MAQC Society Projects

A New MAQC Society Project Proposal for Inflammatory Molecular Assays/Biomarkers

Background:  The Massive Analysis and Quality Control (MAQC) Society is a fledgling society with its historic roots related to a series of genomic molecular assay projects (MAQC, MAQC II. SEQC/MAQC III, SEQC2) led by the US FDA starting in 2005 and continuing to today.  The historical motivation for these efforts were challenges that arose in the reproducibility (across laboratories, across platforms, across data analytic methods) of genomic testing in a variety of technologies:  qPCR, microarray, next-gen sequencing (NGS).  These combined systems often generated massive datasets for analysis and interpretation, often with complex multi-step and iterative data analysis pipelines.  Genomic and proteomics assays were typically used for drug development, clinical discovery and diagnostics, and safety/risk assessment.  Especially in the early maturation of microarray and next-gen technologies, basic issues frequently arose regarding apparent discordance between highly similar experiments and studies.   The MAQC Consortium and later the MAQC Society would address many of these issues.

Rational for MAQC Society involvement in inflammatory molecular assays and biomarkers:

Inflammation as class of biological mechanisms underlies a spectrum of diseases and poses a unique opportunity to understand both its fundamental (core) and disease-state specific features.

Single and small multiplex analyte assays (e.g., immunohistochemistry (IHC), enzyme-linked immunosorbent assay (ELISA), flow and mass cytometry, mass spec and general Ab-based immunoassays) have a long history and association with inflammatory and immune-related diseases.  Some are qualitative while others are semi-quantitative.  Historically, the amount of data associated with these assays have been comparatively modest (vs. genomics) and the quality challenges were well known, usually related to specificity and affinity of specific Ab-binding reagents.   However, inflammation-related assays have recently gained an order of magnitude or more in complexity in recent years.  Current flow cytometry methods for immune-related diseases and conditions now typically incorporate tens and up to nearly one hundred multiplexed analytes on potentially thousands of cells per patient.  IHC methods have similarly increased complexity for examining cells preserved in formalin for equivalent numbers of cells.  Interestingly, with the emergence of single-cell RNA sequencing (scRNA-seq), there are now competing methods to traditional IHC, single- to multiplexed ELISAs, and flow methods for identifying and classifying individual cell types of interest.  

Therefore, we would like to form a MAQC Society project and Working Group(s) devoted to assays associated with inflammatory diseases.


Anticipated studies:  This project and related working group(s) will assemble existing and spawn potentially new studies using relevant assays and technologies.  The coherence of related technologies should exist in theory but in current practice there are challenges associated with each method: 

  • scRNA-seq: new methods are evolving quickly, and challenges include biases from cell stabilization, cryopreservation, contamination from nuclear RNA or extracellular RNA, inclusion/exclusion of necrotic cells, commutability of distinct library protocols and platforms

  • Highly multiplexed flow/mass cytometry:  cytometry has challenges related to crosstalk, confirming utility of markers (especially for rare events), gating bias/ambiguity combined with multi-dimensional representations of cells (sample and cell composition)

  • General proteomic methods:  various performance characteristics of proteomics methods for inflammatory biomarkers should be assessed as well as their commutability

Anticipated potential outcomes:

  • Understanding of the state of technologies to measure inflammatory process and factors driving the reproducibility of inflammatory panel assays.

  • Creation of reference materials based on known mixtures of immune cell lines (ground truth) that can be used for evaluating platforms, methods, and protocols

    • Quantitative performance metrics will be developed for inflammatory panel performance

  • Best practices related to various approaches and methods for sensitivity, specificity, and reproducibility of inflammatory panel, disease, and therapeutic results, both single-cell and bulk analysis, including the importance of pre-analytical variables


Please reply to or if you and/or your institution is interested in participating in this important MAQC Society Project related to Inflammatory Panels and Biomarkers and provide feedback on the selection of initial areas of focus and potentially identify already existing datasets that are or could be made public for which this project can use or expand.  Other useful contributions can include providing well described tissue samples for testing.



Shi, L., Kusko, R., Wolfinger, R.D., Haibe-Kains, B., Fischer, M., Sansone, S.A., Mason, C.E., Furlanello, C., Jones, W.D., Ning, B. and Tong, W., 2017. The international MAQC Society launches to enhance reproducibility of high-throughput technologies. Nature biotechnology, 35(12), p.1127.