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Zhang Y, Kohrn BF, Yang M, et al. PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage. Proc Natl Acad Sci U S A. 2021;118(31)doi: 10.1073/pnas.2023373118.
Zhang, Y., Kohrn, B. F., Yang, M., Nachmanson, D., Soong, T. R., Lee, I. H., Tao, Y., Clevers, H., Swisher, E. M., Brentnall, T. A., Loeb, L. A., Kennedy, S. R., Salk, J. J., Naxerova, K., & Risques, R. A. (2021). PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage. Proceedings of the National Academy of Sciences of the United States of America, 118(31), . https://doi.org/10.1073/pnas.2023373118
Zhang, Yuezheng, et al. "PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage." Proceedings of the National Academy of Sciences of the United States of America vol. 118,31 (2021). doi: https://doi.org/10.1073/pnas.2023373118
Zhang Y, Kohrn BF, Yang M, Nachmanson D, Soong TR, Lee IH, Tao Y, Clevers H, Swisher EM, Brentnall TA, Loeb LA, Kennedy SR, Salk JJ, Naxerova K, Risques RA. PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage. Proc Natl Acad Sci U S A. 2021 Aug 03;118(31). doi: 10.1073/pnas.2023373118. PMID: 34330826; PMCID: PMC8346827.
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Proc Natl Acad Sci U S A. 2021 Aug 03;118(31). doi: 10.1073/pnas.2023373118.

PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage.

Proceedings of the National Academy of Sciences of the United States of America

Yuezheng Zhang, Brendan F Kohrn, Ming Yang, Daniela Nachmanson, T Rinda Soong, I-Hsiu Lee, Yong Tao, Hans Clevers, Elizabeth M Swisher, Teresa A Brentnall, Lawrence A Loeb, Scott R Kennedy, Jesse J Salk, Kamila Naxerova, Rosa Ana Risques

Affiliations

  1. Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195.
  2. Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114.
  3. Department of Radiology, Harvard Medical School, Boston, MA 02114.
  4. Division of Human Biology, Fred Hutchinson Cancer Research Center, WA 98019.
  5. Division of Clinical Research, Fred Hutchinson Cancer Research Center, WA 98019.
  6. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, Netherlands.
  7. Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington Medical Center, Seattle, WA 98195.
  8. Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, WA 98195.
  9. Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA 98195.
  10. Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195; [email protected].

PMID: 34330826 PMCID: PMC8346827 DOI: 10.1073/pnas.2023373118

Abstract

Polyguanine tracts (PolyGs) are short guanine homopolymer repeats that are prone to accumulating mutations when cells divide. This feature makes them especially suitable for cell lineage tracing, which has been exploited to detect and characterize precancerous and cancerous somatic evolution. PolyG genotyping, however, is challenging because of the inherent biochemical difficulties in amplifying and sequencing repetitive regions. To overcome this limitation, we developed PolyG-DS, a next-generation sequencing (NGS) method that combines the error-correction capabilities of duplex sequencing (DS) with enrichment of PolyG loci using CRISPR-Cas9-targeted genomic fragmentation. PolyG-DS markedly reduces technical artifacts by comparing the sequences derived from the complementary strands of each original DNA molecule. We demonstrate that PolyG-DS genotyping is accurate, reproducible, and highly sensitive, enabling the detection of low-frequency alleles (<0.01) in spike-in samples using a panel of only 19 PolyG markers. PolyG-DS replicated prior results based on PolyG fragment length analysis by capillary electrophoresis, and exhibited higher sensitivity for identifying clonal expansions in the nondysplastic colon of patients with ulcerative colitis. We illustrate the utility of this method for resolving the phylogenetic relationship among precancerous lesions in ulcerative colitis and for tracing the metastatic dissemination of ovarian cancer. PolyG-DS enables the study of tumor evolution without prior knowledge of tumor driver mutations and provides a tool to perform cost-effective and easily scalable ultra-accurate NGS-based PolyG genotyping for multiple applications in biology, genetics, and cancer research.

Keywords: cancer evolution; carcinogenic fields; phylogenetic reconstruction; preneoplastic; somatic evolution

Conflict of interest statement

Competing interest statement: S.R.K., L.A.L., and R.A.R. are consultants and equity holders at TwinStrand Biosciences Inc. J.J.S. is an employee and equity holder at TwinStrand Biosciences Inc. S.R.K.

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