Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery

• DOI: 10.1016/j.molimm.2017.03.012
• Publication Date: 2017-04-04T20:06:25Z
• Authors: Ufuk Kirik; Lennart Greiff; Fredrik Levander; Mats Ohlin
• Keywords: IGHV@; Antibody Repertoire

Analysis of antibody repertoire development and specific responses important for e.g. autoimmune conditions, allergy, protection against disease is supported by high throughput sequencing associated bioinformatics pipelines that describe the diversity encoded variable domains. Proper assignment sequences to germline genes are many such processes, instance in analysis somatic hypermutation. Germline gene inference from antibody-encoding transcriptomes, using tools as TIgGER or IgDiscover, has a potential enhance quality analyses. These may also be used identify not previously known. In this study, we exploited software define aspects settings pre-existing knowledge affect outcome inference. Furthermore, demonstrate capacity IGHJ IGHD haplotype inference, whenever subjects heterozygous with respect genes, lend support IGHV general, identification novel alleles presently recognized reference directories. We propose shall, possible, future best practice IGHJ-directed was haplotypes expressing some genes. particular, identified did express several major IGHV1-8, IGHV3-9, IGHV3-15, IGHV1-18, IGHV3-21, IGHV3-23. envisage will provide an efficient approach further studies link between available immunoglobulin outcomes immune responses.