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The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

2006 Nature Biotechnology  
and the MAQC web site (http://www.fda.gov/nctr/science/centers/ toxicoinformatics/maqc/).  ...  All data are available through GEO (series accession number: GSE5350), ArrayExpress (accession number: E-TABM-132), ArrayTrack (http://www.fda.gov/nctr/science/centers/toxicoinformatics/Array Track/),  ...  The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues.  ... 
doi:10.1038/nbt1239 pmid:16964229 pmcid:PMC3272078 fatcat:artpc4ivune53euk2xcfbcocui

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

2010 Nature Biotechnology  
In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity  ...  Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established.  ...  There the MicroArray Quality control (MAQc)-ii study of common practices for the development and validation of microarray-based predictive models As part of the United States Food and Drug Administration's  ... 
doi:10.1038/nbt.1665 pmid:20676074 pmcid:PMC3315840 fatcat:7ff44lokvrehraq6gdulu3t34q

Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study

Emi Arikawa, Yanyang Sun, Jie Wang, Qiong Zhou, Baitang Ning, Stacey L Dial, Lei Guo, Jingping Yang
2008 BMC Genomics  
The MicroArray Quality Control (MAQC) project evaluated the inter-and intra-  ...  Approval does not signify that the contents necessarily reflect the position or opinions of the FDA nor does mention of trade names or commercial products constitute endorsement or recommendation for use  ...  Acknowledgements This document has been reviewed in accordance with United States Food and Drug Administration (FDA) policy and approved for publication.  ... 
doi:10.1186/1471-2164-9-328 pmid:18620571 pmcid:PMC2491643 fatcat:visep753eves7mp3xnspsm4n6m

Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project

Tucker A Patterson, Edward K Lobenhofer, Stephanie B Fulmer-Smentek, Patrick J Collins, Tzu-Ming Chu, Wenjun Bao, Hong Fang, Ernest S Kawasaki, Janet Hager, Irina R Tikhonova, Stephen J Walker, Liang Zhang (+6 others)
2006 Nature Biotechnology  
Here we provide a simultaneous comparison of results from one-and two-color labeling designs, using two independent RNA samples from the MicroArray Quality Control (MAQC) project, tested on each of three  ...  , data analysis and data interpretation.  ...  Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project when planning a microarray experiment is whether to use a one-color or two-color approach  ... 
doi:10.1038/nbt1242 pmid:16964228 fatcat:flc6h5nienao3h7ceagi3vmh64

Power and limitations of RNA-Seq: findings from the SEQC (MAQC-III) Consortium

Paweł Piotr Łabaj
2015 EMBnet journal  
We present primary results from the Sequencing Quality Control (SEQC) project by US-FDA MAQC consortium.  ...  Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling.  ...  We present primary results from the Sequencing Quality Control (SEQC) project by US-FDA MAQC consortium.  ... 
doi:10.14806/ej.21.a.831 fatcat:mux5zxplsvdqtdqvtvzoln5tza

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong, Leming Shi
2010 BMC Bioinformatics  
Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005.  ...  The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive.  ...  ZW was supported by a postdoctoral fellowship from the National Center for Toxicological Research of the US FDA through the Oak Ridge Institute for Science and Education (ORISE).  ... 
doi:10.1186/1471-2105-11-s6-s10 pmid:20946593 pmcid:PMC3026357 fatcat:utrpufn6dndcnhy2dx5okymz3u

Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data

James J Chen, Huey-Miin Hsueh, Robert R Delongchamp, Chien-Ju Lin, Chen-An Tsai
2007 BMC Bioinformatics  
Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms.  ...  The MAQC analysis presented for the conclusion of inter-and intra-platform comparability/ reproducibility of microarray gene expression measurements is inadequate.  ...  Acknowledgements The views presented in this paper are those of the authors and do not necessarily represent those of the U.S. Food and Drug Administration.  ... 
doi:10.1186/1471-2105-8-412 pmid:17961233 pmcid:PMC2204045 fatcat:vw7sxeacjvannjfk3ocvftpxoa

Feature Selection and Classification of MAQC-II Breast Cancer and Multiple Myeloma Microarray Gene Expression Data

Qingzhong Liu, Andrew H. Sung, Zhongxue Chen, Jianzhong Liu, Xudong Huang, Youping Deng, Raya Khanin
2009 PLoS ONE  
Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging.  ...  Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are  ...  The MAQC-II consortium for making the data sets available to this study is gratefully appreciated. Author Contributions Conceived and designed the experiments: QL. Performed the experiments: QL.  ... 
doi:10.1371/journal.pone.0008250 pmid:20011240 pmcid:PMC2789385 fatcat:wgvmaxq335cnfjcnggqivdiooi

