Stitching immunoglobulins

BCR and antibodies are of course produced in a similar manner to TCRs, and thus the conceptual framework applies equally to those sequences. However, the existence of somatic hypermutation, far greater structural- and allelic-polymorphism, and more complicated constant region biology in the IG loci makes stitchr more difficult to apply. While we are not officially supporting the use of stitchr to make immunoglobulin sequences, we have made it possible for users to do so if they wish.

In order to achieve this, users can try using this modified version of stitchrdl to download formatted human immunoglobulin sequences from IMGT. This will create an additional species folder called ‘HUMAN-IG’ in the stitchr data folder, wherever that’s installed. Note that we strongly recommend thoroughly checking the sequences downloaded in this manner. Alternatively users may wish to curate their own germline datasets as per the Stitchr data formatting section, and move it to the stitchr data directory (stitchr -dd) themselves.

These can then be used like so:

stitchr -v IGHV3-30-3*01 -j IGHJ4*02 -cdr3 CARLSPAGGFFDYW -c IGHM*01 -s HUMAN-IG -n JQ304252
stitchr -v IGHV4-61*01 -j IGHJ3*02 -cdr3 CARITGDRGAFDIW -c IGHD*01 -s HUMAN-IG -n AF262208
stitchr -v IGHV1-69*01 -j IGHJ3*02 -cdr3 CAREVVPTFRENAFDIW -c IGHG1*01 -s HUMAN-IG -n MW177368
stitchr -v IGHV4-59*01 -j IGHJ5*02 -cdr3 CARGISWFDPW -c IGHE*01 -s HUMAN-IG -n DQ005305
stitchr -v IGKV3-20*01 -j IGKJ5*01 -cdr3 CQQYGTSRPITF -c IGKC*01 -s HUMAN-IG -n BC032451
stitchr -v IGLV1-47*01 -j IGLJ3*02 -cdr3 CAAWDDSLSGWVF -c IGLC2*01 -s HUMAN-IG -l IGLV1-47*02 -n AB064224

However for the reasons stated above we recommend using caution when applying stitchr to these loci: long read sequencing (both into the V and the C) and liberal use of the ‘seamless’ setting is recommended.

Note that the default form of the IGH constant regions supplied when using just the gene+allele is the secreted form: (where available) the membrane bound form is produced by appending ‘_M’. E.g. use IGHM*01 for the secreted form, and IGHM*01_M for the membranous.