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Review
. 2021 May 26:10:e66274.
doi: 10.7554/eLife.66274.

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Johannes Trück #  1 , Anne Eugster #  2 , Pierre Barennes #  3   4 , Christopher M Tipton  5 , Eline T Luning Prak  6 , Davide Bagnara  7 , Cinque Soto  8   9 , Jacob S Sherkow  10   11   12 , Aimee S Payne  6 , Marie-Paule Lefranc  13   14   15 , Andrew Farmer  16 ; AIRR Community; Magnolia Bostick #  16 , Encarnita Mariotti-Ferrandiz #  3
Affiliations
Review

Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling

Johannes Trück et al. Elife. .

Abstract

Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.

Keywords: B-cell Receptor (BCR); IG; T-cell Receptor (TCR); TR; antibody; immunoglobulin; immunology; inflammation; next generation sequencing (NGS).

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Conflict of interest statement

JT, AE, PB, CT, DB, CS, JS, AP, ML, EM No competing interests declared, EL is consulting or is an advisor for Roche Diagnostics Corporation, Enpicom, The Antibody Society, The American Autoimmune Related Diseases Association and IEDB. AF works for Takara Bio USA, but has no ownership or stock in the company, MB During the writing of the manuscript, Magnolia Bostick was employed by Takara Bio USA, but has no ownership or stock in the company.

Figures

Figure 1.
Figure 1.. Geographic distribution of survey participants and their AIRR-seq research interests.
(A) Map with geographic distribution of survey participants. (B) Histogram showing the principal studied organisms among the participants. The ‘Other’ category includes rat, ferret, rabbit, goat, pig, canine, bovis, cattle, chicken, fish, teleost, salmon, zebrafish, other fish species, transgenic animals. (C) Venn diagram representing the percentage of participants according to their interest in AIRR template type. (D) Pie-chart representing the distribution of survey participants according to their research interest(s). Immune system diseases and other categories are described in more detail in the bar plots (right and left). Numbers of respondents for each category are shown next to the bars.
Figure 1—figure supplement 1.
Figure 1—figure supplement 1.. Heatmaps of the areas of study depending on the interest.
Each column is a participant group and the colors represent the area studied (blue: area studied, white: area not studied). For each heatmap, areas are ordered by decreasing frequency depending on the number of participants in each group. Information about the number of areas per participant and bioinformatic skills are added below (Chi2: p=0.0064).
Figure 2.
Figure 2.. Molecular approaches used in bulk sequencing.
(A) Venn diagram representing the most important molecular approaches used and their usage and sharing among participants. Numbers of respondents in each of the four main categories are shown in parentheses. (B) Bar plots representing biological material used and molecular barcoding proportion for the two major molecular biology approaches (multiplex PCR and template switching). Only the answers of respondents who used one technology exclusively are shown (Multiplex PCR: n = 29; Template switching: n = 10). UMI = unique molecular identifier.
Figure 2—figure supplement 1.
Figure 2—figure supplement 1.. Yearly number of PubMed entries referring to single-cell AIRR sequencing (left panel) and bioinformatic AIRR reconstruction from RNA-seq studies (right panel) 1980–2020 (via https://www.ncbi.nlm.nih.gov/pubmed/, accessed on 16 January 2020).
Search query (left panel): (‘single cell’[Title/Abstract] OR ‘10X’[Title/Abstract]) AND (‘VDJ’[Title/Abstract] OR ‘TCR’[Title/Abstract] OR ‘BCR’[Title/Abstract] OR ‘b cell receptor’[Title/Abstract] OR ‘t cell receptor’[Title/Abstract] OR ‘repertoire’[Title/Abstract]) Search query (right panel): (‘rna-seq’[Title/Abstract] OR ‘rna sequencing’[Title/Abstract]) AND (‘VDJ’[Title/Abstract] OR ‘TCR’[Title/Abstract] OR ‘BCR’[Title/Abstract] OR ‘b cell receptor’[Title/Abstract] OR ‘t cell receptor’[Title/Abstract] OR ‘repertoire’[Title/Abstract]).
Figure 3.
Figure 3.. Homebrew controls and their desired applications.
(A) Most frequently used homebrew controls (total n = 47). (B) Total frequencies of desired applications of homebrew controls for respondents currently using (gray bars; total n = 47) and currently not using controls (black bars; total n = 42).
See this image and copyright information in PMC

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