Biogazelle bioinformatic expertise enables Bio-Rad to offer the most comprehensive lncRNA array content on the market

Bio-Rad collaborated with an experienced partner to extend their product portfolio of validated gene expression qPCR assays for human long non-coding RNAs (lncRNAs). To ensure the success of this project, they relied on a trusted adviser that they knew would deliver. That partner was Biogazelle. 

  • tens of thousands of qPCR assays validated in silico across entire human genome
  • 5,000 high priority assays subjected to wet lab validation

The Client

Bio-Rad Laboratories develops, manufactures, and markets a broad range of products and solutions for the life science research and clinical diagnostics markets.

Bio-Rad had previously relied on Biogazelle’s expertise to develop assay content in their PrimePCR product line, which Biogazelle designed and validated both in silico and in the lab (read more).

The Challenge

For this particular project, Bio-Rad needed a partner to develop a line of highly specific long non-coding RNA (lncRNA) qPCR assays and arrays that would enable their customers to study targets relevant to their area of research.

LncRNAs are genes that do not translate to proteins, but whose transcripts play important regulatory roles in both normal and disease biology.

The challenges were considerable. First, the project was huge in scale, requiring detailed in silico validation of tens of thousands of assays to be completed within a short timeframe. Second, as the target of the assay design was lncRNAs, the information on the gene structure was scattered across a number of databases without complete consensus of the gene annotation. Third, Bio-Rad wanted to offer its customers functional lncRNA arrays. However, as this research domain is still in its infancy, the majority of lncRNAs have not been assigned to functional pathways.

 

"I would recommend Biogazelle for their unique and innovative approaches to solving problems, and their high degree of scientific integrity."

James Flynn, Product Manager at Bio-Rad Laboratories

The Solution

Our team was able to manage the huge scale of the project, designing and in silico validating assays within acceptable timelines, thanks to our fully automated design and validation engine. We then drew upon our specific experience in high throughput assay validation to complete 5,000 wet lab assay validations in an equally short timeframe. This included qPCR analysis of a serial dilution of synthetic templates and positive and negative controls, and deep amplicon sequencing to ensure absolute specificity.

We applied our expert knowledge of the human transcriptome and relevant databases (including Ghent University’s LNCipedia) to create a unique reference transcriptome. This unified reference transcriptome was a crucial prerequisite to design qPCR assays that are specific for lncRNAs and not for sense or antisense overlapping transcripts. Our profound knowledge of the transcriptome allowed us to identify and tackle the challenges that were implied by the nature of the assay design.

In the absence of detailed lncRNA functional annotation, we built on our expertise in data-analysis and non-coding RNA to design disease or pathway specific lncRNA arrays matching the functional mRNA arrays that Bio-Rad already offers to its customers.

 

"Biogazelle came through in a big way to fine-tune the design algorithm to our needs; the results provide the best possible assays which displayed excellent performance."

James Flynn, Product Manager at Bio-Rad Laboratories

The Results

Biogazelle worked with the client’s technical staff and delivered an assay solution for the entire human genome for lncRNA gene targets that, after extensive validation, Bio-Rad was completely confident in commercializing as PrimePCR assays. Our team designed and fine-tuned our in silico pipeline in order to meet the client’s specific needs.

Biogazelle created a unique design engine that avoided many of the serious potential problems of assay specificity. This allowed Bio-Rad to offer exceptionally specific lncRNA assays to their customers.

Through the use of this novel approach for array design, Biogazelle assisted Bio-Rad in its endeavor to accelerate research in the exciting and growing field of lncRNA analysis.

 

Click to Tweet"Biogazelle’s bioinformatics team created a unique tool which allows us to offer some of the most specific lncRNA assays on the market."

James Flynn, Product Manager at Bio-Rad Laboratories

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