A predictive microarray-based biomarker for early detection of Alzheimer's disease intended for clinical diagnostic application

被引:4
作者
Calciano, Margaret [1 ]
Lemarie, Jean Christophe [2 ]
Blondiaux, Elodie [2 ]
Einstein, Richard [1 ,3 ]
Fehlbaum-Beurdeley, Pascale [4 ]
机构
[1] Exonhit Inc, Gaithersburg, MD USA
[2] Effi Stat, Paris, France
[3] Intrexon Corp, Germantown, MD USA
[4] Exonhit SA, Paris, France
关键词
Alzheimer's disease; diagnostic gene; expression; microarray; splice variant; VALIDATION; PERFORMANCE; SIGNATURE;
D O I
10.3109/1354750X.2013.773083
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Objective: Microarray-based signatures for clinical application are often plagued by processing variability or batch effects that compromise the robustness of the test performance. Methods: A splice variant array-based signature for early detection of Alzheimer's disease (AD) was developed using 315 AD or normal subjects processed in three disparate microarray batches. Results: A modified top scoring pair classifier using the signature, is robust to batch effects and outperforms other common classifiers, with sensitivity and specificity of 88.3% (95% CI:81.2%, 93.4%) and 88.9% (95% CI:65.3%, 98.6%), respectively, on an independent cohort. Conclusions: This splice-variant array-based signature shows promise for clinical diagnostic use in AD.
引用
收藏
页码:264 / 272
页数:9
相关论文
共 28 条
[11]   Empirical Bayes Estimates for Large-Scale Prediction Problems [J].
Efron, Bradley .
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2009, 104 (487) :1015-1028
[12]   Validation of AclarusDx™, a Blood-Based Transcriptomic Signature for the Diagnosis of Alzheimer's Disease [J].
Fehlbaum-Beurdeley, Pascale ;
Sol, Olivier ;
Desire, Laurent ;
Touchon, Jacques ;
Dantoine, Thierry ;
Vercelletto, Martine ;
Gabelle, Audrey ;
Jarrige, Anne-Charlotte ;
Haddad, Raphael ;
Lemarie, Jean Christophe ;
Zhou, Weiyin ;
Hampel, Harald ;
Einstein, Richard ;
Vellas, Bruno .
JOURNAL OF ALZHEIMERS DISEASE, 2012, 32 (01) :169-181
[13]  
Geman Donald, 2004, Stat Appl Genet Mol Biol, V3, pArticle19
[14]   Converting a breast cancer microarray signature into a high-throughput diagnostic test [J].
Glas, Annuska M. ;
Floore, Arno ;
Delahaye, Leonie J. M. J. ;
Witteveen, Anke T. ;
Pover, Rob C. F. ;
Bakx, Niels ;
Lahti-Domenici, Jaana S. T. ;
Bruinsma, Tako J. ;
Warmoes, Marc O. ;
Bernards, Rene ;
Wessels, Lodewyk F. A. ;
Van 't Veer, Laura J. .
BMC GENOMICS, 2006, 7 (1)
[15]   A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription [J].
Johansson, D ;
Lindgren, P ;
Berglund, A .
BIOINFORMATICS, 2003, 19 (04) :467-473
[16]   Adjusting batch effects in microarray expression data using empirical Bayes methods [J].
Johnson, W. Evan ;
Li, Cheng ;
Rabinovic, Ariel .
BIOSTATISTICS, 2007, 8 (01) :118-127
[17]   Tackling the widespread and critical impact of batch effects in high-throughput data [J].
Leek, Jeffrey T. ;
Scharpf, Robert B. ;
Bravo, Hector Corrada ;
Simcha, David ;
Langmead, Benjamin ;
Johnson, W. Evan ;
Geman, Donald ;
Baggerly, Keith ;
Irizarry, Rafael A. .
NATURE REVIEWS GENETICS, 2010, 11 (10) :733-739
[18]   A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data [J].
Luo, J. ;
Schumacher, M. ;
Scherer, A. ;
Sanoudou, D. ;
Megherbi, D. ;
Davison, T. ;
Shi, T. ;
Tong, W. ;
Shi, L. ;
Hong, H. ;
Zhao, C. ;
Elloumi, F. ;
Shi, W. ;
Thomas, R. ;
Lin, S. ;
Tillinghast, G. ;
Liu, G. ;
Zhou, Y. ;
Herman, D. ;
Li, Y. ;
Deng, Y. ;
Fang, H. ;
Bushel, P. ;
Woods, M. ;
Zhang, J. .
PHARMACOGENOMICS JOURNAL, 2010, 10 (04) :278-291
[19]   Expansion of the eukaryotic proteome by alternative splicing [J].
Nilsen, Timothy W. ;
Graveley, Brenton R. .
NATURE, 2010, 463 (7280) :457-463
[20]   Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data [J].
Pelz, Carl R. ;
Kulesz-Martin, Molly ;
Bagby, Grover ;
Sears, Rosalie C. .
BMC BIOINFORMATICS, 2008, 9 (1)