Gastrointestinal Unit, School of Clinical and Molecular Medicine, Western General Hospital, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
Hum Mol Genet. 2010 Dec 15;19(24):4930-8. doi: 10.1093/hmg/ddq411. Epub 2010 Sep 21.
The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of copy number typing based on the paralogue ratio test (PRT) to assess beta-defensin copy number in more than 1500 UK DNA samples including more than 1000 cases of Crohn's disease. A subset of 625 samples was typed using both PRT-based methods and standard real-time PCR methods, from which direct comparisons highlight potentially serious shortcomings of a real-time PCR assay for typing this variant. Comparing our PRT-based results with two previous studies based only on real-time PCR, we find no evidence to support the reported association of Crohn's disease with either low or high beta-defensin copy number; furthermore, it is noteworthy that there are disagreements between different studies on the observed frequency distribution of copy number states among European controls. We suggest safeguards to be adopted in assessing and reporting the accuracy of copy number measurement, with particular emphasis on integer clustering of results, to avoid reporting of spurious associations in future case-control studies.
人类 8 号染色体上β防御素基因的拷贝数变异被认为是炎症性疾病易感性的基础，但在为充分效力的病例对照研究提供足够动力所需的规模上进行准确分型存在相当大的挑战。在这项工作中，我们使用基于等位基因比例测试 (PRT) 的准确拷贝数分型方法来评估超过 1500 个英国 DNA 样本中的β防御素拷贝数，其中包括 1000 多个克罗恩病病例。使用 PRT 方法和标准实时 PCR 方法对 625 个样本的子集进行了分型，直接比较突出了该变体的实时 PCR 检测方法的潜在严重缺陷。将我们基于 PRT 的结果与仅基于实时 PCR 的两项先前研究进行比较，我们没有发现任何证据支持先前报道的克罗恩病与低或高β防御素拷贝数之间的关联；此外，值得注意的是，不同研究之间在欧洲对照人群中观察到的拷贝数状态的分布频率存在分歧。我们建议在评估和报告拷贝数测量的准确性时采取一些保障措施，特别强调结果的整数聚类，以避免在未来的病例对照研究中报告虚假关联。
