Here, the members of the AIRR Community Biological Resources WG have summarized the current practice regarding the use of standards and controls among its members as well as among other international AIRR-seq experts and in the literature. by DNA recombination, a process of somatic rearrangement of variable (V), diversity (D), and joining (J) genes (Tonegawa, 1983). The diversity of the resulting rearranged genes (referred as V-J and V-D-J) is very high, due to not only the combination of different germline V, D, and J genes, but also to the deletion and addition of templated (P) nucleotides and the addition of non-templated (N) nucleotides at the junctions between the rearranged genes, and somatic hypermutation of expressed IG (Papavasiliou and Schatz, 2002; Lefranc and Lefranc, 2020). The total number of potential expressed rearranged IG and TR sequences in an individual is referred to as the adaptive immune receptor repertoire (AIRR). The adaptive immune repertoire is very diverse in a healthy individual, with the theoretically possible number DLK-IN-1 of clonotypes reaching more DLK-IN-1 than 1019 different TR (Bradley and Thomas, 2019) and 1011 IG (Glanville et al., 2009), far exceeds the number of B and T cells in a given individual (Davis and Bjorkman, 1988; Freeman et al., 2009; Elhanati et al., 2015). Thanks to next-generation sequencing (NGS), the AIRR can be sampled with sufficient depth for some of its complexity Cited2 to be studied (Weinstein et al., 2009; Six et al., 2013). AIRR sequencing (AIRR-seq) provides insights into the immune status of an individual at steady-state or in altered conditions such as malignancy, autoimmune disease, immunodeficiency, infectious disease, or vaccination, and allows comparison of B- and T-cell populations between individuals and time points (Benichou et al., 2012; Kirsch et al., 2015; Dziubianau et al., 2013; Hou et al., 2016; Ghraichy et al., 2018). AIRR-seq permits the description and quantification of global diversity and characteristics of AIRR, the identification of clonal expansions, the tracking of particular clonotypes, and the prediction of their specificities (Miho et al., 2018; Zvyagin et al., 2020; Sidhom et al., 2018; Glanville et al., 2017; Huang et al., 2020; Jokinen et al., 2021; Akbar et al., 2021; Hayashi et al., 2021) as well as the antibody selection through phage display (Rouet et al., 2018; Ravn et al., 2013), thereby providing opportunities for new biomarker identification (Gittelman, 2021; Dines, 2020), therapeutic antibody discovery (Akbar et al., 2021; Richardson et al., 2021), CAR-T cell bioengineering (Sheih et al., 2020), vaccine development, cancer diagnostics and treatment (Linette et al., 2019; Zhang et al., 2018; Lu et al., 2018),?including neoantigen discovery (Chiou et al., 2021; Richters et al., 2019) and immune intervention monitoring in diverse pathologies, such as stem cell transplantation (Robinson, 2015; Fink, 2019; Jiang et al., 2019; Jacobsen et al., 2017; Theil, 2017; Link-Rachner et al., 2019; Rubelt et al., 2017; Parola et al., 2018; Georgiou et al., 2014; Arnaout et al., 2021; Anand et al., DLK-IN-1 2021). NGS-based approaches and methods have multiplied, now including high-throughput bulk sequencing of IG or TR starting from genomic DNA (gDNA) or mRNA (as cDNA), which typically provides information on one receptor chain only, and more recently to the sequencing of the two IG or TR chains expressed in a single cell, which provides information around the antigen-specific receptor. These approaches are increasingly applied, mostly to human AIRRs, but also to study AIRRs from other organisms (Chaudhary and DLK-IN-1 Wesemann, 2018; Minervina et al., 2019). Molecular protocols to amplify IG or TR chains typically rely on Polymerase Chain Reaction (PCR), such as DLK-IN-1 multiplex-PCR or RACE-PCR (Robins et al., 2009; Wang et al., 2010; DeKosky et al., 2013; Eugster et al., 2013; Heather et al., 2015; Mamedov et al., 2013). To obtain reliable and comparable AIRR-seq data, the methods for performing AIRR-seq need to fulfill a number of requirements. First, the data generated by AIRR-seq must.
Here, the members of the AIRR Community Biological Resources WG have summarized the current practice regarding the use of standards and controls among its members as well as among other international AIRR-seq experts and in the literature
