{"id":43142,"date":"2024-06-01T22:24:14","date_gmt":"2024-06-01T14:24:14","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43142"},"modified":"2024-06-01T22:48:57","modified_gmt":"2024-06-01T14:48:57","slug":"%e6%8e%a2%e7%b4%a2%e5%ad%9f%e5%be%b7%e5%b0%94%e9%9a%8f%e6%9c%ba%e5%8c%96%e7%a0%94%e7%a9%b6%e7%9a%84%e5%88%9b%e6%96%b0%e5%b7%a5%e5%85%b7%ef%bc%9agsmr","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=43142","title":{"rendered":"\u63a2\u7d22\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u7684\u521b\u65b0\u5de5\u5177\uff1aGSMR"},"content":{"rendered":"\n<h1 class=\"wp-block-heading\"><\/h1>\n\n\n\n<p>\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\uff08Mendelian Randomization, MR\uff09\u5728\u533b\u5b66\u548c\u6d41\u884c\u75c5\u5b66\u7814\u7a76\u4e2d\u8d77\u7740\u8d8a\u6765\u8d8a\u91cd\u8981\u7684\u4f5c\u7528\u3002\u5b83\u901a\u8fc7\u5229\u7528\u57fa\u56e0\u53d8\u5f02\u4f5c\u4e3a\u5de5\u5177\u53d8\u91cf\uff0c\u63a2\u8ba8\u66b4\u9732\u56e0\u7d20\u4e0e\u75be\u75c5\u4e4b\u95f4\u7684\u56e0\u679c\u5173\u7cfb\u3002\u7136\u800c\uff0c\u5728\u5b9e\u9645\u5e94\u7528\u4e2d\uff0c\u7814\u7a76\u4eba\u5458\u5e38\u5e38\u9762\u4e34\u591a\u6548\u6027\uff08pleiotropy\uff09\u548c\u57fa\u56e0\u5173\u8054\u4e0d\u5e73\u8861\uff08linkage disequilibrium, LD\uff09\u7b49\u590d\u6742\u95ee\u9898\u3002\u4e3a\u4e86\u5e94\u5bf9\u8fd9\u4e9b\u6311\u6218\uff0c\u5e7f\u4e49\u6458\u8981\u6570\u636e\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\uff08Generalized Summary-data-based Mendelian Randomization, GSMR\uff09\u5e94\u8fd0\u800c\u751f\u3002\u672c\u6587\u5c06\u8be6\u7ec6\u4ecb\u7ecdGSMR\u7684\u529f\u80fd\u3001\u4f7f\u7528\u65b9\u6cd5\u53ca\u5176\u5728\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u7814\u7a76\u4e2d\u7684\u91cd\u8981\u6027\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u4ec0\u4e48\u662fGSMR\uff1f<\/h2>\n\n\n\n<p>GSMR\u662f\u4e00\u79cd\u57fa\u4e8e\u5e7f\u4e49\u6458\u8981\u6570\u636e\u7684\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u65b9\u6cd5\uff0c\u4e13\u4e3a\u5904\u7406\u548c\u6821\u6b63\u591a\u6548\u6027\u95ee\u9898\u800c\u8bbe\u8ba1\u3002\u5b83\u5229\u7528\u5e7f\u4e49\u7ebf\u6027\u6df7\u5408\u6a21\u578b\uff08Generalized Linear Mixed Model, GLMM\uff09\u8fdb\u884cMR\u5206\u6790\uff0c\u663e\u8457\u63d0\u9ad8\u4e86\u7ed3\u679c\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u3002GSMR\u7279\u522b\u9002\u7528\u4e8e\u5927\u89c4\u6a21\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76\uff08GWAS\uff09\u6570\u636e\u7684\u5206\u6790\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GSMR\u7684\u4e3b\u8981\u529f\u80fd<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">1. \u591a\u6548\u