a scan statistic to extract causal gene clusters from case-control genome-wide rare cnv data扫描数据提取因果基因从病例对照全基因组罕见的cnv数据集群.pdfVIP

A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data Nishiyama et al. Nishiyama et al. BMC Bioinformatics 2011, 12:205 /1471-2105/12/205 (26 May 2011) Nishiyama et al. BMC Bioinformatics 2011, 12:205 /1471-2105/12/205 METHODOLOGY ARTICLE Open Access A scan statistic to extract causal gene clusters from case-control genome-wide rare CNV data 1,2* 3 3,4 5 5 6 Takeshi Nishiyama , Kunihiko Takahashi , Toshiro Tango , Dalila Pinto , Stephen W Scherer , Satoshi Takami and Hirohisa Kishino6 Abstract Background: Several statistical tests have been developed for analyzing genome-wide association data by incorporating gene pathway information in terms of gene sets. Using these methods, hundreds of gene sets are typically tested, and the tested gene sets often overlap. This overlapping greatly increases the probability of generating false positives, and the results obtained are difficult to interpret, particularly when many gene sets show statistical significance. Results: We propose a flexible statistical framework to circumvent these problems. Inspired by spatial scan statistics for detecting clustering of disease occurrence in the field of epidemiology, we developed a scan statistic to extract disease-associated gene clusters from a whole gene pathway. Extracting one or a few significant gene clusters from a global pathway limits the overall false positive probability, which results in increased statistical power, and facilitates the interpretation of test results. In the present study, we applied our method to genome-wid