What is ImReP?

Overview of ImReP. (a) Schematic representation of human adaptive immune repertoire. Adaptive immune repertoire consists of four T-cell receptor loci (blue color, T-cell receptor alpha locus (TCRA); T-cell receptor beta locus (TCRB); T-cell receptor delta locus (TCRD); and T-cell receptor gamma locus (TCRG)) and three immunoglobulin loci (red color, Immunoglobulin heavy locus (IGH); Immunoglobulin kappa locus (IGK); Immunoglobulin lambda locus (IGL). Alternative name – BCR, B-cell receptor). B- and T-cell receptors contain multiple variable (V, green color), diversity (D, present only in IGH, TCRB, TCRG, violet color), joining (J, yellow color) and constant (C, blue color) gene segments. V(D)J gene segments are randomly jointed and non-templated bases (N, dark red color) are inserted at the recombination junctions. The resulting spliced T- or B-cell repertoire transcript incorporates the C segment and is translated into the antigen receptor proteins. RNA-Seq reads are derived from the rearranged immunoglobulin IG and TCR loci. Reads entirely aligned to genes of B- and T-cell receptors are inferred from mapped reads (black color). Reads with extensive somatic hypermutations and reads spanning the V(D)J recombination are inferred from the unmapped reads (grey color). Complementarity determining region 3 (CDR3) is the most variable region of the three CDR regions and is used to identify T/B-cell receptor clonotypes—a group of clones with identical CDR3 amino acid sequences. (b) Receptor derived reads spanning V(D)J recombinations are identified from unmapped reads and assembled into the CDR3 sequences. We first scan the amino acid sequences of the read and determine the putative CDR3 boundaries defined by last conserved cysteine encoded by the V gene and the conserved phenylalanine (for TCR) or tryptophan (for BCR) of J gene. Given the putative CDR3
boundaries, we check the prefix and suffix of the read to match the suffix of V and prefix of J genes, respectively. (c-d) In case a read overlaps with only the V or J gene, we perform the second stage of ImReP to match such reads based on the overlap of CDR3 sequence using suffix tree.