No Evidence for the use of DIR, D-D Fusions, Chromosome 15 Open
Reading Frames or VH Replacement in the Peripheral Repertoire Was Found
when Applying an Improved Algorithm, JointML, to 6329 Human IgH
Line Ohm-Laursen1, Morten Nielsen2,
Stine R Larsen1, and Torben Barington1*
Immunology., 119(2):265-77, 2006.
1Department of Clinical Immunology, Odense University Hospital, Denmark.
2Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Lyngby, Denmark.
Antibody diversity is created by imprecise joining of the V-, (D-) and
J-gene segments of the heavy and light chain loci. Analysis of
rearrangements is complicated by somatic hypermutations and the
uncertainty of the sources of gene segments and the precise way they
recombine. It has been suggested that DIR and chromosome 15 open
reading frames (OR15) can replace conventional D genes, that two or
inverted D genes may be used and that the repertoire can be further
diversified by VH replacement. Safe conclusions require large,
well-defined sequence samples and algorithms minimizing stochastic
assignment of segments.
Two computer programs were developed for analysis of heavy chain
joints. JointHMM is a profile hidden Markow model while JointML is a
maximum likelihood based method taking the lengths of the joint and the
mutational status of the VH gene into account. The programs were
applied to a set of 6329 clonally unrelated rearrangements. A
conventional D gene was found in 80% of un-mutated sequences and 64% of
mutated sequences while D gene assignment was kept below 5% in
artificial (randomly permutated) rearrangements. No evidence for the
use of DIR, OR15, multiple D genes or VH replacements was found while
inverted D genes were used in less than 0.1% of the sequences. JointML
was shown to have a higher predictive performance when it comes to
D-gene assignment in mutated and un-mutated sequences than four other
publicly available programs. An online version 1.0 of JointML is
available at www.cbs.dtu.dk/services/VDJsolver.
The VDJsolver 1.0 implements the JointMLc method described in the article.