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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

Abstract

High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing of T-cell-receptor (TCR) and B-cell-receptor (BCR) mRNA transcripts with short-read transcriptome profiling of barcoded single-cell libraries generated by droplet-based partitioning. We show that Repertoire and Gene Expression by Sequencing (RAGE-Seq) can generate accurate full-length antigen receptor sequences at nucleotide resolution, infer B-cell clonal evolution and identify alternatively spliced BCR transcripts. We apply RAGE-Seq to 7138 cells sampled from the primary tumor and draining lymph node of a breast cancer patient to track transcriptome profiles of expanded lymphocyte clones across tissues. Our results demonstrate that RAGE-Seq is a powerful method for tracking the clonal evolution from large numbers of lymphocytes applicable to the study of immunity, autoimmunity and cancer.

Type Journal
ISBN 2041-1723
Authors Singh, M.; Al-Eryani, G.; Carswell, S.; Ferguson, J. M.; Blackburn, J.; Barton, K.; Roden, D.; Luciani, F.; Giang Phan, T.; Junankar, S.; Jackson, K.; Goodnow, C. C.; Smith, M. A.; Swarbrick, A.
Responsible Garvan Author A/Prof Alex Swarbrick
Publisher Name Nature Communications
Published Date 2019-07-16
Published Volume 10
Published Issue 1
Published Pages 3120
Status Always Electronic
DOI 10.1038/s41467-019-11049-4
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/31311926
OpenAccess link to author's accepted manuscript version https://publications.gimr.garvan.org.au/open-access/15092