{"doi":"10.1016/j.ebiom.2020.102972","title":"Ultra-efficient sequencing of T Cell receptor repertoires reveals shared responses in muscle from patients with Myositis","abstract":"BACKGROUND: Myositis, or idiopathic inflammatory myopathy (IIM), is a group disorders of unknown etiology characterized by the inflammation of skeletal muscle. The role of T cells and their antigenic targets in IIM initiation and progression is poorly understood. T cell receptor (TCR) repertoire sequencing is a powerful approach for characterizing complex T cell responses. However, current TCR sequencing methodologies are complex, expensive, or both, greatly limiting the scale of feasible studies. METHODS: Here we present Framework Region 3 AmplifiKation sequencing (\"FR3AK-seq\"), a simplified multiplex PCR-based approach for the ultra-efficient and quantitative analysis of TCR complementarity determining region 3 (CDR3) repertoires. By using minimal primer sets targeting a conserved region immediately upstream of CDR3, undistorted amplicons are analyzed via short read, single-end sequencing. We also introduce the novel algorithm Inferring Sequences via Efficiency Projection and Primer Incorporation (\"ISEPPI\") for linking CDR3s to their associated variable genes. FINDINGS: We find that FR3AK-seq is sensitive and quantitative, performing comparably to two different industry standards. FR3AK-seq and ISEPPI were used to efficiently and inexpensively characterize the T cell infiltrates of surgical muscle biopsies obtained from 145 patients with IIM and controls. A cluster of closely related TCRs was identified in samples from patients with sporadic inclusion body myositis (IBM). INTERPRETATION: The ease and minimal cost of FR3AK-seq removes critical barriers to routine, large-scale TCR CDR3 repertoire analyses, thereby democratizing the quantitative assessment of human TCR repertoires in disease-relevant target tissues. Importantly, discovery of closely related TCRs in muscle from patients with IBM provides evidence for a shared antigen-driven T cell response in this disease of unknown pathogenesis. FUNDING: This work was supported by NIH grant U24AI118633 and a Prostate Cancer Foundation Young Investigator Award.","journal":"EBioMedicine","year":2020,"id":69943,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":20,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9541,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":370638,"name":"Xuwen Alice Zheng","orcid":null,"position":1,"is_corresponding":false},{"id":250478,"name":"Iago Pinal‐Fernandez","orcid":"0000-0001-6338-9218","position":2,"is_corresponding":false},{"id":257664,"name":"José C. Milisenda","orcid":"0000-0003-0151-7872","position":3,"is_corresponding":false},{"id":257459,"name":"Lisa Christopher‐Stine","orcid":"0000-0002-7150-7306","position":4,"is_corresponding":false},{"id":257667,"name":"Thomas E. Lloyd","orcid":"0000-0003-4756-3700","position":5,"is_corresponding":false},{"id":257669,"name":"Andrew L. Mammen","orcid":"0000-0003-3732-3252","position":6,"is_corresponding":false},{"id":108428,"name":"H. Benjamin Larman","orcid":"0000-0001-7863-196X","position":7,"is_corresponding":false},{"id":369972,"name":"Janelle M. Montagne","orcid":"0000-0002-8113-1373","position":0,"is_corresponding":true}],"reference_count":64,"raw_metadata":null,"created_at":"2026-07-18T21:42:48.813846Z","pmid":"32891935","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}