6027\u6821\u6b63<\/h3>\n\n\n\n<p>\u591a\u6548\u6027\u662f\u6307\u4e00\u4e2a\u57fa\u56e0\u53d8\u5f02\u5f71\u54cd\u591a\u4e2a\u8868\u578b\uff0c\u8fd9\u53ef\u80fd\u5bfc\u81f4MR\u5206\u6790\u4e2d\u7684\u504f\u501a\u3002GSMR\u901a\u8fc7\u68c0\u6d4b\u548c\u6821\u6b63\u591a\u6548\u6027\uff0c\u6709\u6548\u51cf\u5c11\u56e0\u591a\u6548\u6027\u5f15\u5165\u7684\u504f\u5dee\uff0c\u786e\u4fdd\u56e0\u679c\u63a8\u65ad\u7684\u51c6\u786e\u6027\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">2. \u5e7f\u4e49\u7ebf\u6027\u6df7\u5408\u6a21\u578b<\/h3>\n\n\n\n<p>GSMR\u91c7\u7528\u5e7f\u4e49\u7ebf\u6027\u6df7\u5408\u6a21\u578b\uff08GLMM\uff09\uff0c\u80fd\u591f\u5904\u7406\u590d\u6742\u7684\u6570\u636e\u7ed3\u6784\u3002GLMM\u8003\u8651\u4e86\u57fa\u56e0\u53d8\u5f02\u4e4b\u95f4\u7684\u5173\u8054\uff0c\u63d0\u9ad8\u4e86\u5bf9\u5927\u89c4\u6a21\u6570\u636e\u7684\u5904\u7406\u80fd\u529b\uff0c\u9002\u7528\u4e8e\u9ad8\u7ef4\u6570\u636e\u5206\u6790\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">3. \u5927\u89c4\u6a21\u6570\u636e\u5206\u6790<\/h3>\n\n\n\n<p>GSMR\u80fd\u591f\u5904\u7406\u5927\u89c4\u6a21\u7684GWAS\u6570\u636e\uff0c\u8fd9\u5bf9\u4e8e\u5f53\u524d\u5927\u91cf\u7684\u57fa\u56e0\u6570\u636e\u96c6\u5c24\u4e3a\u91cd\u8981\u3002\u5b83\u652f\u6301\u9ad8\u7ef4\u6570\u636e\u5206\u6790\uff0c\u80fd\u591f\u5728\u8f83\u77ed\u65f6\u95f4\u5185\u5b8c\u6210\u5927\u89c4\u6a21\u8ba1\u7b97\u4efb\u52a1\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">4. \u7528\u6237\u53cb\u597d\u7684\u754c\u9762<\/h3>\n\n\n\n<p>\u5c3d\u7ba1GSMR\u529f\u80fd\u5f3a\u5927\uff0c\u4f46\u5176\u7528\u6237\u754c\u9762\u8bbe\u8ba1\u7b80\u6d01\u76f4\u89c2\uff0c\u63d0\u4f9b\u4e86\u8be6\u7ec6\u7684\u4f7f\u7528\u6307\u5357\u548c\u5e2e\u52a9\u6587\u6863\uff0c\u65b9\u4fbf\u7528\u6237\u5feb\u901f\u4e0a\u624b\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u5982\u4f55\u4f7f\u7528GSMR\uff1f<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e00\uff1a\u5b89\u88c5\u548c\u52a0\u8f7dGSMR\u8f6f\u4ef6<\/h3>\n\n\n\n<p>\u9996\u5148\uff0c\u7528\u6237\u9700\u8981\u5728\u8ba1\u7b97\u673a\u4e0a\u5b89\u88c5GSMR\u8f6f\u4ef6\u3002GSMR\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u6b65\u9aa4\u5b89\u88c5\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code># \u4e0b\u8f7dGSMR\u6e90\u7801\ngit clone https:\/\/github.com\/yanglab\/gsmr.git\n\n# \u8fdb\u5165GSMR\u76ee\u5f55\u5e76\u7f16\u8bd1\u5b89\u88c5\ncd gsmr\nmake<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e8c\uff1a\u51c6\u5907\u6570\u636e<\/h3>\n\n\n\n<p>\u7528\u6237\u9700\u8981\u51c6\u5907GWAS\u6458\u8981\u7edf\u8ba1\u6570\u636e\uff0c\u5305\u62ec\u66b4\u9732\u56e0\u7d20\u548c\u7ed3\u679c\u53d8\u91cf\u7684\u6570\u636e\u3002\u786e\u4fdd\u6570\u636e\u683c\u5f0f\u7b26\u5408GSMR\u7684\u8f93\u5165\u8981\u6c42\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u4e09\uff1a\u8fd0\u884cGSMR\u5206\u6790<\/h3>\n\n\n\n<p>\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fd0\u884cGSMR\u5206\u6790\uff0c\u8fdb\u884c\u56e0\u679c\u5173\u7cfb\u63a8\u65ad\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>.