PIRD: Pan Immune Repertoire Database

Wei Zhang; Longlong Wang; Ke Liu; Xiaofeng Wei; Kai Yang; Wensi Du; Shiyu Wang; Nannan Guo; Chuanchuan Ma; Lihua Luo; Jinghua Wu; Liya Lin; Fan Yang; Fei Gao; Xie Wang; Tao Li; Ruifang Zhang; Nitin K Saksena; Huanming Yang; Jian Wang; Lin Fang; Yong Hou; Xun Xu; Xiao Liu

doi:10.1093/bioinformatics/btz614

PIRD: Pan Immune Repertoire Database

Bioinformatics. 2020 Feb 1;36(3):897-903. doi: 10.1093/bioinformatics/btz614.

Authors

Wei Zhang^{1

2}, Longlong Wang^{1

2

3}, Ke Liu^{1

2}, Xiaofeng Wei^{1

2}, Kai Yang^{1

2}, Wensi Du^{1

2}, Shiyu Wang^{1

2

3}, Nannan Guo^{1

2}, Chuanchuan Ma^{1

2}, Lihua Luo^{1

2

3}, Jinghua Wu^{1

2

3}, Liya Lin^{1

2}, Fan Yang^{1

2}, Fei Gao¹, Xie Wang^{1

2}, Tao Li^{1

2}, Ruifang Zhang^{1

2}, Nitin K Saksena^{1

2}, Huanming Yang^{1

4}, Jian Wang^{1

4}, Lin Fang^{1

5}, Yong Hou^{1

2}, Xun Xu^{1

2}, Xiao Liu^{1

2}

Affiliations

¹ BGI-Shenzhen, Shenzhen 518083, China.
² China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
³ BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China.
⁴ James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
⁵ Department of Biology, University of Copenhagen, Copenhagen, Denmark.

PMID: 31373607
DOI: 10.1093/bioinformatics/btz614

Abstract

Motivation: T and B cell receptors (TCRs and BCRs) play a pivotal role in the adaptive immune system by recognizing an enormous variety of external and internal antigens. Understanding these receptors is critical for exploring the process of immunoreaction and exploiting potential applications in immunotherapy and antibody drug design. Although a large number of samples have had their TCR and BCR repertoires sequenced using high-throughput sequencing in recent years, very few databases have been constructed to store these kinds of data. To resolve this issue, we developed a database.

Results: We developed a database, the Pan Immune Repertoire Database (PIRD), located in China National GeneBank (CNGBdb), to collect and store annotated TCR and BCR sequencing data, including from Homo sapiens and other species. In addition to data storage, PIRD also provides functions of data visualization and interactive online analysis. Additionally, a manually curated database of TCRs and BCRs targeting known antigens (TBAdb) was also deposited in PIRD.

Availability and implementation: PIRD can be freely accessed at https://db.cngb.org/pird.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antigens
Databases, Factual
High-Throughput Nucleotide Sequencing*
Humans
Immunotherapy
Receptors, Antigen, T-Cell / genetics*

Substances

Antigens
Receptors, Antigen, T-Cell