来自用户 思考问题的熊 的文献。
当前共找到 2 篇文献分享。
1.
思考问题的熊
(2022-03-20 16:35):
#paper Li, Yumei, Xinzhou Ge, Fanglue Peng, Wei Li, and Jingyi Jessica Li. “Exaggerated False Positives by Popular Differential Expression Methods When Analyzing Human Population Samples.” Genome Biology 23, no. 1 (March 15, 2022): 79. https://doi.org/10.1186/s13059-022-02648-4.
前几天发表在 Genome Biology 的一篇论文，算是比较严谨地论证了在大样本量RNA-seq差异分析时，今后即便不考虑速度因素，也应该抛弃DEseq2和edgeR转而使用朴实无华的Wilcoxon秩和检验。
更具体的内容已经写成推送发出来了，感兴趣可以再看看。
IF:10.100Q1
Genome biology,
2022-03-15.
DOI: 10.1186/s13059-022-02648-4
PMID: 35292087
PMCID:PMC8922736
在分析人类群体样本时，流行的差异表达方法夸大了假阳性
Abstract:
When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high …
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When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. Expanding the analysis to limma-voom, NOISeq, dearseq, and Wilcoxon rank-sum test, we found that FDR control is often failed except for the Wilcoxon rank-sum test. Particularly, the actual FDRs of DESeq2 and edgeR sometimes exceed 20% when the target FDR is 5%. Based on these results, for population-level RNA-seq studies with large sample sizes, we recommend the Wilcoxon rank-sum test.
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翻译
当使用人类群体 RNA-seq 样本鉴定两种情况之间的差异表达基因时，我们通过排列分析发现了一个现象：两种流行的生物信息学方法 DESeq2 和 edgeR 具有出乎意料的高错误发现率。将分析扩展到 limma-voom、NOISeq、dearseq 和 Wilcoxon 秩和检验，我们发现除了 Wilcoxon 秩和检验外，FDR 控制经常失败。特别是，当目标 FDR 为 5% 时，DESeq2 和 edgeR 的实际 FDR 有时会超过 20%。基于这些结果，对于样本量较大的群体水平 RNA-seq 研究，我们建议使用 Wilcoxon 秩和检验。
2.
思考问题的熊
(2022-02-27 22:55):
#paper 深夜文献安利
简要解读
https://kaopubear.top/blog/2022-02-27-do-clinical-decisions/
通过阅读这篇文献，你一方面可以了解目前的生物标志物物相关高频基因和高频突变位点（有附件可下载），另一方面可以了解临床决策的基本逻辑和重要数据库，最后还能获得一个即刻可用的在线突变注释工具MTPB
Tamborero, D., Dienstmann, R., Rachid, M.H. et al. The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology. Nat Cancer 3, 251–261 (2022). https://doi.org/10.1038/s43018-022-00332-x
Abstract:
There is a growing need for systems that efficiently support the work of medical teams at the precision-oncology point of care. Here, we present the implementation of the Molecular Tumor …
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There is a growing need for systems that efficiently support the work of medical teams at the precision-oncology point of care. Here, we present the implementation of the Molecular Tumor Board Portal (MTBP), an academic clinical decision support system developed under the umbrella of Cancer Core Europe that creates a unified legal, scientific and technological platform to share and harness next-generation sequencing data. Automating the interpretation and reporting of sequencing results decrease the need for time-consuming manual procedures that are prone to errors. The adoption of an expert-agreed process to systematically link tumor molecular profiles with clinical actions promotes consistent decision-making and structured data capture across the connected centers. The use of information-rich patient reports with interactive content facilitates collaborative discussion of complex cases during virtual molecular tumor board meetings. Overall, streamlined digital systems like the MTBP are crucial to better address the challenges brought by precision oncology and accelerate the use of emerging biomarkers.
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翻译