PLoS Computational Biology
Public Library of Science
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Inferring the immune response from repertoire sequencing
Volume: 16, Issue: 4
DOI 10.1371/journal.pcbi.1007873
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Abstract

High-throughput immune repertoire sequencing (RepSeq) experiments are becoming a common way to study the diversity, structure and composition of lymphocyte repertoires, promising to yield unique insight into individuals’ past infection history. However, the analysis of these sequences remains challenging, especially when comparing two different temporal or tissue samples. Here we develop a new theoretical approach and methodology to extract the characteristics of the lymphocyte repertoire response from different samples. The method is specifically tailored to RepSeq experiments and accounts for the multiple sources of noise present in these experiments. Its output provides expansion parameters, as well as a list of potentially responding clonotypes. We apply the method to describe the response to yellow fever vaccine obtained from samples taken at different time points. We also use our results to estimate the diversity and clone size statistics from data.

https://www.researchpad.co/tools/openurl?pubtype=article&doi=10.1371/journal.pcbi.1007873&title=Inferring the immune response from repertoire sequencing&author=Maximilian Puelma Touzel,Aleksandra M. Walczak,Thierry Mora,Miles P. Davenport,&keyword=&subject=Research Article,Biology and Life Sciences,Molecular Biology,Molecular Biology Techniques,Cloning,Research and Analysis Methods,Molecular Biology Techniques,Cloning,Biology and Life Sciences,Immunology,Vaccination and Immunization,Medicine and Health Sciences,Immunology,Vaccination and Immunization,Medicine and Health Sciences,Public and Occupational Health,Preventive Medicine,Vaccination and Immunization,Research and Analysis Methods,Mathematical and Statistical Techniques,Mathematical Models,Biology and Life Sciences,Immunology,Immune Response,Medicine and Health Sciences,Immunology,Immune Response,Medicine and Health Sciences,Infectious Diseases,Viral Diseases,Yellow Fever,Biology and Life Sciences,Genetics,Gene Expression,Biology and life sciences,Molecular biology,Molecular biology techniques,Sequencing techniques,RNA sequencing,Research and analysis methods,Molecular biology techniques,Sequencing techniques,RNA sequencing,Biology and Life Sciences,Cell Biology,Cellular Types,Animal Cells,Blood Cells,White Blood Cells,Lymphocytes,Biology and Life Sciences,Cell Biology,Cellular Types,Animal Cells,Immune Cells,White Blood Cells,Lymphocytes,Biology and Life Sciences,Immunology,Immune Cells,White Blood Cells,Lymphocytes,Medicine and Health Sciences,Immunology,Immune Cells,White Blood Cells,Lymphocytes,