Pettigrew Christopher A, Wayte Nicola, Wronski Ania, Lovelock Paul K, Spurdle Amanda B, Brown Melissa A
School of Molecular and Microbial Sciences, The University of Queensland, St Lucia, QLD, Australia.
Breast Cancer Res Treat. 2008 Jul;110(2):227-34. doi: 10.1007/s10549-007-9714-5. Epub 2007 Sep 26.
Disruption of the breast cancer susceptibility gene BRCA2 is associated with increased risk of developing breast and ovarian cancer. Over 1800 sequence changes in BRCA2 have been reported, although for many the pathogenicity is unclear. Classifying these changes remains a challenge, as they may disrupt regulatory sequences as well as the primary protein coding sequence. Sequence changes located in the splice site consensus sequences often disrupt splicing, however sequence changes located within exons are also able to alter splicing patterns. Unfortunately, the presence of these exonic splicing enhancers (ESEs) and the functional effect of variants within ESEs it is currently difficult to predict. We have previously developed a method of predicting which sequence changes within exons are likely to affect splicing, using BRCA1 as an example. In this paper, we have predicted ESEs in BRCA2 using the web-based tool ESEfinder and incorporated the same series of filters (increased threshold, 125 nt limit and evolutionary conservation of the motif) in order to identify predicted ESEs that are more likely to be functional. Initially 1114 ESEs were predicted for BRCA2, however after all the filters were included, this figure was reduced to 31, 3% of the original number of predicted ESEs. Reported unclassified sequence variants in BRCA2 were found to colocalise to 55% (17/31) of these conserved ESEs, while polymorphisms colocalised to 0 of the conserved ESEs. In summary, we have identified a subset of unclassified sequence variants in BRCA2 that may adversely affect splicing and thereby contribute to BRCA2 disruption.
乳腺癌易感基因BRCA2的破坏与患乳腺癌和卵巢癌的风险增加相关。尽管BRCA2中有超过1800个序列变化已被报道，但其中许多变化的致病性尚不清楚。对这些变化进行分类仍然是一项挑战，因为它们可能会破坏调控序列以及主要的蛋白质编码序列。位于剪接位点共有序列中的序列变化通常会破坏剪接，然而位于外显子内的序列变化也能够改变剪接模式。不幸的是，目前很难预测这些外显子剪接增强子（ESE）的存在以及ESE内变体的功能效应。我们之前以BRCA1为例，开发了一种预测外显子内哪些序列变化可能影响剪接的方法。在本文中，我们使用基于网络的工具ESEfinder预测了BRCA2中的ESE，并纳入了相同系列的筛选标准（提高阈值、125 nt限制和基序的进化保守性），以识别更有可能具有功能的预测ESE。最初预测BRCA2有1114个ESE，然而在纳入所有筛选标准后，这一数字降至31个，占预测ESE原始数量的3%。BRCA2中已报道的未分类序列变体被发现与这些保守ESE的55%（17/31）共定位，而多态性与保守ESE的共定位率为0。总之，我们在BRCA2中鉴定出了一个未分类序列变体子集，这些变体可能会对剪接产生不利影响，从而导致BRCA2破坏。
