Bleakley Kevin, Lefranc Marie-Paule, Biau Gérard
Institut Curie, Centre de Recherche, Paris, F-75248, France.
BMC Bioinformatics. 2008 Oct 2;9:408. doi: 10.1186/1471-2105-9-408.
Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system. This trimming is followed by addition of nucleotides at random, forming the N regions (N for nucleotides) of the V-J and V-D-J junctions. These processes are crucial for creating diversity in the immune response since the number of trimmed nucleotides and the number of added nucleotides vary in each B or T cell. IMGT sequence analysis tools, IMGT/V-QUEST and IMGT/JunctionAnalysis, are able to provide detailed and accurate analysis of the final observed junction nucleotide sequences (tool "output"). However, as trimmed nucleotides can potentially be replaced by identical N region nucleotides during the process, the observed "output" represents a biased estimate of the "true trimming process."
A probabilistic approach based on an analysis of the standardized tool "output" is proposed to infer the probability distribution of the "true trimmming process" and to provide plausible biological hypotheses explaining this process. We collated a benchmark dataset of TR alpha (TRA) and TR gamma (TRG) V-J rearranged sequences and junctions analysed with IMGT/V-QUEST and IMGT/JunctionAnalysis, the nucleotide sequence analysis tools from IMGT, the international ImMunoGeneTics information system, http://imgt.cines.fr. The standardized description of the tool output is based on the IMGT-ONTOLOGY axioms and concepts. We propose a simple first-order model that attempts to transform the observed "output" probability distribution into an estimate closer to the "true trimming process" probability distribution. We use this estimate to test the hypothesis that Poisson processes are involved in trimming. This hypothesis was not rejected at standard confidence levels for three of the four trimming processes: TRAV, TRAJ and TRGV.
By using trimming of rearranged TR genes as a benchmark, we show that a probabilistic approach, applied to IMGT standardized tool "outputs" opens the way to plausible hypotheses on the events involved in the "true trimming process" and eventually to an exact quantification of trimming itself. With increasing high-throughput of standardized immunogenetics data, similar probabilistic approaches will improve understanding of processes so far only characterized by the "output" of standardized tools.
在免疫系统的B细胞和T细胞中，免疫球蛋白（IG）和T细胞受体（TR）重排过程中，可变（V）、多样（D）和连接（J）基因的末端核苷酸会被修剪。修剪之后会随机添加核苷酸，形成V-J和V-D-J连接的N区（N代表核苷酸）。这些过程对于在免疫反应中产生多样性至关重要，因为每个B细胞或T细胞中修剪的核苷酸数量和添加的核苷酸数量各不相同。国际免疫基因信息系统（IMGT）的序列分析工具IMGT/V-QUEST和IMGT/JunctionAnalysis能够对最终观察到的连接核苷酸序列（工具“输出”）进行详细而准确的分析。然而，由于在这个过程中修剪的核苷酸可能会被相同的N区核苷酸所取代，所以观察到的“输出”代表了对“真实修剪过程”的有偏差估计。
提出了一种基于对标准化工具“输出”分析的概率方法，以推断“真实修剪过程”的概率分布，并提供解释此过程的合理生物学假设。我们整理了一个TRα（TRA）和TRγ（TRG）V-J重排序列及连接的基准数据集，这些序列和连接使用IMGT/V-QUEST和IMGT/JunctionAnalysis进行了分析，IMGT是国际免疫基因信息系统（http://imgt.cines.fr）的核苷酸序列分析工具。工具输出的标准化描述基于IMGT本体公理和概念。我们提出了一个简单的一阶模型，试图将观察到的“输出”概率分布转换为更接近“真实修剪过程”概率分布的估计。我们使用这个估计来检验关于修剪过程涉及泊松过程的假设。在四个修剪过程中的三个过程（TRAV、TRAJ和TRGV）中，这个假设在标准置信水平下未被拒绝。
通过将重排的TR基因修剪作为基准，我们表明应用于IMGT标准化工具“输出”的概率方法为关于“真实修剪过程”中涉及的事件的合理假设开辟了道路，并最终实现对修剪本身的精确量化。随着标准化免疫遗传学数据高通量的增加，类似的概率方法将提高对目前仅由标准化工具“输出”所表征的过程的理解。
