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三阴性乳腺癌联合Affymetrix队列中数据集偏差的控制

Control of dataset bias in combined Affymetrix cohorts of triple negative breast cancer.

作者信息

Karn Thomas, Rody Achim, Müller Volkmar, Schmidt Marcus, Becker Sven, Holtrich Uwe, Pusztai Lajos

机构信息

Department of Gynecology, Goethe-University Frankfurt, Frankfurt am Main, Germany.

Department of Obstetrics and Gynecology, University Hospital Lübeck, Germany.

出版信息

Genom Data. 2014 Oct 23;2:354-6. doi: 10.1016/j.gdata.2014.09.014. eCollection 2014 Dec.

DOI:10.1016/j.gdata.2014.09.014
PMID:26484129
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4535974/
Abstract

Heterogenous subtypes of breast cancer need to be analyzed separately. Pooling of datasets can provide reasonable sample sizes but dataset bias is an important concern. We assembled a combined dataset of 579 Affymetrix microarrays from triple negative breast cancer (TNBC) in Gene Expression Omnibus (GEO) series GSE31519. We developed a method for selecting comparable datasets and to control for the amount of dataset bias of individual probesets.

摘要

乳腺癌的异质性亚型需要分别进行分析。数据集的合并可以提供合理的样本量，但数据集偏差是一个重要问题。我们从基因表达综合数据库（GEO）系列GSE31519中收集了579个三阴性乳腺癌（TNBC）的Affymetrix微阵列的组合数据集。我们开发了一种方法来选择可比数据集，并控制单个探针集的数据集偏差量。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ebf/4535974/3cff7e5ebb77/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ebf/4535974/278beee01927/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ebf/4535974/3cff7e5ebb77/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ebf/4535974/278beee01927/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ebf/4535974/3cff7e5ebb77/gr2.jpg

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本文引用的文献

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PLoS One. 2011;6(12):e28403. doi: 10.1371/journal.pone.0028403. Epub 2011 Dec 29.
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A clinically relevant gene signature in triple negative and basal-like breast cancer.三阴性和基底样乳腺癌中具有临床相关性的基因特征。
Breast Cancer Res. 2011 Oct 6;13(5):R97. doi: 10.1186/bcr3035.
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Melanoma antigen family A identified by the bimodality index defines a subset of triple negative breast cancers as candidates for immune response augmentation.
通过上皮间质转化和肿瘤免疫微环境对三阴性乳腺癌进行分类。
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Cellular Fitness Phenotypes of Cancer Target Genes from Oncobiology to Cancer Therapeutics.从肿瘤生物学到癌症治疗的癌症靶基因的细胞健康表型。
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NOTCH3 inactivation increases triple negative breast cancer sensitivity to gefitinib by promoting EGFR tyrosine dephosphorylation and its intracellular arrest.NOTCH3失活通过促进表皮生长因子受体（EGFR）酪氨酸去磷酸化及其细胞内阻滞，增加三阴性乳腺癌对吉非替尼的敏感性。
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双模态指数鉴定的黑色素瘤相关抗原家族 A 将三阴性乳腺癌的一个亚组定义为免疫反应增强的候选者。
Eur J Cancer. 2012 Jan;48(1):12-23. doi: 10.1016/j.ejca.2011.06.025. Epub 2011 Jul 7.
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Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer.从 3030 个 Affymetrix 阵列的池中提取分界值，以对不同临床类型的乳腺癌进行分层。
Breast Cancer Res Treat. 2010 Apr;120(3):567-79. doi: 10.1007/s10549-009-0416-z. Epub 2009 May 20.
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Genome Biol. 2004;5(10):R80. doi: 10.1186/gb-2004-5-10-r80. Epub 2004 Sep 15.
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