Real-Time PCR Using OpenArray Technology

OpenArray System as a Tool for High-Throughput Genotyping
and Gene Expression Analysis
OpenArray is a unique technology provided by Thermo Fisher Scientific, minimizing reagent use and helping to decrease the price per data point.

OpenArray technology streamline real-time PCR studies that use large numbers of samples, assays, or both, as a single QuantStudio 12K Flex OpenArray plate is equivalent to running eight traditional 384-well plates. Broad range of applications including SNP genotyping, Gene Expression, microRNA analysis and pharmacogenomics
(Broccanello, Chiara et al.2020).

Once the most suitable array format is chosen according to the type of experiment, the number of samples, and targets, an online tool allows the operator to configure and order the array plates. 

The OpenArray plates contain custom or predesigned TaqMan GeneExpression or SNP Genotyping assays preloaded into the plate 3,072 through-holes. These through-holes are externally hydrophobic and internally hydrophilic and are able to hold 33-nL of reagents via capillary action. Each plate contains 48 subarrays, each with 64 through-holes*.

 

* Figure 1: TaqMan OpenArray Plate anatomy

Custom OpenArray® plates: 

3 million TaqMan® Gene Expression Assays

5 million predesigned genotyping assays

  • 2,700 inventoried drug-metabolizing enzyme (DME) assays
  • Custom TaqMan® assays

Custom OpenArray plates include a suite of 11 formats >>> Click here 

Workflow: 

TaqMan Assays can also be designed and tested for robustness in previous validation experiments in order to select the best ones to insert into the arrays. Thermo Fisher Scientific made available some easy to use OpenArray plates containing human predesigned assays, such as “Cancer Panel,” “Signal Transduction Panel,” “Stem Cell Panel,” “Inflammation Panel,” “Kinome Panel,” “Advanced MicroRNA Panel,” and “Pharmacogenomics Express Panel.”

Applications:

  1. SNP Genotyping
    Highest sample throughput for mid-density genotyping. In a single work day, 36 TaqMan OpenArray Genotyping Plates can be run on the OpenArray Real-Time PCR Platform to generate data for >110,000 genotypes. Arrays are increasingly used for research in the medical science, for example:
  • Genotyping application has been involved in the study of Parkinson disease. Ross et al. in 2018 developed an array to study 22 SNPs associated to essential tremor.
  • Forensic analysis use SNPs for individual identification and paternity test, Pomeroy et al. in 2009 developed a method for individual identification using only seven SNPs.
  • Animal genetics, in the Sardinian sheep SNPs associated with variations at regulatory regions of the milk protein genes. Fingerprinting chicken breeds by Viale et al. in 2017 using OpenArray technology.
  1. Gene Expression Analysis
    Analyze up to 2,304 samples for gene expression per day using the OpenArray Technology and our TaqMan Gene Expression Assays allows to process a total of over 5,184 genotyping samples in one day.

To evaluate mechanisms underlying melanoma tumor biology and improve the prediction of metastasis formation in 2018 Cook et al. developed and validated a gene expression profile using OpenArray.

  1. MicroRNA Analysis
    QuantStudio 12K Flex Real-Time System helps streamline microRNA (miRNA) profiling, at a scale previously unattainable.
    • Broad coverage: run 3 samples per QuantStudio 12K Flex OpenArray Plate translating up to 818 assays per sample (up to 758 unique assays)
    • High throughput: 12 samples per ~2 hr instrument run and 48 samples per 8hr working day
    • Cost effective: rapid sample screening with minimal hands-on time

Favero C et al. in 2017 developed a chip to investigate the expression of miRNA to discriminate between malignant pleural mesothelioma patients (MPM) and subjects with past asbestos exposure (PAE).

Another example, in 2013, Hudsun et al. used “MicroRNA Panel” in medullary thyroid carcinoma research to discover an overexpression of miR-10a and miR-375.

  1. Pharmacogenomics

Predict an individual’s response to a drug, allowing to select medications over others. To develop precise and cost-effective treatment, doses tailored to an individual genetic profile for a better outcome. Analyze up to 1,700 samples per day using our 2,700 predesigned TaqMan Assays for drug-metabolizing enzymes (DMEs).

Pharmacogenomics (PGx) study conducted in at UPMC Presbyterian Hospital in Pittsburgh using high-density population screening of 4,627 markers within 1,191 genes, aimed to isolate concise PGx signatures that associate with novel and known phenotypes within specific patient cohort. Targeted PGx testing can be deployed clinically in the future, using validated testing platforms.