical Oncology
9. Optimized variant calling for estimating kinship.
   A. Woerner, Sammed N. Mandape, Kapema Bupe Kapema, Tiffany Duque, Amy Smuts, J. King, Benjamin Crysup, Xue-Wen Wang, Meng Huang, Jian-Ye Ge et al. · 2022 · Forensic Science International: Genetics
10. Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing
    Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, H. Garresori, Satu Oltedal, R. Forthun, A. Molven, Y. Rozenholc, O. Nordgård · 2022 · Scientific Reports
11. Exhaustive circulating tumor DNA sequencing reveals the genomic landscape of Hodgkin lymphoma and facilitates ultrasensitive detection of minimal residual disease
    Sophia Sobesky, L. Mammadova, M. Cirillo, E. Drees, J. Mattlener, H. Dörr, J. Altmuller, Zhiyuan Shi, P. Bröckelmann, J. Weiss et al. · 2021 · medRxiv
12. PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations
    Izumi Yamaguchi, Takashi Watanabe, O. Ohara, Y. Hasegawa · 2019 · PLoS ONE
13. Immortalization of Different Breast Epithelial Cell Types Results in Distinct Mitochondrial Mutagenesis
    Sujin Kwon, Susan Kim, H. E. Nebeck, E. Ahn · 2019 · bioRxiv
14. Urine as an Alternative to Blood for Cancer Liquid Biopsy and Precision Medicine
    Adam Zhang, Tai-Jung Lee, Surbhi Jain, Ying-Hsiu Su · 2018 · IEEE International Conference on Bioinformatics and Biomedicine
15. A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes
    Min-Jung Kim, Si-Cho Kim, Young-Joon Kim · 2018 · Genomics & Informatics
16. Accurate detection of low-level mosaic mutations in pediatric acute lymphoblastic leukemia using single molecule tagging and deep-sequencing
    Jiangyan Yu, Željko Antić, Simon V. van Reijmersdal, Alexander Hoischen, Edwin Sonneveld, Esmé Waanders, Roland P. Kuiper · 2017 · Leukemia & lymphoma/Leukemia and lymphoma
17. Accurate in vivo population sequencing uncovers drivers of within-host genetic diversity in viruses
    Maoz Gelbart, Sheri Harari, Ya’ara Ben-Ari, T. Kustin, D. Wolf, M. Mandelboim, O. Mor, P. Pennings, A. Stern · 2018 · bioRxiv
18. Targeted Error-Suppressed Detection of Circulating Paternal DNA to Establish a Diagnosis of Gestational Trophoblastic Neoplasm.
    J. Lavoie, M. Alcaide, R. Fisher, M. Seckl, Ryan D. Morin, A. Tinker · 2017 · JCO Precision Oncology
19. Asymmetrical barcode adapter-assisted recovery of duplicate reads and error correction strategy to detect rare mutations in circulating tumor DNA
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20. Development and validation of an ultra-high sensitive next-generation sequencing assay for molecular diagnosis of clinical oncology
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21. Statistical modeling for sensitive detection of low-frequency single nucleotide variants
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22. Mitochondrial dysfunction in neurodegenerative disorders: mechanisms and therapeutic advances
    Yan Tong, Jing Na He, Linbin Zhou, Jiaxin Zhang, Bo Man Ho, Lin Du, Yolanda Wong Ying Yip, Hemlata Bisnauthsing, Poemen P. M. Chan, Clement Chee Yung Tham et al. · 2026 · Molecular Biomedicine
23. Hologenomic analysis of rectal mucus sampling for detection of adenomatous polyps and colorectal cancer
