BASIC: BCR assembly from single cells

Canzar, Stefan; Neu, Karlynn E.; Tang, Qingming; Wilson, Patrick C.; Khan, Aly A.

doi:10.1093/bioinformatics/btw631

Cited by 89 publications

(107 citation statements)

References 15 publications

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“…85 Thus, random cloning is particularly applicable to the study of active immune responses characterized by high frequencies of autoreactive ASC and this application has been greatly enhanced by highly efficient barcoding methods. [89][90][91] The latter approach is able to simultaneously analyze the transcriptional profile of each cell and can therefore categorize the functional phenotype of the cell expressing different BCR. Thus, ultra-high-throughput single-cell amplification of paired H and L chains using an emulsion-based linkage PCR can achieve these goals in millions of cells per experiment.…”

Section: Single-cell Bcr Cloning and Expression For Autoreactivity mentioning

confidence: 99%

“…88 The immune repertoire of large numbers of single cells can also be similarly interrogated using automated droplet-based emulsion platforms. [89][90][91] The latter approach is able to simultaneously analyze the transcriptional profile of each cell and can therefore categorize the functional phenotype of the cell expressing different BCR. 89,90,92,93 On the other hand, high-through- ssDNA, dsDNA, insulin, or LPS.…”

Section: Single-cell Bcr Cloning and Expression For Autoreactivity mentioning

confidence: 99%

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Understanding and measuring human B‐cell tolerance and its breakdown in autoimmune disease

Cashman

Jenks

Woodruff

et al. 2019

Immunological Reviews

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It is well established that normal immune systems are endowed with a significant degree of autoreactivity. Accordingly, effective tolerogenic mechanisms are required to censor autoreactive cells and to ultimately prevent their differentiation into pathogenic effector cells. In this review, we will discuss how immunological tolerance is enforced in the human B-cell compartment. We shall also discuss the breakdown of B-cell tolerance in human autoimmune diseases.Finally, we will review different experimental approaches to measure B-cell tolerance in human disease. | B-CELL TOLER AN CE . CHECK P OINTS AND MECHANIS MS . LE SSONS LE ARNED THROUG H MOUS E S TUD IE SMouse models have been instrumental in defining multiple checkpoints and distinct mechanisms underpinning the enforcement of B-cell tolerance. Tolerance checkpoints are classified into central and peripheral mechanisms based on anatomical location and stage AbstractThe maintenance of immunological tolerance of B lymphocytes is a complex and critical process that must be implemented as to avoid the detrimental development of autoreactivity and possible autoimmunity. Murine models have been invaluable to elucidate many of the key components in B-cell tolerance; however, translation to human homeostatic and pathogenic immune states can be difficult to assess.Functional autoreactive, flow cytometric, and single-cell cloning assays have proven to be critical in deciphering breaks in B-cell tolerance within autoimmunity; however, newer approaches to assess human B-cell tolerance may prove to be vital in the further exploration of underlying tolerance defects. In this review, we supply a comprehensive overview of human immune tolerance checkpoints with associated mechanisms of enforcement, and highlight current and future methodologies which are likely to benefit future studies into the mechanisms that become defective in human autoimmune conditions.

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Section: Single-cell Bcr Cloning and Expression For Autoreactivity mentioning

confidence: 99%

Section: Single-cell Bcr Cloning and Expression For Autoreactivity mentioning

confidence: 99%

Understanding and measuring human B‐cell tolerance and its breakdown in autoimmune disease

Cashman

Jenks

Woodruff

et al. 2019

Immunological Reviews

View full text Add to dashboard Cite

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“…For example alternative splicing (BRIE 40 , Outrigger 41 , SingleSplice 42 ), single nucleotide variants (SSrGE 43 ) and allele-specific expression (SCALE 44 ). Reconstruction of immune cell receptors is another area that has received considerable attention from tools such as BASIC 45 , TraCeR 46 and TRAPeS 47 . While tools that complete these tasks are unlikely to ever dominate scRNA-seq analysis it is likely that we will see an increase in methods for tackling specialised analyses as researchers continue to push the boundaries of what can be observed using scRNA-seq data.…”

Section: Alternative Analysesmentioning

confidence: 99%

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Zappia

Phipson

Oshlack

2017

Preprint

101

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As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers.In order to better facilitate selection of appropriate analysis tools we have been cataloguing and curating new analysis tools, as they become available, in the scRNAtools database (www.scRNA-tools.org). Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools are developed to perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and as a record of the growth of the field over time.

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“…methods that use scRNA-seq data may also be used to reconstruct the joint heavy/light chain repertoire coupled with the full transcriptome. 92,93 In 2017 10x Genomics produced chemistry kits for their Chromium machine which are capable of producing barcoded libraries for sequencing that can be separately enriched for BCR or TCR data. To date, however, we have not seen any publications that have implemented this.…”

Section: Repertoire Analys Is Approache Smentioning

confidence: 99%

Immunoglobulin gene analysis as a tool for investigating human immune responses

Dunn-Walters

Townsend

Sinclair

et al. 2018

Immunological Reviews

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SummaryThe human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self‐reactive B cells removed. Later antigen‐dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen‐specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub‐speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.

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BASIC: BCR assembly from single cells

Cited by 89 publications

References 15 publications

Understanding and measuring human B‐cell tolerance and its breakdown in autoimmune disease

Understanding and measuring human B‐cell tolerance and its breakdown in autoimmune disease

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Immunoglobulin gene analysis as a tool for investigating human immune responses

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