Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data

Bo Li; Taiwen Li; Binbin Wang; Ruoxu Dou; Jean-Chrisophe Pignon; Toni K Choueiri; Sabina Signoretti; Jun S Liu; Xiaole Shirley Liu

doi:10.1101/073395

bioRxiv · 10.1101/073395

Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data

Bo Li·Taiwen Li·Binbin Wang·Ruoxu Dou·Jean-Chrisophe Pignon·Toni K Choueiri·Sabina Signoretti·Jun S Liu·Xiaole Shirley Liu

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Abstract

Characterization of tissue-infiltrating T cell repertoire is critical to understanding tumor-immune interactions and autoimmune disease etiology. We present TRUST, an open source algorithm for calling the TCR transcript hypervariable CDR3 regions using unselected RNA-seq data profiled from solid tissues. TRUST achieved high sensitivity in CDR3 calling even for samples with low sequencing depth and has demonstrated utilities in its application to large tumor cohorts.

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Bo Li, Taiwen Li, Binbin Wang, Ruoxu Dou, Jean-Chrisophe Pignon, Toni K Choueiri, Sabina Signoretti, Jun S Liu, Xiaole Shirley Liu. 2016-09-05. Ultrasensitive detection of TCR hypervariable region in solid-tissue RNA-seq data. https://doi.org/10.1101/073395

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