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

2010
In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity  ...  Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established.  ...  All MAQC-II participants freely donated their time and reagents for the completion and analyses of the MAQC-II project. The MAQC-II consortium also thanks R.  ... 
doi:10.17615/5bpt-a893 fatcat:ptgq4bk3dvdszhlk64ihw4ixyy

Data quality in genomics and microarrays

Hanlee Ji, Ronald W Davis
2006 Nature Biotechnology  
Analysis of the MAQC and ERCC RNA sets has resulted in extensive gene expression data sets with validation across many microarray platforms and systems (e.g., by  ...  To date, the MicroArray Quality Control (MAQC) project-the first results of which are presented in this issue-and the External RNA Controls Consortium (ERCC) are the most comprehensive efforts in assessing  ...  A vital part of the MAQC project has been the identification of common transcripts that are mutually represented among the various microarray platforms included in the analysis 9 .  ... 
doi:10.1038/nbt0906-1112 pmid:16964224 pmcid:PMC2943412 fatcat:35hkslbwobf5pck434jftodygq

The FDA's Experience with Emerging Genomics Technologies—Past, Present, and Future

Joshua Xu, Shraddha Thakkar, Binsheng Gong, Weida Tong
2016 AAPS Journal  
The latest MAQC project is also called the SEquencing Quality Control (SEQC) project focused on next-generation sequencing.  ...  MicroArray Quality Control Consortium (MAQC), to address issues such as reproducibility, precision, specificity/sensitivity, and data interpretation.  ...  The SEQC project evaluated technical performance, quality control, and cross lab and cross platform reproducibility of RNA-seq.  ... 
doi:10.1208/s12248-016-9917-y pmid:27116022 pmcid:PMC4973466 fatcat:anbltnjsvranpeedu3quqwhm2u

Shambhala: a platform-agnostic data harmonizer for gene expression data

Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin, Anton Buzdin
2019 BMC Bioinformatics  
Each profile is transformed to make it similar to the output of microarray hybridization platform Affymetrix Human Gene.  ...  Results: Unlike previously published methods enabling good quality data harmonization for only two datasets, Shambhala allows conversion of multiple datasets into the universal form suitable for further  ...  All the gene expression data that were used for research, including the datasets from MAQC, SEQC and GTEx projects, were taken from publicly available repository Gene Expression Omnibus (GEO), and had  ... 
doi:10.1186/s12859-019-2641-8 fatcat:eldsaomt3vcylestzlm7wfvoia

Of genomics and bioinformatics

W Slikker
2010 The Pharmacogenomics Journal  
The first phase of the MAQC project (MAQC-I) evaluated various issues related to microarray technology, including, but not limited to, quality control, data analysis, cross-laboratory and cross-platform  ...  An important parallel research effort is the MicroArray Quality Control (MAQC) project.  ... 
doi:10.1038/tpj.2010.59 pmid:20676063 fatcat:sydljwli35aapeavn42jwxa6k4

Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

Pierre R Bushel, Dahlia Nielsen, Weida Tong
2009 BMC Proceedings  
We also thank Rosetta Biosoftware and JMP Genomics for sponsoring the conference and all the MAQC special session presenters, poster presenters and student presenters for participating in the conference  ...  Acknowledgements We thank Juliebeth Briseno for her assistance with organizing TIES-2007, Chris Smith for the development and maintenance of the conference web site, Rita Ross for help with on-site registration  ...  In addition, a special session on the FDA-led MicroArray Quality Control project [2, 3] was provided that highlighted reproducibil-ity of microarray analysis.  ... 
doi:10.1186/1753-6561-3-s2-s1 pmid:19278557 pmcid:PMC2654484 fatcat:h46bevxh2rg6zkrigwubnmryrq

Arrays of Hope

Evelyn Strauss
2006 Cell  
"That allows us to maximally control the quality of the results," says Bernards, avoiding problems that arise from different methods of sample han dling and analysis.  ...  "The compa nies controlled the use of their own platforms so the MAQC project had the best of the best working on it," says Kim. "Most labs can do one platform or at the most two very well.  ... 
doi:10.1016/j.cell.2006.11.005 pmid:17110319 fatcat:nfdfqhnrz5e77piv32l6cdfab4
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