Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.

Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.
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DOI:
10.1186/s13059-018-1507-0
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发表时间:
2018-09-11
期刊:
影响因子:
12.3
通讯作者:
Stephanie Huang R
Stephanie Huang R
中科院分区:
生物学1区
文献类型:
--
作者:
Geeleher P;Nath A;Wang F;Zhang Z;Barbeira AN;Fessler J;Grossman RL;Seoighe C;Stephanie Huang R

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使用肿瘤基因表达数据鉴定的表达数量性状基因座(eQTL)可能影响癌细胞、肿瘤相关正常细胞或两者中的基因表达。在这里,我们已经证明了一种方法,以确定eQTL影响癌细胞中的表达,通过建模基因型和肿瘤纯度之间的统计相互作用。只有三分之一的乳腺癌风险变异,从传统分析中鉴定为eQTL,可以确信地归因于癌细胞。其余的变异可能会影响肿瘤微环境的细胞,如免疫细胞和成纤维细胞。肿瘤eQTL的解卷积将有助于确定遗传多态性如何影响癌症风险,发展和治疗反应。本文的在线版本(10.1186/s13059-018-1507-0)包含补充材料,可供授权用户使用。
Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts. Deconvolution of tumor eQTLs will help determine how inherited polymorphisms influence cancer risk, development, and treatment response. The online version of this article (10.1186/s13059-018-1507-0) contains supplementary material, which is available to authorized users.
实现癌症基因组数据的共同愿景。
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发表时间: 2016-09-22
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影响因子: --
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