    Andrew J. Tock, Kamrun S. Patel, Emma Morales-Walker, Ling-Lan Zhang, Chris Orthodoxou, Alasdair D. Macritchie, Stephen Njoroge, O. Olaniru, Guy Mozolowski, Inês Mendes et al. · 2025 · Nature Communications
24. Adverse Outcome Pathway‐Informed Integrated Testing to Identify Chemicals Causing Genotoxicity Through Oxidative DNA Damage: Case Study on 4‐Nitroquinoline 1‐Oxide
    Elizabeth Huliganga, E. Cho, Carol D. Swartz, Andrew Williams, Leslie Recio, J. Salk, F. Marchetti, C. Yauk · 2025 · Environmental and Molecular Mutagenesis
25. Disruption of recombination machinery alters the mutational landscape in plant organellar genomes
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26. Dose-related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay
    D. Schuster, D. LeBlanc, G. Zhou, M. J. Meier, A. Dodge, P. White, Alexandra S. Long, A. Williams, C. Hobbs, A. Diesing et al. · 2024 · bioRxiv
27. CarcSeq detection of lorcaserin-induced clonal expansion of Pik3ca H1047R mutants in rat mammary tissue
    Jennifer B Faske, Meagan B. Myers, Matthew Bryant, Xiaobo He, Florence McLellen, Todd Bourcier, Barbara L. Parsons · 2024 · Toxicological Sciences
28. TopoQual polishes circular consensus sequencing data and accurately predicts quality scores
    Minindu Weerakoon, Sangjin Lee, Emily Mitchell, Haynes Heaton · 2025 · BMC Bioinformatics
29. Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells
    Bo-Hu Pan, P. Kaldhone, Alexander W. Alund, Hua Du, Xiao-Qing Guo, Jian Yan, Ying Chen, Tong Zhou, T. Robison, Tao Chen · 2021 · Nanotoxicology
30. Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients
    C. Chiou, Chih-Liang Wang, Ji-Dung Luo, Chien-Ying Liu, How-Wen Ko, Cheng-Ta Yang · 2020 · Cancer Genomics & Proteomics
31. A Streamlined and High Throughput Error-Corrected Next Generation Sequencing Method for Low Variant Allele Frequency Quantitation.
    P. McKinzie, Michelle E. Bishop · 2019 · Toxicological Sciences
32. The A, B, C, D’s of replicative DNA polymerase fidelity: utilizing high-throughput single-molecule sequencing to understand the molecular basis for DNA polymerase accuracy
    Leonardo Betancurt-Anzola, Killian C O’Connell, Vladimir Potapov, Jennifer L. Ong, Nathan A. Tanner, Ludovic Sauguet, Kelly M. Zatopek · 2025 · Nucleic Acids Research
33. MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology
    A. Dodge, Andrew Williams, D. LeBlanc, D. Schuster, Elena Esina, Charles C. Valentine, J. Salk, A. Maslov, Christ Bradley, C. Yauk et al. · 2025 · Bioinformatics Advances
34. Whole genome mutagenicity evaluation using Hawk-Seq™ demonstrates high inter-laboratory reproducibility and concordance with the transgenic rodent gene mutation assay
    S. Matsumura, Sayaka Hosoi, Takako Hirose, Yuki Otsubo, Kazutoshi Saito, Masaaki Miyazawa, Akihiro Kawade, A. Hakura, Dai Kakiuchi, Shoji Asakura et al. · 2025 · Genes and Environment
35. A side-by-side comparison of variant function measurements using deep mutational scanning and base editing
    Ivan Sokirniy, Haider Inam, Marta Tomaszkiewicz, Joshua Reynolds, David M. McCandlish, Justin R. Pritchard · 2025 · Nucleic Acids Research
36. N-Nitroso-ethylisopropylamine mutagenicity in rat liver using the cII transgenic mutation assay and Duplex Sequencing analysis of genomic DNA.
