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Using synthetic templates to design an unbiased multiplex PCR assay

Author

Listed:
  • Christopher S. Carlson

    (Fred Hutchinson Cancer Research Center)

  • Ryan O. Emerson

    (Adaptive Biotechnologies)

  • Anna M. Sherwood

    (Adaptive Biotechnologies)

  • Cindy Desmarais

    (Adaptive Biotechnologies)

  • Moon-Wook Chung

    (Adaptive Biotechnologies)

  • Joseph M. Parsons

    (Adaptive Biotechnologies)

  • Michelle S. Steen

    (Adaptive Biotechnologies)

  • Marissa A. LaMadrid-Herrmannsfeldt

    (Adaptive Biotechnologies)

  • David W. Williamson

    (Adaptive Biotechnologies)

  • Robert J. Livingston

    (Adaptive Biotechnologies)

  • David Wu

    (University of Washington)

  • Brent L. Wood

    (University of Washington)

  • Mark J. Rieder

    (Adaptive Biotechnologies)

  • Harlan Robins

    (Fred Hutchinson Cancer Research Center)

Abstract

T and B cell receptor loci undergo combinatorial rearrangement, generating a diverse immune receptor repertoire, which is vital for recognition of potential antigens. Here we use a multiplex PCR with a mixture of primers targeting the rearranged variable and joining segments to capture receptor diversity. Differential hybridization kinetics can introduce significant amplification biases that alter the composition of sequence libraries prepared by multiplex PCR. Using a synthetic immune receptor repertoire, we identify and minimize such biases and computationally remove residual bias after sequencing. We apply this method to a multiplex T cell receptor gamma sequencing assay. To demonstrate accuracy in a biological setting, we apply the method to monitor minimal residual disease in acute lymphoblastic leukaemia patients. A similar methodology can be extended to any adaptive immune locus.

Suggested Citation

  • Christopher S. Carlson & Ryan O. Emerson & Anna M. Sherwood & Cindy Desmarais & Moon-Wook Chung & Joseph M. Parsons & Michelle S. Steen & Marissa A. LaMadrid-Herrmannsfeldt & David W. Williamson & Rob, 2013. "Using synthetic templates to design an unbiased multiplex PCR assay," Nature Communications, Nature, vol. 4(1), pages 1-9, December.
  • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3680
    DOI: 10.1038/ncomms3680
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    Cited by:

    1. Nils-Petter Rudqvist & Maud Charpentier & Claire Lhuillier & Erik Wennerberg & Sheila Spada & Caroline Sheridan & Xi Kathy Zhou & Tuo Zhang & Silvia C. Formenti & Jennifer S. Sims & Alicia Alonso & Sa, 2023. "Immunotherapy targeting different immune compartments in combination with radiation therapy induces regression of resistant tumors," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    2. Ming Chen & Runzhe Chen & Ying Jin & Jun Li & Xin Hu & Jiexin Zhang & Junya Fujimoto & Shawna M. Hubert & Carl M. Gay & Bo Zhu & Yanhua Tian & Nicholas McGranahan & Won-Chul Lee & Julie George & Xiao , 2021. "Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    3. Simona Pagliuca & Carmelo Gurnari & Colin Hercus & Sébastien Hergalant & Sanghee Hong & Adele Dhuyser & Maud D’Aveni & Alice Aarnink & Marie Thérèse Rubio & Pierre Feugier & Francesca Ferraro & Hetty , 2023. "Leukemia relapse via genetic immune escape after allogeneic hematopoietic cell transplantation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Jani Huuhtanen & Liang Chen & Emmi Jokinen & Henna Kasanen & Tapio Lönnberg & Anna Kreutzman & Katriina Peltola & Micaela Hernberg & Chunlin Wang & Cassian Yee & Harri Lähdesmäki & Mark M. Davis & Sat, 2022. "Evolution and modulation of antigen-specific T cell responses in melanoma patients," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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