Titlebook: Immunogenetics; Methods and Protocol Anton W. Langerak Book‘‘‘‘‘‘‘‘ 2022 The Editor(s) (if applicable) and The Author(s) 2022 The immunome.

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Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics,c laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe the EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay, which is designed to simultaneously detect B and T cell clonal rearrangements, translocations, copy number alterations, and sequence va

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Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocyt by the somatic hypermutation process. In chronic lymphocytic leukemia (CLL), the mutational load of the clonal BcR IG expressed by the leukemic cells constitutes an important prognostic and predictive biomarker. Here, we provide a reliable methodology capable of determining the mutational status of

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NGS-Based B-Cell Receptor Repertoire AnalysisRepertoire analyses in the Context of Inborn Errors ofwith recurrent infections, but many also suffer from immune dysregulation, autoimmunity, and malignancies..Inborn errors of the immune system can cause defects in the development and selection of the B-cell receptor (BCR) repertoire. Patients with IEI can have a defect in one of the key processes of

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Generic Multiplex Digital PCR for Accurate Quantification of T Cells in Copy Number Stable and Unsth. In this chapter, we describe how T cell quantifications can be obtained from bulk DNA samples with a multiplex digital PCR experiment. The experimental setup includes the concurrent quantification of three different DNA targets within one reaction: a unique T cell DNA marker, a regional corrector

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Gene Engineering T Cells with T-Cell Receptor for Adoptive Therapy,rred, and extensively tested in vitro to accurately assess specificity and sensitivity of target recognition. Here, we present a fundamental series of protocols that cover critical preclinical parameters, thereby enabling the selection of candidate TCRs for clinical testing.

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AIRR Community Guide to Planning and Performing AIRR-Seq Experiments,er for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controllin

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Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation,eriments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the anti