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The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Open accessAbstract
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. 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 in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.
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“Using the common intra-site DEGs to validate the called inter-site DEGs, the MCC41, 42 showed that PEER also yields a higher accuracy than the original limmavoom method (Supplementary Fig. 22d,e), indicating that global data normalization analysis methods such as PEER can also be used to improve RNA-seq data across both Illumina and the PGM platforms.”
From Detecting and correcting systematic variation in large-scale RNA sequencing data (2014) · cites this paper as [42]
In the citing paper
“for instance, the Food and Drug Administration (FDA) agency of the USA employed the MCC as the main evaluation measure in the MicroArray II / Sequencing Quality Control (MAQC/SEQC) projects [41, 42].”
From The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation (2020) · cites this paper as [41]
In the citing paper
“Within the MicroArray Quality Control (MAQC)-II study [7], we observed, however, that the performance of gene expression models in predicting clinical outcome was limited and largely dependent on the respective clinical endpoint.”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [7]
In the citing paper
“Within the MicroArray Quality Control (MAQC)-II study [7], we observed, however, that the performance of gene expression models in predicting clinical outcome was limited and largely dependent on the respective clinical endpoint.”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [7]
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“Considering the fact that the nature of the clinical endpoint strongly affects a classifier’s performance [7, 18], we included endpoints that are known to cover a broad range of predictive difficulties (low difficulty, SEX, and CLASS LABEL; intermediate difficulty, EFS ALL, and OS ALL; high difficulty, EFS HR, and OS HR).”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [7]
In the citing paper
“Evaluation of the prediction performances in the validation set revealed that the endpoint represents the most relevant factor affecting model performances, which is well in line with the findings of the MAQC-II study [7].”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [7]
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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
Foox, J., Tighe, S. W., Nicolet, C. M., Zook, J. M., Byrska‐Bishop, M. S., Clarke, W. E., Khayat, M. M., Mahmoud, M., Laaguiby, P. K., Herbert, Z. T., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01049-5 · Cited by 144
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k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction
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Grading of soft tissue sarcomas: from histological to molecular assessment
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Ultrasensitive detection of rare mutations using next-generation targeted resequencing
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“Given the issue of the true positives relative to the true negatives being highly skewed (18), we report a balanced measure for the classification accuracy using the Matthews Correlation coefficient (MCC) as was done for the MAQCII analysis (19).”
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Practices and Trends of Machine Learning Application in Nanotoxicology
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“MCC is equivalent to the Pearson Correlation Coefficient for binary variables [147] and has been selected as an evaluation metric for micro-array-based predictive models by the MicroArray Quality Control (MAQC) Consortium [148].”
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Metadata
- Authors
- MAQC Consortium
- Venue
- Nature Biotechnology
- Published
- 2010-07-30
- Volume
- 28
- Issue
- 8
- Pages
- 827-838
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3315840
- OpenAlex
- W2021560851
- Cited by
- 889
- References
- 63
- Citations by year
- 2026: 13 · 2025: 33 · 2024: 39 · 2023: 35 · 2022: 40 · 2021: 58 · 2020: 61 · 2019: 58 · 2018: 46 · 2017: 35 · 2016: 57 · 2015: 54 · 2014: 87 · 2013: 85 · 2012: 79
- FWCI
- 34.94
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Institute of Process Engineering, CAS Institutional Repository (submittedVersion, cc-by-nc-sa)
- IRIS (submittedVersion)
- Repository of Futwangen University of Applied Sciences (Furtwangen University) (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Funders
- National Institutes of Health (Z99 LM999999, Z99 HL999999, Z99 MH999999, Z99CL999999)
- National Cancer Institute (CA97513-01, CA55819-01A1, R00CA126184, P01CA055819, R33CA097513)
- National Institute of General Medical Sciences (T32GM074906, R01GM083084, R01GM083226, R01GM072611)
- National Center for Research Resources (R01RR021967)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- microarray quality control, gene expression profiling, prediction model, genomic classifier, model validation, pulmonary toxicity, hepatotoxicity, breast cancer, multiple myeloma, neuroblastoma, rodent toxicity, method comparison, reproducibility
- MeSH terms
- Animals, Breast Neoplasms, Disease Models, Animal, Female, Humans, Liver Diseases, Lung Diseases, Multiple Myeloma, Neoplasms, Neuroblastoma, Predictive Value of Tests, Quality Control, Survival Analysis, Guidelines as Topic, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Rats
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