    Li Xia, Jian Yan, Ying Chen, Kamela Mitchell, Timothy J. McGovern, A. Atrakchi, R. Heflich, Tao Chen · 2025 · Chemico-Biological Interactions
37. Single-molecule DNA analysis implicates brain mitochondria pathology in bipolar disorder
    H. Ohtani, R. Ichikawa, Kanako Mori, T. Kato, Masaki Nishioka · 2025 · Molecular Psychiatry
38. TP53 somatic evolution in the normal endometrium of Black and White individuals
    E. Rios-Doria, Elizabeth U. Parker, Brendan F. Kohrn, M. Pike, CoohleenAnn Coombes, Elena Latorre-Esteves, D. Reiter, J. Fredrickson, Ronit Katz, E. M. Swisher et al. · 2025 · Gynecologic Oncology
39. Single-nucleotide level base recognition through a complex DNA tetrahedron probe
    Hong-Zhao Qiu, Qi-Ling Yang, Hai-Yan Qiu, Zhuoran Hu, Fenying Kong, Shanwen Hu · 2025 · Microchemical journal (Print)
40. Somatic MED12 Mutations in Myometrial Cells
    Yi-Nuo Li, Huma Asif, Yue-Qing Feng, Julie J Kim, Jian-Jun Wei · 2024 · Cells
41. Repeat treatment of organotypic airway cultures with ethyl methanesulfonate causes accumulation of somatic cell mutations without expansion of bronchial-carcinoma-specific cancer driver mutations.
    Yiying Wang, Yuan Le, Kelly L Harris, Ying Chen, Xi-Lin Li, Jennifer B Faske, R. A. Wynne, R. Mittelstaedt, Xuefei Cao, Jaime Miranda-Colon et al. · 2024 · Mutation Research. Genetic Toxicology and Environmental Mutagenesis
42. Progress in the application of minimal residual disease detection in multiple myeloma
    Xiaojia Zuo, Dingsheng Liu · 2021 · Journal of Hematopathology
43. Utility of Serial cfDNA NGS for Prospective Genomic Analysis of Patients on a Phase I Basket Study
    L. Smyth, Jonathan B. Reichel, Jiabin Tang, J. Patel, Fanli Meng, D. Selcuklu, B. Houck-Loomis, Dao-Qi You, A. Samoila, G. Schiavon et al. · 2021 · JCO Precision Oncology
44. Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection
    Jennifer E. Kay, Sheyla Mirabal, William E. Briley, Takafumi Kimoto, Theofilos Poutahidis, Timothy M. Ragan, Peter T. C. So, Dushan N. Wadduwage, Susan E. Erdman, Bevin P. Engelward · 2020 · Environmental and Molecular Mutagenesis
45. Development and Application of Duplex Sequencing Strategy for Cell-Free DNA (cfDNA)-Based Longitudinal Monitoring of Stage IV Colorectal Cancer.
    Saradhi Mallampati, S. Zalles, D. Duose, Peter C. Hu, L. Medeiros, Ignacio I. Wistuba, S. Kopetz, R. Luthra · 2019 · Journal of Molecular Diagnostics
46. Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity
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47. CRISPR-DS: an efficient, low DNA input method for ultra-accurate sequencing
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48. Identification of Low Allele Frequency Mosaic Mutations in Alzheimer Disease
    C. S. Frigerio, M. Fiers, T. Voet, B. de Strooper · 2017 · Neuromethods
49. Visualizing, quantifying, and manipulating mitochondrial DNA in vivo
    David L. Prole, Patrick Francis Chinnery, Nick S. Jones · 2020 · Journal of Biological Chemistry
