The Experts below are selected from a list of 21681 Experts worldwide ranked by ideXlab platform
Ning Jiang - One of the best experts on this subject based on the ideXlab platform.
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Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Frontiers in immunology, 2018Co-Authors: Ke Yue, Ben S. Wendel, Jun Xiao, Chad M. Williams, Hui Yang, Ning JiangAbstract: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 naive 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.
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accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Susan K. Pierce, Peter D Crompton, Jun Xiao, Ke Yue, Pengyu Ren, Keke Chen, Ning JiangAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage Repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody Repertoire diversification in infants and toddlers. Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative Repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Study human antibody Repertoire in malaria using ultra accurate Immune Repertoire sequencing (TECH2P.931)
Journal of Immunology, 2015Co-Authors: Ning Jiang, Ben S. WendelAbstract:Recently developed Immune Repertoire sequencing (IR-seq) has become a useful tool to quantify the composition of the various antigen receptor Repertoires, such as antibody and T cell receptor. However, early versions of IR-seq suffer significantly from high amplification bias and high sequencing errors. In this study, we developed an improved IR-seq method that clusters antibody sequences within each molecular identifier group to further separate different Ig transcripts that have been tagged with the same molecular identifier. We first validated this method by using naive B cells sorted to different amounts. Analysis showed that our methods has significantly improved the sequence accuracy and diversity coverage. In addition, it enables us to examine small number of cells, such as memory and plasmablasts. We used this method to study antibody Repertoire in children who experienced malaria in Africa. Epidemiology studies showed that children under 5 are most vulnerable to malaria with more than 460,000 cases of malaria caused death in children younger than 5 in Africa in 2012. However, little is known on how immunity toward malaria is established. We sequenced children from as young as 3 month to 10 year old and observed many traits in antibody diversity and mutations that correlate with age and confer protection, demonstrating the power of systems immunology approach to study infection.
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High-throughput high-accuracy Immune Repertoire sequencing (TECH1P.841)
Journal of Immunology, 2014Co-Authors: Ning JiangAbstract:Using VDJ recombination, the human Immune system contains hundreds of billions of B and T cells that each expresses a unique antigen receptor through a gene recombination mechanism. This “Immune Repertoire” forms the base of a safety net that protects each individuals against infections and cancers, with particular lymphocytes proliferating in response to antigenic stimulation. Recently developed Immune Repertoire sequencing technology has enabled us to quantitatively study the Immune Repertoire in response to vaccination. However, high rate of errors generated from sequencing the PCR amplification process imposed a challenge on accurate determining Repertoire diversity and somatic hypermutations. Recently, we developed a RNA barcoding technology that significantly reduced the error rate from 10-3 to 10-5 nt. This new method greatly improved the over-all diversity and mutation estimates and enabled us to answer many questions in human natural infections.
Ben S. Wendel - One of the best experts on this subject based on the ideXlab platform.
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Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Frontiers in immunology, 2018Co-Authors: Ke Yue, Ben S. Wendel, Jun Xiao, Chad M. Williams, Hui Yang, Ning JiangAbstract: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 naive 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.
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Accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Mingjuan Qu, Stefany M. Hernandez, Ke-yue Ma, Eugene W. Liu, Chenfeng He, Peter D Crompton, Di Wu, Jun Xiao, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
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accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Susan K. Pierce, Peter D Crompton, Jun Xiao, Ke Yue, Pengyu Ren, Keke Chen, Ning JiangAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage Repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody Repertoire diversification in infants and toddlers. Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative Repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Peter D Crompton, Jun Xiao, Ke Yue, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the Repertoire response to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
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Study human antibody Repertoire in malaria using ultra accurate Immune Repertoire sequencing (TECH2P.931)
Journal of Immunology, 2015Co-Authors: Ning Jiang, Ben S. WendelAbstract:Recently developed Immune Repertoire sequencing (IR-seq) has become a useful tool to quantify the composition of the various antigen receptor Repertoires, such as antibody and T cell receptor. However, early versions of IR-seq suffer significantly from high amplification bias and high sequencing errors. In this study, we developed an improved IR-seq method that clusters antibody sequences within each molecular identifier group to further separate different Ig transcripts that have been tagged with the same molecular identifier. We first validated this method by using naive B cells sorted to different amounts. Analysis showed that our methods has significantly improved the sequence accuracy and diversity coverage. In addition, it enables us to examine small number of cells, such as memory and plasmablasts. We used this method to study antibody Repertoire in children who experienced malaria in Africa. Epidemiology studies showed that children under 5 are most vulnerable to malaria with more than 460,000 cases of malaria caused death in children younger than 5 in Africa in 2012. However, little is known on how immunity toward malaria is established. We sequenced children from as young as 3 month to 10 year old and observed many traits in antibody diversity and mutations that correlate with age and confer protection, demonstrating the power of systems immunology approach to study infection.
Susan K. Pierce - One of the best experts on this subject based on the ideXlab platform.
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Accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Mingjuan Qu, Stefany M. Hernandez, Ke-yue Ma, Eugene W. Liu, Chenfeng He, Peter D Crompton, Di Wu, Jun Xiao, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
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accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Susan K. Pierce, Peter D Crompton, Jun Xiao, Ke Yue, Pengyu Ren, Keke Chen, Ning JiangAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage Repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody Repertoire diversification in infants and toddlers. Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative Repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Peter D Crompton, Jun Xiao, Ke Yue, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the Repertoire response to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
Jun Xiao - One of the best experts on this subject based on the ideXlab platform.
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Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Frontiers in immunology, 2018Co-Authors: Ke Yue, Ben S. Wendel, Jun Xiao, Chad M. Williams, Hui Yang, Ning JiangAbstract: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 naive 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.
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Accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Mingjuan Qu, Stefany M. Hernandez, Ke-yue Ma, Eugene W. Liu, Chenfeng He, Peter D Crompton, Di Wu, Jun Xiao, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
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accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Susan K. Pierce, Peter D Crompton, Jun Xiao, Ke Yue, Pengyu Ren, Keke Chen, Ning JiangAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage Repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody Repertoire diversification in infants and toddlers. Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative Repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
-
Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Peter D Crompton, Jun Xiao, Ke Yue, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the Repertoire response to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
Ke Yue - One of the best experts on this subject based on the ideXlab platform.
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Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification
Frontiers in immunology, 2018Co-Authors: Ke Yue, Ben S. Wendel, Jun Xiao, Chad M. Williams, Hui Yang, Ning JiangAbstract: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 naive 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.
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accurate Immune Repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children
Nature Communications, 2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Susan K. Pierce, Peter D Crompton, Jun Xiao, Ke Yue, Pengyu Ren, Keke Chen, Ning JiangAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important for understanding Repertoire responses to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12–47 months old) with 4−8 ml of blood. Here, we show this accurate and high-coverage Repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody Repertoire diversification in infants and toddlers. Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative Repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
-
Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children
2017Co-Authors: Ben S. Wendel, Stefany M. Hernandez, Eugene W. Liu, Peter D Crompton, Jun Xiao, Ke Yue, Susan K. PierceAbstract:Accurately measuring antibody Repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the Repertoire response to infection and vaccination. We develop molecular identifier clustering-based Immune Repertoire sequencing (MIDCIRS) and use it to study age-related antibody Repertoire development and diversification before and during acute malaria in infants (
