References

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 Rearrangement.
Line Ohm-Laursen¹, Morten Nielsen², Stine R Larsen¹, and Torben Barington^1* 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.
^*Corresponding author.

Abstract

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 http://services.healthtech.dtu.dk/service.php?VDJsolver-1.0. The VDJsolver 1.0 implements the JointMLc method described in the article.

PMID: 17005006