\/gsmr --gwas-summary exp_data.txt --gwas-summary out_data.txt --gsmr-direction 0 --out result.txt<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">\u6b65\u9aa4\u56db\uff1a\u67e5\u770b\u548c\u89e3\u91ca\u7ed3\u679c<\/h3>\n\n\n\n<p>\u5206\u6790\u5b8c\u6210\u540e\uff0c\u7528\u6237\u53ef\u4ee5\u5728\u7ed3\u679c\u6587\u4ef6\u4e2d\u67e5\u770b\u8be6\u7ec6\u7684\u5206\u6790\u7ed3\u679c\uff0c\u5305\u62ec\u56e0\u679c\u6548\u5e94\u4f30\u8ba1\u3001\u591a\u6548\u6027\u68c0\u9a8c\u7ed3\u679c\u7b49\u3002GSMR\u8fd8\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u7ed3\u679c\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u5e2e\u52a9\u7528\u6237\u66f4\u597d\u5730\u89e3\u91ca\u548c\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GSMR\u7684\u4f18\u52bf<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">1. \u51c6\u786e\u6027\u9ad8<\/h3>\n\n\n\n<p>GSMR\u901a\u8fc7\u591a\u6548\u6027\u6821\u6b63\u548c\u5e7f\u4e49\u7ebf\u6027\u6df7\u5408\u6a21\u578b\uff0c\u5927\u5e45\u63d0\u9ad8\u4e86MR\u5206\u6790\u7684\u51c6\u786e\u6027\u3002\u5b83\u80fd\u591f\u6709\u6548\u68c0\u6d4b\u548c\u6821\u6b63\u591a\u6548\u6027\u95ee\u9898\uff0c\u51cf\u5c11\u56e0\u679c\u63a8\u65ad\u4e2d\u7684\u504f\u5dee\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">2. \u5904\u7406\u5927\u89c4\u6a21\u6570\u636e\u7684\u80fd\u529b<\/h3>\n\n\n\n<p>GSMR\u4e13\u4e3a\u5927\u89c4\u6a21\u6570\u636e\u5206\u6790\u8bbe\u8ba1\uff0c\u80fd\u591f\u5904\u7406\u9ad8\u7ef4\u57fa\u56e0\u6570\u636e\u3002\u65e0\u8bba\u662f\u5904\u7406\u6570\u767e\u4e07\u4e2aSNPs\uff0c\u8fd8\u662f\u6570\u5343\u4e2a\u8868\u578b\uff0cGSMR\u90fd\u80fd\u5728\u8f83\u77ed\u65f6\u95f4\u5185\u5b8c\u6210\u5206\u6790\u4efb\u52a1\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">3. \u7075\u6d3b\u6027\u5f3a<\/h3>\n\n\n\n<p>GSMR\u63d0\u4f9b\u591a\u79cd\u53c2\u6570\u8bbe\u7f6e\u548c\u5206\u6790\u9009\u9879\uff0c\u7528\u6237\u53ef\u4ee5\u6839\u636e\u5177\u4f53\u7684\u7814\u7a76\u9700\u6c42\uff0c\u81ea\u7531\u9009\u62e9\u548c\u8c03\u6574\u5206\u6790\u65b9\u6cd5\u3002\u5b83\u8fd8\u652f\u6301\u591a\u79cd\u6570\u636e\u683c\u5f0f\u548c\u8f93\u5165\u7c7b\u578b\uff0c\u5177\u6709\u5f88\u9ad8\u7684\u7075\u6d3b\u6027\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">4. \u6613\u4e8e\u4f7f\u7528<\/h3>\n\n\n\n<p>\u5c3d\u7ba1GSMR\u529f\u80fd\u5f3a\u5927\uff0c\u4f46\u5176\u7528\u6237\u754c\u9762\u548c\u4f7f\u7528\u6d41\u7a0b\u8bbe\u8ba1\u7b80\u6d01\u76f4\u89c2\u3002\u8be6\u7ec6\u7684\u4f7f\u7528\u6307\u5357\u548c\u5e2e\u52a9\u6587\u6863\uff0c\u4f7f\u5f97\u65e0\u8bba\u662f\u521d\u5b66\u8005\u8fd8\u662f\u8d44\u6df1\u7814\u7a76\u4eba\u5458\u90fd\u80fd\u5feb\u901f\u4e0a\u624b\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GSMR\u5728\u7814\u7a76\u4e2d\u7684\u5e94\u7528\u6848\u4f8b<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">\u6848\u4f8b\u4e00\uff1a\u5fc3\u8840\u7ba1\u75be\u75c5\u7814\u7a76<\/h3>\n\n\n\n<p>\u7814\u7a76\u4eba\u5458\u5229\u7528GSMR\u5206\u6790\u5fc3\u8840\u7ba1\u75be\u75c5\u7684\u76f8\u5173GWAS\u6570\u636e\uff0c\u63a2\u8ba8\u4e86\u80c6\u56fa\u9187\u6c34\u5e73\u4e0e\u51a0\u5fc3\u75c5\u4e4b\u95f4\u7684\u56e0\u679c\u5173\u7cfb\u3002\u901a\u8fc7GSMR\u7684\u591a\u6548\u6027\u6821\u6b63\uff0c\u7814\u7a76\u4eba\u5458\u53d1\u73b0\u4e86\u66f4\u4e3a\u51c6\u786e\u7684\u56e0\u679c\u6548\u5e94\u4f30\u8ba1\uff0c\u9a8c\u8bc1\u4e86\u80c6\u56fa\u9187\u6c34\u5e73\u5bf9\u51a0\u5fc3\u75c5\u98ce\u9669\u7684\u663e\u8457\u5f71\u54cd\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u6848\u4f8b\u4e8c\uff1a\u4ee3\u8c22\u75be\u75c5\u7814\u7a76<\/h3>\n\n\n\n<p>\u5728\u53e6\u4e00\u9879\u7814\u7a76\u4e2d\uff0c\u7814\u7a76\u4eba\u5458\u4f7f\u7528GSMR\u5206\u6790\u4e86\u4e0e2\u578b\u7cd6\u5c3f\u75c5\u76f8\u5173\u7684\u57fa\u56e0\u53d8\u5f02\uff0c\u63a2\u8ba8\u4e86\u80a5\u80d6\u3001\u80f0\u5c9b\u7d20\u62b5\u6297\u7b49\u4ee3\u8c22\u6307\u6807\u4e0e\u7cd6\u5c3f\u75c5\u98ce\u9669\u4e4b\u95f4\u7684\u56e0\u679c\u5173\u7cfb\u3002GSMR\u7684\u9ad8\u6548\u6570\u636e\u5904\u7406\u80fd\u529b\uff0c\u4f7f\u5f97\u7814\u7a76\u4eba\u5458\u80fd\u591f\u5feb\u901f\u5206\u6790\u5927\u89c4\u6a21\u6570\u636e\uff0c\u5e76\u5f97\u51fa\u4e86\u53ef\u9760\u7684\u7814\u7a76\u7ed3\u8bba\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u6848\u4f8b\u4e09\uff1a\u7cbe\u795e\u75be\u75c5\u7814\u7a76<\/h3>\n\n\n\n<p>GSMR\u8fd8\u88ab\u5e94\u7528\u4e8e\u7cbe\u795e\u75be\u75c5\u7684\u7814\u7a76\u4e2d\u3002\u4f8b\u5982\uff0c\u7814\u7a76\u4eba\u5458\u4f7f\u7528GSMR\u5206\u6790\u4e86\u6291\u90c1\u75c7\u548c\u53cc\u76f8\u60c5\u611f\u969c\u788d\u7684GWAS\u6570\u636e\uff0c\u63a2\u8ba8\u4e86\u795e\u7ecf\u9012\u8d28\u6c34\u5e73\u4e0e\u8fd9\u4e9b\u7cbe\u795e\u75be\u75c5\u4e4b\u95f4\u7684\u56e0\u679c\u5173\u7cfb\u3002\u901a\u8fc7GSMR\u7684\u591a\u6548\u6027\u6821\u6b63\uff0c\u7814\u7a76\u4eba\u5458\u53d1\u73b0\u4e86\u65b0\u7684\u6f5c\u5728\u56e0\u679c\u5173\u7cfb\uff0c\u63a8\u52a8\u4e86\u7cbe\u795e\u75be\u75c5\u7684\u75c5\u56e0\u7814\u7a76\u3002<\/p>\n\n\n\n<h2 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