Discovering Genetic Factors for psoriasis through exhaustively searching for significant second order SNP-SNP interactions.
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其它資訊
摘要In this paper, we aim at discovering genetic factors of psoriasis through searching for statistically significant SNP-SNP interactions exhaustively from two real psoriasis genome-wide association study datasets (phs000019.v1.p1 and phs000982.v1.p1) downloaded from the database of Genotypes and Phenotypes. To deal with the enormous search space, our search algorithm is accelerated with eight biological plausible interaction patterns and a pre-computed look-up table. After our search, we have discovered several SNPs having a stronger association to psoriasis when they are in combination with another SNP and these combinations may be non-linear interactions. Among the top 20 SNP-SNP interactions being found in terms of pairwise p-value and improvement metric value, we have discovered 27 novel potential psoriasis-associated SNPs where most of them are reported to be eQTLs of a number of known psoriasis-associated genes. On the other hand, we have inferred a gene network after selecting the top 10000 SNP-SNP interactions in terms of improvement metric value and we have discovered a novel long distance interaction between XXbac-BPG154L12.4 and RNU6-283P which is not a long distance haplotype and may be a new discovery. Finally, our experiments with the synthetic datasets have shown that our pre-computed look-up table technique can significantly speed up the search process.
出版社接受日期28.09.2018
著者LEE Kwan Yeung, LEUNG Kwong Sak, TANG Leung Sang Nelson, WONG Man Hon
期刊名稱Scientific Reports
出版年份2018
月份10
日期12
卷號8
文章號碼15186
國際標準期刊號2045-2322
電子國際標準期刊號2045-2322
語言英式英語
關鍵詞GWAS, SNP, psoriasis

上次更新時間 2020-07-08 於 02:00