Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expan...
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| Format: | Article |
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Frontiers Media S.A.
2018-02-01
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| Series: | Frontiers in Immunology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fimmu.2018.00033/full |
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| author | Ke-Yue Ma Chenfeng He Ben S. Wendel Chad M. Williams Jun Xiao Hui Yang Hui Yang Ning Jiang Ning Jiang |
| author_facet | Ke-Yue Ma Chenfeng He Ben S. Wendel Chad M. Williams Jun Xiao Hui Yang Hui Yang Ning Jiang Ning Jiang |
| author_sort | Ke-Yue Ma |
| collection | DOAJ |
| description | Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection. Here, we describe using an MID Clustering-based IR-Seq (MIDCIRS) method to quantitatively study TCR RNA molecule copy number and clonality in T cells. First, we demonstrated the necessity of performing MID sub-clustering to eliminate erroneous sequences. Further, we showed that MIDCIRS enables a sensitive detection of a single cell in as many as one million naïve T cells and an accurate estimation of the degree of T cell clonal expression. The demonstrated accuracy, sensitivity, and wide dynamic range of MIDCIRS TCR-seq provide foundations for future applications in both basic research and clinical settings. |
| first_indexed | 2024-12-22T19:42:04Z |
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| id | doaj.art-84ba639a163f4fa9be365cf2db66f1c4 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-22T19:42:04Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-84ba639a163f4fa9be365cf2db66f1c42022-12-21T18:14:49ZengFrontiers Media S.A.Frontiers in Immunology1664-32242018-02-01910.3389/fimmu.2018.00033313185Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size QuantificationKe-Yue Ma0Chenfeng He1Ben S. Wendel2Chad M. Williams3Jun Xiao4Hui Yang5Hui Yang6Ning Jiang7Ning Jiang8Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United StatesDepartment of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United StatesMcKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United StatesDepartment of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United StatesImmuDX, LLC, Austin, TX, United StatesSchool of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, ChinaResearch Center of Special Environmental Biomechanics & Medical Engineering, Xi’an, Shaanxi, ChinaInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United StatesDepartment of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United StatesUnique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection. Here, we describe using an MID Clustering-based IR-Seq (MIDCIRS) method to quantitatively study TCR RNA molecule copy number and clonality in T cells. First, we demonstrated the necessity of performing MID sub-clustering to eliminate erroneous sequences. Further, we showed that MIDCIRS enables a sensitive detection of a single cell in as many as one million naïve T cells and an accurate estimation of the degree of T cell clonal expression. The demonstrated accuracy, sensitivity, and wide dynamic range of MIDCIRS TCR-seq provide foundations for future applications in both basic research and clinical settings.http://journal.frontiersin.org/article/10.3389/fimmu.2018.00033/fullMID clustering-based IR-Seq TCR repertoire sequencingmolecular identifierssub-clusteringnaïve T cellsCMV-specific T cells |
| spellingShingle | Ke-Yue Ma Chenfeng He Ben S. Wendel Chad M. Williams Jun Xiao Hui Yang Hui Yang Ning Jiang Ning Jiang Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification Frontiers in Immunology MID clustering-based IR-Seq TCR repertoire sequencing molecular identifiers sub-clustering naïve T cells CMV-specific T cells |
| title | Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification |
| title_full | Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification |
| title_fullStr | Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification |
| title_full_unstemmed | Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification |
| title_short | Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification |
| title_sort | immune repertoire sequencing using molecular identifiers enables accurate clonality discovery and clone size quantification |
| topic | MID clustering-based IR-Seq TCR repertoire sequencing molecular identifiers sub-clustering naïve T cells CMV-specific T cells |
| url | http://journal.frontiersin.org/article/10.3389/fimmu.2018.00033/full |
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