ArticleFrontiers in immunology2018
Computational Evaluation of B-Cell Clone Sizes in Bulk Populations.
Article in Frontiers in immunology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 44 citations in OpenAlex.
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- Single-cell analysis of cerebrospinal fluid reveals common features of neuroinflammation.Cell reports. Medicine · 2025Article
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- Dynamic establishment of recipient resident memory T cell repertoire after human intestinal transplantation.EBioMedicine · 2024Article
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- Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation in a pediatric-dominated cohort.Frontiers in immunology · 2024Article
- Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes.The Journal of experimental medicine · 2024Article
- Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation.medRxiv : the preprint server for health sciences · 2023Article
- CD27 on human memory B cells-more than just a surface marker.Clinical and experimental immunology · 2023Review
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- AIRR Community Guide to Planning and Performing AIRR-Seq Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Bulk gDNA Sequencing of Antibody Heavy-Chain Gene Rearrangements for Detection and Analysis of B-Cell Clone Distribution: A Method by the AIRR Community.Methods in molecular biology (Clifton, N.J.) · 2022Article
- mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern.Science (New York, N.Y.) · 2021Article
- mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern.bioRxiv : the preprint server for biology · 2021Article
- Altered function and differentiation of age-associated B cells contribute to the female bias in lupus mice.Nature communications · 2021Article
- Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting.Nature communications · 2021Article
- Maintenance of the human memory T cell repertoire by subset and tissue site.Genome medicine · 2021Article
- Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling.eLife · 2021Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.