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Journal article
Computational Evaluation of B-Cell Clone Sizes in Bulk Populations
Frontiers in immunology, Vol.9, pp.1472-1472
29 Jun 2018
PMCID: PMC6034424
PMID: 30008715
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
B cell clones expand and contract during adaptive immune responses and can persist or grow uncontrollably in lymphoproliferative disorders. One way to monitor and track B cell clones is to perform large-scale sampling of bulk cell populations, amplifying, and sequencing antibody gene rearrangements by next-generation sequencing (NGS). Here, we describe a series of computational approaches for estimating B cell clone size in NGS immune repertoire profiling data of antibody heavy chain gene rearrangements. We define three different measures of B cell clone size—copy numbers, instances, and unique sequences—and show how these measures can be used to rank clones, analyze their diversity, and study their distribution within and between individuals. We provide a detailed, step-by-step procedure for performing these analyses using two different data sets of spleen samples from human organ donors. In the first data set, 19 independently generated biological replicates from a single individual are analyzed for B cell clone size, diversity and sampling sufficiency for clonal overlap analysis. In the second data set, B cell clones are compared in eight different organ donors. We comment upon frequently encountered pitfalls and offer practical advice with alternative approaches. Overall, we provide a series of pragmatic analytical approaches and show how different clone size measures can be used to study the clonal landscape in bulk B cell immune repertoire profiling data.
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Details
- Title
- Computational Evaluation of B-Cell Clone Sizes in Bulk Populations
- Creators
- Aaron M. Rosenfeld - Drexel UniversityWenzhao Meng - University of PennsylvaniaDora Y. Chen - University of PennsylvaniaBochao Zhang - Drexel UniversityTomer Granot - Columbia UniversityDonna L. Farber - Columbia UniversityUri Hershberg - Drexel UniversityEline T. Luning Prak - , , , , , , , ,
- Publication Details
- Frontiers in immunology, Vol.9, pp.1472-1472
- Publisher
- Frontiers Media S.A
- Grant note
- P01 AI106697, P30 CA016520 / National Institutes of Health
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Identifiers
- 991019167606504721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Immunology