SAIVGeM: Spreadsheet Analysis of Immunoglobulin V _H Gene Mutations

Abstract

The analysis of mutations in immunoglobulin heavy chain variable (IGHV) region genes is a tedious process when performed by hand on multiple sequences. This report describes a set of linked Microsoft Excel files that perform several common analyses on large numbers of IGHV sequences. The spreadsheet analysis of immunoglobulin VH gene mutations (SAIVGeM) package determines the distribution of mutations among each nucleotide, the nature of the mutation at both the nucleotide and amino acid level, the frequency of mutation in the A/G G C/T A/T (RGYW) hotspot motifs of both strand polarity, and the distribution of replacement and silent mutations among the complementarity determining regions (CDRs) and the framework regions (FRs) of the immunoglobulin gene as defined by either the Kabat or IMGT conventions. These parameters are summarized and graphically presented where appropriate. In addition, the SAIVGeM package analyzes those mutations that occur in third positions of redundant codons. Because any nucleotide change in these positions is inherently silent, these positions can be used to study the mutational spectra without biases from the selection of protein structure.

Ubiquitin-mediated fluctuations in MHC class II facilitate efficient germinal center B cell responses

“…IGHV1-72*01 members were selected using IMGT V-QUEST and taken forward in analysis. Mutation frequencies and amino acid changes were identified using the SAIVGEM package ( Messmer, 2005 ). MiSeq analysis was performed by first merging paired-end reads using PANDAseq ( Masella et al, 2012 ).…”