50. The role of circulating tumor DNA in ovarian cancer
    Yiliminuer Abulajiang, Wang Ming, Yumei Wu · 2026 · Discover Oncology
51. Detection of mutations: from Ames test to duplex sequencing
    Niketa Bhawsinghka, R. Schaaper · 2026 · Frontiers in Molecular Biosciences
52. Circulating Tumor DNA Assessment in Classic Hodgkin Lymphoma: Ready for Primetime?
    T. Zamrik, B. von Tresckow, S. Alig · 2026 · Hematology/Oncology Clinics of North America
53. Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq
    Yang Zhang, H. Chao, Mu-Chun Niu, C. Grochowski, Kavya Kottapalli, Sravya V. Bhamidipati, D. Muzny, Richard A. Gibbs, Cheng-Hang Zong, H. Doddapaneni · 2025 · bioRxiv
54. Ultra-sensitive DNA sequencing maps mutations that precede cancer
    Jian Carrot‐Zhang · 2025 · Nature
55. Tissue and Sex-Specific Performance of a Cancer Driver Based Biomarker in rasH2-Tg Mice
    Kelly L Harris, Jennifer B Faske, Binsheng Gong, Barbara L. Parsons · 2025 · Environmental and Molecular Mutagenesis
56. A novel KRAS exon 2 drop-off digital PCR assay for mutation detection in cell-free DNA of cancer patients
    Bianca Addamo-De Nard, Meret Geissmann, Dilara Akhoundova, C. Pistoni, T. Brezina, M. Zoche, Achim Weber, S. Hussung, Ralph Fritsch · 2025 · Diagnostic Pathology
57. Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations
    Javier Martínez del Río, Luis Menéndez‐Arias · 2025 · Viruses
58. Enhanced Error Suppression for Accurate Detection of Low‐Frequency Variants
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59. Effect of sequencing platforms on the sensitivity of chemical mutation detection using Hawk-Seq™
    Sayaka Hosoi, Takako Hirose, S. Matsumura, Yuki Otsubo, Kazutoshi Saito, Masaaki Miyazawa, Takayoshi Suzuki, Kenichi Masumura, Kei-ichi Sugiyama · 2024 · Genes and Environment
60. Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing
    Gus Waneka, Braden Pate, J. Monroe, Daniel B. Sloan · 2024 · bioRxiv
61. A maternal germline mutator phenotype in a family affected by heritable colorectal cancer
    Candice L. Young, A. Beichman, David Mas-Ponte, Shelby L. Hemker, Luke Zhu, J. Kitzman, Brian Shirts, Kelley Harris · 2023 · medRxiv
62. MADDD-seq, a novel massively parallel sequencing tool for simultaneous detection of DNA damage and mutations
    M. Vermulst, S. Paskvan, Claire S. Chung, Kathryn Franke, Nigel Clegg, S. Minot, J. Madeoy, A. Long, Jean-François Goût, J. Bielas · 2023 · bioRxiv
63. Detection of Nine Oncogenes Amplification in Lung and Colorectal Cancer Formalin-Fixed Paraffin-Embedded Tissue Samples using Combined Next-Generation Sequencing-Based Script and Digital Droplet Polymerase Chain Reaction
    C. Bontoux, A. Guyard, A. Lupo, Karim Diallo, Khedidja Rebah, A. Hercent, Edouard Guenzi, J. Cros, J. Lamoril, K. Leroy et al. · 2023 · Cancer Control: Journal of the Moffitt Cancer Cente
64. New Insights into Adjuvant Therapy for Localized Colon Cancer
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65. Next-Generation Sequencing for Measurable Residual Disease Assessment in Acute Leukemia
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66. A mutational gradient drives somatic mutation accumulation in mitochondrial DNA and influences germline polymorphisms and genome composition
    Monica Sanchez-Contreras, Mariya T. Sweetwyne, Brendan F. Kohrn, Kristine A. Tsantilas, Michael J. Hipp, Elizabeth K. Schmidt, J. Fredrickson, Jeremy A. Whitson, M. Campbell, P. Rabinovitch et al. · 2021 · bioRxiv
67. High Fidelity Deep Sequencing Reveals No Effect of ATM, ATR, and DNA-PK Cellular DNA Damage Response Pathways on Adenovirus Mutation Rate
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68. Codon-Directed Determination of the Biological Causes of Sequence Variants in Therapeutic Proteins.
