meta分析

SNPmeta3-索要原始文件+数据提取

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第1章:亚甲基四氢叶酸还原酶(MTHFR)多态性与非酒精性脂肪性肝病(NAFLD)之间的关联风险:meta分析

Man-Yi Sun, Li Zhang, Song-Li Shi, Jing-Na Lin

Published: April 29, 2016http://dx.doi.org/10.1371/journal.pone.0154337

http://dx.doi.org/10.1371/journal.pone.0154337

全文地址:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154337

Inclusion and exclusion criteria

The eligible case-control studies were identified according to the following inclusion and exclusion criteria. Inclusion criteria: 1) The data on the association between MTHFR polymorphisms and susceptibility to NAFLD was provided; 2) The individual genotype frequencies for MTHFR polymorphisms could be extracted. Exclusion criteria: 1) duplicated studies; 2) reviews or books; 3) non-clinical data; 4) other genes; 5) non-NAFLD diseases; 6) case, trial, or non-polymorphism; 7) meeting/conference abstracts; 8) unavailable data.

Data extraction strategy

Data was extracted from qualified articles independently by the authors (MYS LZ SLS JNL) using the same reporting form. The controversial evaluations were resolved through discussion. If the data was unavailable, an attempt was made to contact corresponding author to request missing data via E-mail. The following information was extracted: mutation site, first author, year of publication, country, ethnicity, sample sizes in case and control group, source of control, genotyping method, gender and age in case group, disease group, allele and genotype frequencies in each group, The Χ2 and P value of Hardy-Weinberg Equilibrium (HWE) test in control group. HWE value was calculated by chi-squared test and P value less than 0.05 was considered a departure from HWE.

Statistical analysis

The P value, odd radio (OR) and corresponding 95% confidence interval (CI) were calculated by Mantel-Haenszel statistics under the allele, homozygote, heterozygote, dominant or recessive models. P value <0.05 was considered statistically significant association between C677T and A1298C polymorphisms of MTHFR and NAFLD risks. Χ2-based Q statistic and I2test were applied to analyze the overall heterogeneities. When I2 values < 25% or P value of heterogeneity >0.10, a fixed-effect model was selected for Mantel-Haenszel statistics. Otherwise, a random-effect model was used [3235]. When significant heterogeneity existed, sensitivity analysis was also performed to analyze the study that influenced homogeneity of the included studies. The potential publication bias was evaluated by Begg’s funnel plot with pseudo 95% confidence limits [36]. Statistical analyses were conducted by Review Manager Version 5.0 (The Nordic Cochrane Centre, The Cochrane Collaboration, Denmark) and Stata/SE 12.0 (StataCorp, College Station, USA) software.

 

纳入标准(正文)

根据以下纳入和排除标准确定合格的病例对照研究。纳入标准:1)提供MTHFR多态性与NAFLD易感性之间关系的数据; 2)可以提取MTHFR多态性的个体基因型频率。排除标准:1)重复研究; 2)评论或书籍; 3)非临床资料; 4)其他基因; 5)非NAFLD疾病; 6)病例、试验或非多态性; 7)会议/会议摘要; 8)不可用数据。

数据提取策略

使用相同的报告表格,作者独立地从合格的文章中提取数据。有争议的评估通过讨论得到解决。如果数据不可用,则尝试联系相应的作者以通过电子邮件请求丢失的数据。提取以下信息:突变位点,第一作者,出版年份,国家,种族,病例和对照组的样本量,对照来源,基因分型方法,病例组,疾病组,等位基因和基因型频率中的性别和年龄各组,对照组的Hardy-Weinberg平衡(HWE)检验的X2P值。HWE值通过卡方检验计算,P值小于0.05被认为是偏离HWE。

统计分析

通过等位基因,纯合子,杂合子,显性或隐性模型下的Mantel-Haenszel统计量计算P值, OR和相应的95%置信区间(CI)。P值<0.05被认为是MTAFR和NAFLD风险的C677T与A1298C多态性之间的统计学显着相关性。应用基于X2的Q统计量和I2检验来分析总体异质性。当I2值<25%或异质性P值> 0.10时,选择Mantel-Haenszel统计量的固定效应模型。否则,随机效应模型用于[ 32 - 35 ]。当存在显着的异质性时,还进行敏感性分析以分析影响所包含研究的同质性的研究。通过Begg的漏斗图评估潜在的出版偏倚,具有95%的置信限度[ 36 ]。统计分析由Review Manager 5.0版(Nordic Cochrane Center,The Cochrane Collaboration,Denmark)和Stata / SE 12.0(StataCorp,College Station,USA)软件进行。

 

###猴哥摘要解析:

1. 纳入标准:纳入标准和排除标准不可相同,不能说纳入多态性研究、排除非多态性研究,其实这两个说的是一回事。

所以排除标准中“4)其他基因; 5)非NAFLD疾病; 6)病例、试验或非多态性;”为多余。

2.“如果数据不可用,则尝试联系相应的作者以通过电子邮件请求丢失的数据。”审稿人会要求提供邀请的原始数据的邮件。

 

猴哥在这里贴出猴哥索要原始文献的信件:

您好!非常冒昧打搅您了。
最近看到了您的一篇发表在高分杂志Oncotarget上题为“Polymorphisms in xx  gene and breast cancer susceptibility in Chinese women: A case-control study”(补充参考文献格式。),文章超赞,我是您的小红粉,XX gene对乳腺癌来说真是太重要了,而您将他变为了现实,这是一项举世瞩目的、开创性的工作。特向请教您,文中提到的XX geners123, rs456, rs789 这三个rs号,我未能查出其对应的SNP位点中的哪个基因到哪个基因的突变,您是否能对这个位点的点对点突变说得更详细些,比如 530位点GC的突变,恳请戴教授指教。 我的邮箱是123456@qq.com. 万分感谢!

 

3.数据提取表

提取以下信息:突变位点,第一作者,出版年份,国家,种族,病例和对照组的样本量,对照来源,基因分型方法,病例组,疾病组,等位基因和基因型频率中的性别和年龄各组,对照组的Hardy-Weinberg平衡(HWE)检验的X2P值。HWE值通过卡方检验计算,P值小于0.05被认为是偏离HWE。

猴哥之前有讲:

4 数据提取:

5.本文提供了一个非常好的模板

 

拓展知识:

SNPmeta

SNPMETA1

SNPMETA2_检索式

SNPMETA3_索要原始文献+数据提取

 

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网状emta分析必备技能

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网状Meta分析必备技能3_数据初始值的设定

网状Meta分析必备技能4_Gemtc实现生存分析

网状meta分析必备技能5_HR风险比

网状meta分析必备技能6_R+Rstudio运用meta包做简单meta分析

网状meta分析必备技能7_使用R、GeMTC和STATA软件实现连续变量的网状Meta分析

 

网状meta分析stata简易教程

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NMA(网状meta分析)stata简易教程(5)排序图的制作

 

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诊断性meta分析简单实现(1)之revman

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诊断性meta分析简单实现(5)_结果的展示和解读

 

其他

meta分析统计方法-随机对照试验的风险评估rob

生物标记物(基因)联合诊断模型的stata实现ROC(AUC)

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