SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations

Volpe, Joseph M.; Cowell, Lindsay G.; Kepler, Thomas B.

doi:10.1093/bioinformatics/btk004

Cited by 117 publications

(136 citation statements)

References 18 publications

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“…Lineage tree construction and quantitative analysis GL genes for each sequence were identified by alignment using V-QUEST (http://imgt.cines.fr/IMGT_vquest/share/textes/) and the SoDA algorithm [62] (http://dulci.org/soda). Sequences were accordingly grouped into clonally related sequence groups and aligned within each group with the most likely GL segments using ClustalW (http://www.ebi.ac.uk/clustalw).…”

Section: Cloning and Sequencingmentioning

confidence: 99%

B‐cell clonal diversification and gut‐lymph node trafficking in ulcerative colitis revealed using lineage tree analysis

et al. 2008

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In studies of inflammatory bowel diseases (IBD), research has so far focused mainly on the role of T cells. Despite evidence suggesting that B cells and the production of autoantibodies may play a significant role in IBD pathogenesis, the role of B cells in gut inflammation has not yet been thoroughly investigated. In the present study we used the new approach of lineage tree analysis for studying immunoglobulin variable region gene diversification in B cells found in the inflamed intestinal tissue of two ulcerative colitis patients as well as B cells from mucosa-associated lymph nodes (LN) in the same patients. Healthy intestinal tissue of three patients with carcinoma of the colon was used as normal control. Lineage tree shapes revealed active immune clonal diversification processes occurring in ulcerative colitis patients, which were quantitatively similar to those in healthy controls. B cells from intestinal tissues and the associated LN are shown here to be clonally related, thus supplying the first direct evidence supporting B-cell trafficking between gut and associated LN in IBD and control tissues. IntroductionUlcerative colitis (UC), one of the idiopathic inflammatory bowel diseases (IBD), is a chronic relapsing inflammatory disorder that may lead to significant impairment of gastrointestinal structure and function. UC usually involves the large intestine and extends proximally from the rectum upwards in a continuous fashion. Histologically, inflammation is usually limited to the mucosal layer and may involve ulceration and crypt abscess formation. UC has also been linked to an increased risk of gastrointestinal malignancy [1].Despite recent progress in IBD research, in human subjects as well as a wide variety of experimental animal models, many questions concerning the immunological and genetic basis of the disease remain unanswered. The mucosa-associated lymphoid 2600tissue of the gastrointestinal tract has the important tasks of, on the one hand, recognizing harmful pathogens and antigens within the gut and mounting an appropriate immune response against them and, on the other hand, knowing when and how to dampen or suppress that response once the assault has been cleared or when commensal flora or self-antigens are encountered [2]. The pathogenesis of IBD appears to be related to a disruption of that finely tuned and regulated balance which exists within the mucosa-associated lymphoid tissue, resulting in deregulated and exaggerated local immune responses. This imbalance is most probably a result of complex genetic, environmental, and immunological susceptibility factors [3].Experimental models of intestinal inflammation indicate that mucosal inflammation is probably mediated either by excessive effector T-cell function or deficient regulatory T-cell function. Exaggerated T helper 1 cell response associated with increased secretion of IL-12, IFN-g and/or TNF results in a Crohn's Disease (CD)-like colitis in these experimental models, and exaggerated T helper 2 cell response associated with increas...

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Section: Cloning and Sequencingmentioning

confidence: 99%

B‐cell clonal diversification and gut‐lymph node trafficking in ulcerative colitis revealed using lineage tree analysis

et al. 2008

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“…Sequencing was done by the UNC sequencing core facility. Sequences were aligned using Sequencher software version 4.5 (Gene Codes Corp., Ann Arbor, MI), and TCR gene identification made using SoDA [40]. The population entropy, a measure of the population diversity, is estimated using a Bayesian method we have developed (Kepler, manuscript in preparation).…”

Section: Single Cell Sequencingmentioning

confidence: 99%

Rescue of cytotoxic function in the CD8α knockout mouse by removal of MHC class II

et al. 2008

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CD8 plays an important role in the activity of cytolytic T cells (CTL). However, whether or not CD8 is required for the development of CTL has not been clearly determined. Cytotoxic activity in the CD8a knockout mouse is difficult to induce, and has only been demonstrated against allogenic MHC targets. The lack of cytotoxicity may result from impaired lineage commitment of CTL in the absence of CD8, or diminished competitiveness during selection against ( Cells from LCMV-infected mice bind more MHC I tetramer at lower concentrations than their wild-type CTL counterparts. These results demonstrate unequivocally that CD8 is not required for commitment of thymocytes to the CTL lineage.

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“…SoDA has shown several advantages compared to other tools such as JOINSOLVER and V-QUEST, e.g. capacity of batch analysis, better results [7]. Thus we use simulated sequences to compare Ab-origin with SoDA for testing the performance of Ab-origin.…”

Section: Resultsmentioning

confidence: 99%

“…Several tools have been developed trying to trace back to genetic coding from the mature immunoglobulin sequences, including some pioneer work which applied alignment methods [4,5] or consecutive matches for D segment matching [6]. Recently, a new tool based on dynamic programming named SoDA was established, which is intended to process sequences in batch [7].…”

Section: Introductionmentioning

confidence: 99%

Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin

Wang

Zheng

et al. 2007

Computational Science – ICCS 2007

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Abstract. An improved tool to explore the origin of human immunoglobulin heavy chains, named Ab-origin, has been developed. It can analyze in detail the V-D-J joints from the rearranged sequence by searching against germline databases. In addition to the known information about antibody recombination, appropriate score system and restriction of searching location are also incorporated to improve computing performance. When compared with a newly developed software SoDA, Ab-origin performed much better in both accuracy and stability, with 2, 7 and 1 percent higher for V, D and J respectively. Though only taking the human heavy chain for an example here, the algorithm also suits for the analysis of all immunoglobulin and TCR sequences.

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SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations

Cited by 117 publications

References 18 publications

B‐cell clonal diversification and gut‐lymph node trafficking in ulcerative colitis revealed using lineage tree analysis

B‐cell clonal diversification and gut‐lymph node trafficking in ulcerative colitis revealed using lineage tree analysis

Rescue of cytotoxic function in the CD8α knockout mouse by removal of MHC class II

Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin

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