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69. Conserved patterns of somatic mutations in human peripheral blood cells
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70. Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs
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71. A guide to understanding tumour evolution through the lens of population genetics
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72. Benzo[ b ]fluoranthene Induces Mutation Accumulation and Cancer‐Relevant Mutational Signatures in Mouse Lung Alongside Steady State Levels of Chromosome Damage in Blood
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73. Multimodal liquid biopsy surveillance after pancreatectomy for pancreatic ductal adenocarcinoma: evidence and a confirmation‑gated, trial‑ready framework.
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74. URMD-Seq: A high-throughput method for scalable detection of ultra-rare mutations in the human mitochondrial genome.
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75. Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome
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76. Benchmarking UMI clustering tools for accurate detection of low-frequency variants from deep sequencing
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77. mtDeOxoGer: A machine learning-based strategy to effectively filter artifactual mutations induced by oxidative damage in high-throughput mtDNA sequencing data
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78. Challenges and proposed solutions to the adoption of cell free DNA in screening, detecting and prognosticating colorectal cancer
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79. Harnessing the power of an advanced in vitro 3D liver model and error-corrected duplex sequencing for the detection of mutational signatures
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80. The longevity effects of reduced IGF-1 signaling depend on the stability of the mitochondrial genome
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81. Quantifying the mutational landscape of retroviral and lentiviral vectors in gene therapy patients
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82. Optimizing design of genomics studies for clonal evolution analysis
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83. Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker
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84. Clinical applications of circulating tumor DNA in Hodgkin lymphoma.
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85. mitoSomatic : a tool for accurate identification of mitochondrial DNA somatic mutations without paired controls
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86. Discovery of an unusual high number of de novo mutations in sperm of older men using duplex sequencing
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87. Distinguishing excess mutations and increased cell death based on variant allele frequencies
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88. Aperture: Accurate detection of structural variations and viral integrations in circulating tumor DNA using an alignment-free algorithm
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89. Blood and saliva-derived exomes from healthy Caucasian subjects do not display overt evidence of somatic mosaicism.
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90. Assessing Measurable Residual Disease in Acute Myeloid Leukemia
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91. Unexpectedly High Subclonal Mutational Diversity in Human Colorectal Cancer and Its Significance
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92. Application of amplicon-based targeted sequencing with the molecular barcoding system to detect uncommon minor EGFR mutations in patients with treatment-naïve lung adenocarcinoma
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93. Ultra-sensitive sequencing for cancer detection reveals progressive clonal selection in normal tissue over a century of human lifespan
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94. Constructing and Visualizing Cancer Genomic Maps in 3D Spatial Context by Phenotype-based High-throughput Laser-aided Isolation and Sequencing (PHLI-seq)
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95. Novel Multiplexing Strategies for Quantification of Rare Alleles Using ddPCR.
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96. Extreme heterogeneity of human mitochondrial DNA from organelles to populations
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97. Tissue-specific mutagenicity of N-nitroso-methylphenylamine assayed by the transgenic rodent assay and duplex sequencing
    Li Xia, Jian Yan, Kamela Mitchell, R. Heflich, Ying Chen, Timothy J. McGovern, A. Atrakchi, Tao Chen · 2026 · Frontiers in Toxicology
98. Somatic variants in focal cortical malformations.
    Ignacy Czajewski, S. Baulac, S. Baldassari · 2026 · Current Opinion in Genetics and Development
99. Technical Advance Efficient and ultrasensitive identification of clinical somatic mutations by modified single duplex DNA sequencing.
    Kelsi Peneweit, A. Waalkes, Megan M. Nguyen, Scott R. Kennedy, E. Konnick, S. Salipante · 2026 · Journal of Molecular Diagnostics
100. Temporal control of mitochondrial mutagenesis reveals the fate of mtDNA mutations with age
     Sarah J. Shemtov, Eric Hwang, Claire S. Chung, Herbert Anson, Lucy Carrillo, Sang-Min Lee, Ivetta Vorobyova, J. Wan, Scott R. Kennedy, Amy R. Vandiver et al. · 2026 · bioRxiv