IgDiscover published in Nature Communications

ctwatson · December 21, 2016, 2:56pm

Congrats to @martin_corcoran and colleagues!

ncbi.nlm.nih.gov

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.

MM Corcoran, GE Phad, C Vázquez Bernat, N Stahl-Hennig, MA Sumida, M Persson and GB Martin, Nature communications, 2016 20 12

Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool.

martin_corcoran · December 21, 2016, 4:28pm

Thanks Corey.
For those interested, the program can be downloaded from the following site - that also contains a lot of descriptions of the processes involved and more detailed instructions on its use:
IgDiscover
I know a few people here are already using the program but they may want to update with the latest version that contains whitelisting and cross-mapping ratio features that improve the range of germline sequences that can be discovered.