Multi-Modal Analysis

Perform Several Different Types of Analysis—All in One Well

QIAGEN’s Modaplex System can perform several different types of analysis, and it gives you the flexibility to select one, a combination, or all of the analysis types to perform in one test.

The available applications are:

  • Gene Expression
  • miRNA Expression
  • Methylation Analysis
  • Fusion Gene Detection
  • Multimodal Analysis
  • Copy Number Variation
  • SNP Detection

Gene Expression

Gene and chromosome copy number variation biomarkers are now being used in the clinic to classify cancers and identify patients who will benefit from a particular treatment regime. The Modaplex platform is the only platform that combines high multiplexity, high sensitivity and a high dynamic range, allowing multiple transcripts to be quantitated from a single tissue sample in a single well with all of the appropriate controls. Very simply, develop your own complex, expression-based biomarker panel, and bring personalized medicine to your clinic.

The Modaplex System is a great way to test for gene expression biomarkers. We have performed experiments showing that we can very easily run a 16-plex and obtain a quantitative answer with FFPE and frozen samples.

To accurately quantitate mRNA expression levels it is essential that an assay technology has a broad dynamic range. The Modaplex not only has a broad dynamic range, but also allows for a high level of multiplexing.

miRNA Expression

The general importance of miRNAs as both effectors and markers of disease has increased significantly over the past decade. Traditionally thought to be part of an obscure regulatory pathway in the roundworm, miRNAs are now being targeted in therapeutics research and used as biomarkers in numerous cancer research studies, oncology treatments, sepsis, inflammatory diseases, and more.

Technology for miRNA detection has advanced greatly in recent years, and the Modaplex System is an easy way to detect and quantify miRNAs from various starting materials. The multimodal multiplexing capabilities of the Modaplex System make it possible to simultaneously detect miRNAs and mRNAs in the same well from the same tissue sample.

The Modaplex System provides a quantitative answer to your miRNA profiling questions. We have performed experiments showing that we can run a multiplex miRNA assay and obtain a relative quantification answer with FFPE and frozen samples. 

Epigenetics: Methylation Analysis

Analysis of methylation status is important for understanding diverse biological processes. Recently, methylation-specific PCR has gained traction in molecular diagnostics for such diverse areas as cancer, metabolic disease and behavioral disorders. As clinical researchers identify methylation-specific biomarkers for these key clinical areas, more diagnostic systems will need to support methylation specific PCR tests.

With the Modaplex System, clinical researchers can design and run assays for the methylation status of specific genes. Since the Modaplex System allows multi-target type assays, it is possible to design assays that define the methylation status, the expression, and the mutational status all in one well.

Fusion Gene Detection 

A chromosomal translocation happens when nonhomologous chromosomes rearrange; one type of translocation is a gene fusion. Gene fusions have been described in many cancers, and commonly used diagnostically to help differentiate between cancer types.

The Modaplex System can easily be used to analyze fusion genes from many sample types, including FFPE samples. Also, because of the unique way that the Modaplex System differentiates between amplicons, it is very easy to simultaneously detect fusion genes as well as gain-of-function SNPs in the same well from the same sample.

Some examples:


The fusion of the EML4 and ALK genes has been proposed as a causative agent in approximately 10,000 new cases of lung cancer in the United States each year.

Using a multiplex approach, we designed an assay that detects the most common EML4-ALK variants, as well as the EML4 and ALK genes. The Modaplex platform provides clinical laboratories with a simple and robust way of detecting all clinically relevant variants.


Genetic alterations of BCR-ABL and JAK2 are used to diagnostically characterize myeloproliferative disorders. QIAGEN was able to develop a demonstration assay to detect simultaneously all of the common fusion gene variants of BCR-ABL as well as the JAK2 exon 14 mutation V617F. QIAGEN was able to develop a demonstration assay to detect simultaneously all of the common fusion gene variants as well as the JAK2 exon 14 mutation. 

Multimodal Analysis

Modern molecular diagnostic and companion diagnostic tests are becoming increasingly more complex. Gene mutations, such as SNPs, often cause gain-of-function to the encoded protein that can mirror a fusion gene or lead to drug resistance. Additionally, both mRNAs and miRNAs have been identified as surrogate biomarkers in numerous disease models.

Historically, these different target types or assay types are separated into different wells, different runs and even different instrument types. Being able to assay for fusion genes and SNPs in the same well from the same sample prep would be powerful. A system that could add both mRNAs and miRNAs to such a single-well test would lend unprecedented power to the research arsenal.

The Modaplex is able to simultaneously analyze the expression of mRNAs, miRNAs, fusion genes, SNPs and more in one multiplex reaction. This makes the Modaplex the first commercially available platform to allow quantitative multimodal, multiplex analysis.

Find out how the Modaplex System can help your lab.