WELCOME TO THE MAQC SOCIETY

3rd Annual Meeting of the MAQC Society

April 8-10, 2019

Reproducibility for Artificial Intelligence in Medicine

Riva Del Garda, Trentino, Italy

Inaugural Meeting of Little Rock Chapter of MAQC Society

Sept 7-8, 2018

Comprehensive Assessments of NGS Onco-panel Technologies

Univ of Arkansas for Medical Sciences (UAMS), Little Rock, AR

2nd Annual Meeting of the MAQC Society

Feb 24-27, 2018

Precision Medicine in Clinical Omics

Shaghai, China

Inaugural Meeting of the MAQC Society

April 12, 2017

SAS Institute, Cary, NC

SEQC Nature Biotechnology and other Publications

August 2014

Su Z, Łabaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, Thompson JF, Jones WD. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature biotechnology. 2014 Sep;32(9):903.

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Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D. Detecting and correcting systematic variation in large-scale RNA sequencing data. Nature biotechnology. 2014 Sep;32(9):888.

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Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature biotechnology. 2014 Sep;32(9):926.

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Gong B, Wang C, Su Z, Hong H, Thierry-Mieg J, Thierry-Mieg D, Shi L, Auerbach SS, Tong W, Xu J. Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq. Scientific data. 2014 Aug 26;1:140021.

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Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature communications. 2014 Sep 25;5:5125.

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MAQC-II Nature Biotechnology and Pharmacogenomics Publications

August, 2010

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy Jr JD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology. 2010 Aug;28(8):827.

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Tillinghast GW. Microarrays in the clinic. Nature biotechnology. 2010 Aug;28(8):810.

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Fan X, Lobenhofer EK, Chen M, Shi W, Huang J, Luo J, Zhang J, Walker SJ, Chu TM, Li L, Wolfinger R. Consistency of predictive signature genes and classifiers generated using different microarray platforms. The pharmacogenomics journal. 2010 Aug;10(4):247.

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Parry, R.M., Jones, W. D., Stokes, T. H., et al. (2010) k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction, Pharmacogenomics, J 10: 292-309; doi:10.1038/ tpj.2010.56. 

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Shi W, Bessarabova M, Dosymbekov D, Dezso Z, Nikolskaya T, Dudoladova M, Serebryiskaya T, Bugrim A, Guryanov A, Brennan RJ, Shah R. Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. The pharmacogenomics journal. 2010 Aug;10(4):310.

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Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, Berthold F, Shi L, Wolfinger RD, Fischer M, Brors B. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. The pharmacogenomics journal. 2010 Aug;10(4):258.

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Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. The pharmacogenomics journal. 2010 Aug;10(4):278-91.

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Hong H, Shi L, Su Z, Ge W, Jones WD, Czika W, Miclaus K, Lambert CG, Vega SC, Zhang J, Ning B. Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples. The pharmacogenomics journal. 2010 Aug;10(4):364.

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10th MAQC Project Meeting - Inaugural SEQC Meeting

Dec 16-17, 2008

US FDA, Silver Spring, MD

9th MAQC Project Meeting

Sept 18-19, 2008

Best Practices for Developing and Validating Microarray-Based Predictive Models

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US FDA, 10903 New Hampshire Ave, Silver Spring MD

Reproducibility, Sensitivity, and Specificity Publication from MAQC

August 2008

Shi, L, Jones, WD, Jensen, RV, et al. (2008). The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies, BMC Bioinformatics, 9(Suppl 9):S10.

8th MAQC Project Meeting

March 24-26, 2008

Development and Validation of Predictive Models

US FDA, Rockville, MD

7th MAQC Project Meeting

May 24-25, 2007

Development and Validation of Predictive Models

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SAS Institute, Cary, NC

6th MAQC Project Meeting

Nov 28-29, 2006

Washington, Marriott Hotel and the FDA White Oak Facility, Silver Spring, MD

MAQC Nature Biotechnology Publications

Sept, 2006

Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, De Longueville F, Kawasaki ES, Lee KY, Luo Y, et al. The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature biotechnology. 2006 Sep;24(9):1151.

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Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nature biotechnology. 2006 Sep;24(9):1162.

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Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y. Evaluation of DNA microarray results with quantitative gene expression platforms. Nature biotechnology. 2006 Sep;24(9):1115.

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Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nature biotechnology. 2006 Sep;24(9):1123.

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Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, Collins PJ, Chu TM, Bao W, Fang H, Kawasaki ES, Hager J, Tikhonova IR, Walker SJ. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nature biotechnology. 2006 Sep;24(9):1140.

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Tong W, Lucas AB, Shippy R, Fan X, Fang H, Hong H, Orr MS, Chu TM, Guo X, Collins PJ, Sun YA. Evaluation of external RNA controls for the assessment of microarray performance. Nature biotechnology. 2006 Sep;24(9):1132.

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5th Face-to-Face MAQC Consortium Meeting

Sept 21, 2006

National Center for Toxicological Research, FDA, Jefferson, AR

4th Face-to-Face MAQC Consortium Meeting

Feb 3-4, 2006

UMass, Boston, MA

3rd Face-to-Face MAQC Consortium Meeting

Dec 1-2, 2005

Palo Alto, CA

Initial MAQC Consortium Meeting

May 2-3, 2005

The MAQC Project: Calibrated RNA Samples, Reference Datasets, and QC Metrics/Thresholds

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FDA Parklawn Building, 5600 Fisher's Lane, Rockville, MD  20857