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TRUST4：从批量和单细胞 RNA-seq 数据重建免疫受体库。

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.

机构信息

Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.

Harvard T.H. Chan School of Public Health, Boston, MA, USA.

出版信息

Nat Methods. 2021 Jun;18(6):627-630. doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13.

DOI:10.1038/s41592-021-01142-2
PMID:33986545
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9328942/
Abstract

We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in αβ/γδ T cells and B cells from RNA-sequencing (RNA-seq) data. Compared with competing methods, TRUST4 supports both FASTQ and BAM format and is faster and more sensitive in assembling longer-even full-length-receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5' 10x Genomics platforms.

摘要

我们介绍了用于从 RNA 测序 (RNA-seq) 数据中重建 αβ/γδ T 细胞和 B 细胞中免疫受体库的 TRUST4 开源算法。与竞争方法相比，TRUST4 同时支持 FASTQ 和 BAM 格式，在组装更长的——甚至全长的受体库时速度更快、灵敏度更高。TRUST4 还可以从无需 V(D)J 富集的单细胞 RNA-seq (scRNA-seq) 数据中调用受体库序列，并且与 SMART-seq 和 5' 10x Genomics 平台兼容。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cdce/9328942/4456e976c72d/nihms-1690340-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cdce/9328942/c25efff12410/nihms-1690340-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cdce/9328942/4456e976c72d/nihms-1690340-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cdce/9328942/c25efff12410/nihms-1690340-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cdce/9328942/4456e976c72d/nihms-1690340-f0002.jpg

相似文献

[1]
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.

Nat Methods. 2021-6

[2]
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[3]
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[4]
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[5]
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[6]
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[7]
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[8]
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[9]
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[10]
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Cancer Immunol Res. 2022-7-1

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本文引用的文献

[1]
Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.

Nat Commun. 2020-6-19

[2]
Single-cell RNA counting at allele and isoform resolution using Smart-seq3.

Nat Biotechnol. 2020-5-4

[3]
Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells.

Cell. 2020-5-18

[4]
B cells, plasma cells and antibody repertoires in the tumour microenvironment.

Nat Rev Immunol. 2020-1-27

[5]
Structure-based engineering of pH-dependent antibody binding for selective targeting of solid-tumor microenvironment.

MAbs. 2020

[6]
Comprehensive Integration of Single-Cell Data.

Cell. 2019-6-6

[7]
Landscape of B cell immunity and related immune evasion in human cancers.

Nat Genet. 2019-2-11

[8]
IgA Responses to Microbiota.

Immunity. 2018-8-21

[9]
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle.

Bioinformatics. 2018-8-15

[10]
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

Genome Med. 2018-3-20

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