去除内含子需要分支元素,和这些元件的变体可导致异常剪接。我们旨在评估从最近的大规模研究中产生的分支点注释的价值,以选择分支点废除变体,使用遗传性癌基因作为模型。
我们从3个全基因组实验推断的和2个预测的分支点数据集中鉴定了与遗传性癌症相关的119个基因中的分支点元件。然后,我们从公共数据库中鉴定了分支点元素中出现的变体。我们比较了保护,独特的变体观察,和分支点基序内不同核苷酸的种群频率。最后,进行了选定的小基因测定,以评估错配修复基因内分支点元件上变体的剪接效应.
预测的和实验推断的分支点之间存在差的重叠。我们对癌症基因的分析表明,在-2核苷酸的变异,-1个核苷酸,和分支点的位置在实验推断的规范基序更可能是临床相关的。Minigene测定数据显示-2核苷酸对分支点基序完整性更重要,但在分支点使用中也显示出流动性。
来自癌基因分析的数据表明,很少有通过分支点废除严重影响功能的高风险等位基因。这项研究的结果为优先考虑分支点基序变体以进行进一步研究的一般方案提供了依据。
Branchpoint elements are required for intron removal, and variants at these elements can result in aberrant splicing. We aimed to assess the value of branchpoint annotations generated from recent large-scale studies to select
branchpoint-abrogating variants, using hereditary cancer genes as model.
We identified branchpoint elements in 119 genes associated with hereditary cancer from 3 genome-wide experimentally-inferred and 2 predicted
branchpoint data sets. We then identified variants that occur within
branchpoint elements from public databases. We compared conservation, unique variant observations, and population frequencies at different nucleotides within branchpoint motifs. Finally, selected minigene assays were performed to assess the splicing effect of variants at branchpoint elements within mismatch repair genes.
There was poor overlap between predicted and experimentally-inferred branchpoints. Our analysis of cancer genes suggested that variants at -2 nucleotide, -1 nucleotide, and branchpoint positions in experimentally-inferred canonical motifs are more likely to be clinically relevant. Minigene assay data showed the -2 nucleotide to be more important to branchpoint motif integrity but also showed fluidity in
branchpoint usage.
Data from cancer gene analysis suggest that there are few high-risk alleles that severely impact function via branchpoint abrogation. Results of this study inform a general scheme to prioritize branchpoint motif variants for further study.