RNase H–dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

(2018) Laura E. MacConaill et al.   BMC GENOMICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification

(2018) Ke-Yue Ma et al.   Frontiers in Immunology

A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens

(2018) Zhuting Hu et al.   BLOOD

Organoid Modeling of the Tumor Immune Microenvironment

(2018) James T. Neal et al.   CELL

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state

(2017) Shaked Afik et al.   NUCLEIC ACIDS RESEARCH

T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire

(2017) John F. Beausang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Erratum for the Research Article: “Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance” by W. Roh, P.-L. Chen, A. Reuben, C. N. Spencer, P. A. Prieto, J. P. Miller, V. Gopalakrishnan, F. Wang, Z. A. Cooper, S. M. Reddy, C. Gumbs, L. Little, Q. Chang, W.-S.Chen, K. Wani, M. P. De Macedo, E. Chen, J. L. Austin-Breneman, H. Jiang, J. Roszik, M. T. Tetzlaff, M. A. Davies, J. E. Gershenwald, H. Tawbi, A. J. Lazar, P. Hwu, W.-J. Hwu, A. Diab, I. C. Glitza, S. P. Patel, S. E. Woodman, R. N. Amaria, V. G. Prieto, J. Hu, P. Sharma, J. P. Allison, L. Chin, J. Zhang, J. A. Wargo, P. A. Futreal

(2017)   Science Translational Medicine

A rapid method to verify single-cell deposition setup for cell sorters

(2016) Olivia Roos Rodrigues et al.   CYTOMETRY PART A

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

(2016) Auda A Eltahla et al.   IMMUNOLOGY AND CELL BIOLOGY

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

High-quality full-length immunoglobulin profiling with unique molecular barcoding

(2016) M A Turchaninova et al.   Nature Protocols

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

(2016) David Redmond et al.   Genome Medicine

Intratumoral expression levels of PD-L1, GZMA, and HLA-A along with oligoclonal T cell expansion associate with response to nivolumab in metastatic melanoma

(2016) Hiroyuki Inoue et al.   OncoImmunology

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers

(2015) Evgeny S. Egorov et al.   JOURNAL OF IMMUNOLOGY

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

High-throughput pairing of T cell receptor α and β sequences

(2015) Bryan Howie et al.   Science Translational Medicine

Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma

(2015) Michael A. Postow et al.   Journal for ImmunoTherapy of Cancer

Age-Related Decrease in TCR Repertoire Diversity Measured with Deep and Normalized Sequence Profiling

(2014) O. V. Britanova et al.   JOURNAL OF IMMUNOLOGY

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Improved Survival with T Cell Clonotype Stability After Anti-CTLA-4 Treatment in Cancer Patients

(2014) E. Cha et al.   Science Translational Medicine

Distinct immunological mechanisms of CTLA-4 and PD-1 blockade revealed by analyzing TCR usage in blood lymphocytes

(2014) Lidia Robert et al.   OncoImmunology

RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

(2011) Joseph R Dobosy et al.   BMC BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

Deep Sequencing of the Human TCR  and TCR  Repertoires Suggests that TCR  Rearranges After    and    T Cell Commitment

(2011) A. M. Sherwood et al.   Science Translational Medicine

Paired analysis of TCRα and TCRβ chains at the single-cell level in mice

(2010) Pradyot Dash et al.   JOURNAL OF CLINICAL INVESTIGATION

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets

(2010) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comprehensive assessment of the TCRBV repertoire in small T-cell samples by means of an improved and convenient multiplex PCR method

(2009) Sara Mariani et al.   EXPERIMENTAL HEMATOLOGY

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS