Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2022 May 25;54(6):864-873.
doi: 10.3724/abbs.2022062.

Antibody repertoire sequencing analysis

Senxin Zhang  1 , Tiange Yang  2 , Xiaojing Liu  2 , Jiyuan Yang  1 , Xiaoqi Zheng  1
Affiliations
Review

Antibody repertoire sequencing analysis

Senxin Zhang et al. Acta Biochim Biophys Sin (Shanghai). .

Abstract

High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis, i. e., V(D)J sequence annotation, clonal phylogenetic inference, and BCR repertoire profiling and mining. Different from other reviews in this field, we emphasize background intuition and the statistical principle of each method to help biologists better understand it. Finally, we discuss data mining problems for BCR-seq data and with a highlight on recently emerging multiple-sample analysis.

Keywords: BCR repertoire analysis; high-throughput sequencing; profiling and data mining; statistical method.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

None
Figure 1
Methods for BCR repertoire preparation Multiplex PCR: regardless of the template types, degenerated primer sets targeting the V gene segments are adopted. Different colors of arrows symbolizes different primer sets targeting various V classes. When mRNA (from bulk or single cell) is used as input, reverse primers annealing to C segments or poly-A sequence are commonly used to amplify the V(D)J. While when genomic DNA is subject to library preparation, the reverse primers usually anneal to the J intron region. One-side PCR methods: In the context of using bulk mRNA as template, after reverse transcription, several cytidines are over-hanged to the 3’ end of synthesized cDNA. Then a “template switch” primer with poly-G sequence will add adaptor on this side. In bulk mRNA samples, 5’ RACE is a popular example. The biotinylated primers annealing to J intron segment are used to select the target ssDNA sequence with streptavidin. In the next step, a dsDNA “bridge primer” is used to mediate the following ligation and synthesize of the other strand. The one-side PCR strategy of single-cell samples, e.g., 5’ seq, is similar to that of bulk mRNA, and the “template switch” primers are attached to a barcoded bead for discrimination between different cell samples.
None
Figure 2
A reference analysis pipeline for BCR-seq data
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Alt FW, Zhang Y, Meng FL, Guo C, Schwer B. Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell. . 2013;152:417–429. doi: 10.1016/j.cell.2013.01.007. - DOI - PMC - PubMed
    1. Lefranc MP, Lefranc G. The Immunoglobulin FactsBook. 2001
    1. Jung D, Giallourakis C, Mostoslavsky R, Alt FW. Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus. Annu Rev Immunol. . 2006;24:541–570. doi: 10.1146/annurev.immunol.23.021704.115830. - DOI - PubMed
    1. Tonegawa S. Somatic generation of antibody diversity. Nature. . 1983;302:575–581. doi: 10.1038/302575a0. - DOI - PubMed
    1. Xu JL, Davis MM. Diversity in the CDR3 region of VH is sufficient for most antibody specificities. Immunity. . 2000;13:37–45. doi: 10.1016/S1074-7613(00)00006-6. - DOI - PubMed

MeSH terms

Substances

Grants and funding

This work was supported by the grants from the National Key R & D Program of China (No. 2018YFA0900600), the National Natural Science Foundation of China (No. 61972257), the Key Laboratory of Data Science and Intelligence Education (Hainan Normal University), the Ministry of Education (No. DSIE202002), and the Research Base of Online Education for Shanghai Middle and Primary Schools.