For publication of results, please cite:
- Current version:
No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.
Ohm-Laursen L, Nielsen M, Larsen SR, and Barington T.
Immunology. 119(2):265-77. 2006
View the abstract
In order to use the VDJsolver server for prediction on nucleotide sequences:
- Enter the sequence in the sequence window, or give a file name.
The sequence must be written using the one letter code:
Other letters are ignored and treated as unknown.
Other characters, such as whitespace and
numbers, will simply be ignored.
- Press the "Submit sequence" button.
- A www page will return the results when the prediction is ready.
Response time depends on system load.
VDJsolver was developed using Yabasic (www.yabasic.de).
The program uses the maximum likelihood
method to obtain the best fit to the following model:
where Nx designates N and P palindromic nucleotides upstream or downstream of
the D gene as indicated. Any segment may be omitted except VH and JH.
VH was compared with the IGHV3-23*01 germline gene (GenBank accession
number M99660) while JH was compared with the germline JH gene with the
highest identity score from codon 114 through the splice site among all
JH-genes in the IMGT database. The D segments were compared with any
germline D segment available in the IMGT database.
P segments were defined as 2-8 nucleotide long
extensions from the VH, Dx or JH genes reverse complementary to the
corresponding germline sequence. Maximum likelihood was determined by
running through all possible combinations of segments for a given
rearrangement and finding the combination maximizing the likelihood
score. The score was defined as the product of estimated probabilities
for any event deviating from the germline sequences in question.
Probabilities for transitions and transversions in VH, Dx and JH
segments were calculated from the number of substitutions found in the
VH region from codon 1 through 100 (assuming a 5/4 ratio of transitions
to transversions). For un-mutated sequences, the estimated Taq error
rate was used. A given N nucleotide was attributed a probability equal
to its frequency in all N segments (determined by iteration of the
model on all sequences). To reduce stochastic assignment of D segments,
D segments shorter than 4 nucleotides were not accepted and D segments
with more mutations than the 95 percentile of that expected by the
assumed mutation rate and length of the D segment (Poisson
distribution) were not accepted either. A dynamic probability for
including a D segment was introduced, dependent on the length of the
joint region (codons 101 through the downstream splice site) and the
mutation rate of the VH region. The parameters were fine tuned to find
a D gene in 5% of the sequences from a set of artificial
rearrangements made by a random permutation of the bases between the VH
and JH segments of real rearrangements. D segments were generally at
least eight nucleotides long.
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
, Morten Nielsen2
Stine R Larsen1
, and Torben Barington1*
, 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 http://services.healthtech.dtu.dk/service.php?VDJsolver-1.0
The VDJsolver 1.0 implements the JointMLc method described in the article.