◇◇新语丝(www.xys.org)(xys3.dxiong.com)(www.xysforum.org)(xys2.dropin.org)◇◇ 西安交通大学邓红文学术造假证据之一 作者:顽童   最近在阅读邓红文等发表的文章的时候,根据其文章间的相互矛盾之处,发 现其编造文章数据的证据,觉得有必要在新语丝进行进一步的披露,避免更多的 年轻人投身到他的门下,从而毁了自己的前途。也为国内那些把邓红文聘为各种 名义教授的单位敲一下警钟,希望他们对邓红文的做人与做学问有个了解。   西安交通大学邓红文等发表在Plos Genetics 上的“Genome-Wide Association Analyses Identify SPOCK as a Key Novel Gene Underlying Age at Menarche”文章的样本描述与其以前利用相同的数据发表的文章的描述出入 很大,说明这批数据在发表文章的时候存在很严重的数据造假问题,以下是文章 的部分原文: In our GWAS genotyping experiment, following an Affymetrix guideline, we set a standard for the minimum DM call rate at 93% (or the maximum genotype missing rate at 7%) for a sample, considering all the SNPs in the two arrays, the 250 k Nsp and 250 k Sty arrays. More than 98% of all the subjects (i.e., 470 subjects among a total of 477 subjects) met this call rate standard. The remaining 7 samples that did not meet this standard however had one hybridized array passing or approaching this call rate standard (i.e., 93% of all the SNPs in the array were successfully called). Hence the genotype data in the array (with the higher call rate) for these 7 samples were also kept in the dataset for GWAS analysis. For all the 477 subjects, the average DM call rate reached >95%. The final average BRLMM call rate across the entire cohort reached a high level of 99.14%. However, out of the initial full-set of 500,568 SNPs, we discarded 32,961 SNPs with sample call rate <95%, another 36,965 SNPs with allele frequencies deviating from Hardy-Weinberg equilibrium (HWE) (P<0.001) and 51,323 SNPs with minor allele frequencies (MAF) <1%. Therefore, the final SNP set maintained in the subsequent analyses contained 379,319 SNPs, yielding an average marker spacing of ~7.9 kb throughout the human genome.   这篇文章利用了邓红文等最近的1000个高加索人群500K芯片的分型资料研究 高加索女性初潮年龄的基因的关系。我们且不说他的分析方法正确与否,首先看 他的样本描述与以前的利用相同数据所做的文章的区别。这篇文章的样本描述大 致意思是500k芯片包含2个部分,Nsp和Sty,一共是477个女性高加索人个体, 470个个体的Call Rate 大于93%,另外7个个体没有满足这个标准,但是这7个个 体的单芯片数据(Nsp或者Sty)的250k的数据满足了Call Rate 大于93%的标准, 也就是说,这7个个体只有250k的数据被加入到分析中,而另外的470个个体是利 用的500k的数据。这篇文章是邓红文实验室的前工作人员在举报了邓红文的学术 造假后,为邓红文等修改文章的密苏里堪萨斯城市大学医学院的院长,系主任等 美国人要求他所做的修改。   在邓红文等以前发表的文章中,邓红文等刻意回避了一部分样本的Call Rate没有达到标准,从而影响SNP的选择。邓红文等对1000个样本的描述全部满 足了500k的Call Rate   大于93%。举例如下:上文相同第一作者发表在Plos One的文章 “Identification of PLCL1 Gene for Hip Bone Size Variation in Females in a Genome-Wide Association Study”这样描述样本的: ……For the GWAS, a random sample containing 1,000 unrelated participants, including 501 women and 499 men, was identified from our established and expanding genetic repertoire currently containing more than 6000 subjects……. ……GWAS sample. Genomic DNA was extracted from whole human blood using a commercial isolation kit (Gentra systems, Minneapolis, MN, USA) following protocols detailed in the kit. Genotyping with the AffymetrixMapping 250 k Nsp and Affymetrix Mapping 250 k Sty arrays was performed in Vanderbilt Microarray Shared Resources (VMSR) (http://array.mc.vanderbilt.edu/) using the standard protocol recommended by Affymetrix. Genotyping calls were determined from the fluorescent intensities using the DM algorithm with a 0.33 P-value setting as well as the B-RLMM algorithm. DM calls were used for quality control while the BRLMM calls were used for all subsequent data analysis. B-RLMM clustering was performed with 94 samples per cluster…….   可以看到,邓红文等刻意掩盖了一部分样本没有被2个芯片(Nsp和Sty)分 型的事实,实际上是为了达到1000人的样本数,而把一些不符合要求的数据强加 在里面进行分析的事实。这只是其中的一方面,其分析结果的可信度可想而知。   类似数据发表的文章还包括西安交大教师刘晓刚,邓红文等发表在AJHG上面 的文章“Genome-wide Association and Replication Studies Identified TRHR as an Important Gene for Lean Body Mass”等系列文章。   类似的关于邓红文学术造假的证据将陆续公布。 附:有据可查的邓红文目前的国内外工作单位 1、 湖南师范大学生命科学院的长江学者特聘教授。相关网站链接:http://www.changjiang.edu.cn/professor/1073.htm 2、 西安交通大学生命科学与技术学院教授。相关网站链接:http://www.xjtu.edu.cn/szdw/professor/596.html 3、 北京交通大学百人计划海外讲座教授。相关网站链接:http://news.njtu.edu.cn/News_Detail.aspx?n_id=9156 4、 上海理工大学教授,博士生导师,相关网站链接:http://yjs.usst.edu.cn/detail.php?id=2509 5、 怀化医学高等专科学校特聘教授,相关网站链接:http://www.yizhuan.com/web/0/200801/18185323234.html 6、 中南大学湘雅医学院,特聘教授,相关网站链接:http://www.xys.org/xys/ebooks/others/science/dajia9/denghongwen.txt 7、 美国密苏里堪萨斯城市大学教授 8、 美国克莱登大学教授 (XYS20090820) ◇◇新语丝(www.xys.org)(xys3.dxiong.com)(www.xysforum.org)(xys2.dropin.org)◇◇