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However the conventional statistical corrections on locus-specific multiple tests usually result in lower power as the number of markers increases. Alternatively, we propose here the application of the longest significant run (<jats:italic>LSR<\/jats:italic>) method to estimate a region-specific p-value to provide an index for the most likely candidate region.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>An advantage of the<jats:italic>LSR<\/jats:italic>method relative to procedures based on genotypic data is that only p-value data are needed and hence can be applied extensively to different study designs. In this study the proposed<jats:italic>LSR<\/jats:italic>method was compared with commonly used methods such as Bonferroni's method and FDR controlling method. We found that while all methods provide good control over false positive rate,<jats:italic>LSR<\/jats:italic>has much better power and false discovery rate. In the authentic analysis on psoriasis and asthma disease data, the<jats:italic>LSR<\/jats:italic>method successfully identified important candidate regions and replicated the results of previous association studies.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The proposed<jats:italic>LSR<\/jats:italic>method provides an efficient exploratory tool for the analysis of sequences of dense genetic markers. Our results show that the<jats:italic>LSR<\/jats:italic>method has better power and lower false discovery rate comparing with the locus-specific multiple tests.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-9-246","type":"journal-article","created":{"date-parts":[[2008,5,27]],"date-time":"2008-05-27T18:11:55Z","timestamp":1211911915000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Using the longest significance run to estimate region-specific p-values in genetic association mapping studies"],"prefix":"10.1186","volume":"9","author":[{"given":"Ie-Bin","family":"Lian","sequence":"first","affiliation":[]},{"given":"Yi-Hsien","family":"Lin","sequence":"additional","affiliation":[]},{"given":"Ying-Chao","family":"Lin","sequence":"additional","affiliation":[]},{"given":"Hsin-Chou","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Chee-Jang","family":"Chang","sequence":"additional","affiliation":[]},{"given":"Cathy SJ","family":"Fann","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,5,27]]},"reference":[{"key":"2231_CR1","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/ng1801","volume":"38","author":"JC Barrett","year":"2006","unstructured":"Barrett JC, Cardon LR: Evaluating coverage of genome-wide association studies. 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