Expression Analysis Stakes Claim on RNA-Seq

Company Regards Sequencing Method as Significant Competitive Advantage

About a decade ago, Expression Analysis (EA) was just a fictitious business plan written to fulfill course work for an MBA degree. The company’s founder, Steve Casey, worked for the Howard Hughes Medical Institute (HHMI) at Duke University Medical Center, while studying for his MBA at night.

The Duke Microarray Core Facility (MCF), funded by HHMI, began receiving an increasing number of requests to run Affymetrix microarrays for paying clients, but the not-for-profit MCF turned them down. Casey used the situation to create a real business plan for a hypothetical company that provided for-profit microarray services.

In October 2001, that business plan evolved into Expression Analysis, the first commercial Affymetrix provider with a service-centered business model. In the next few years, according to Casey, EA also became the first company to submit microarray data electronically to the FDA, and its microarray processing facility was the first to implement quality systems and procedures in compliance with Good Laboratory Practices and Clinical Laboratory Improvement Amendments.

Today the company “provides regulatory compliant genetic services to a variety of clients to support their clinical trial and research efforts,” says Steve McPhail, president and CEO. He notes that EA offers a full range of solutions, including experimental design, sample analysis, nucleic acid isolation, gene-expression profiling, genotyping, next-generation sequencing, and advanced bioinformatics.

Clients include pharmaceutical firms, biotechnology and diagnostic firms, government laboratories, research institutions, and nonprofit consortiums.

Microarray Testing Services

The company initially focused on performing high-throughput microarray testing services on a single platform. But as the field of genomics expanded, so did the company’s services. Today EA offers a broad range of services across multiple platforms, including Affymetrix, Agilent, Fluidigm, Illumina, Ion Torrent, and RainDance Technologies.

Using these top-of-the-line instruments, EA works on solutions for specimen types, such as whole blood and fresh-frozen tissues, as well as providing nucleic acid isolation and data analysis services. EA is experiencing significant growth in its DNA sequencing services and is investing in tools to advance sequencing data and analysis, according to McPhail.

In the Cloud

One of newest technologies offered by EA is RNA-Seq. “RNA-Seq profiles the whole transcriptome and generates a thousand times more data than a typical microarray,” says McPhail.

RNA-Seq investigates biological events beyond the reach of microarrays, such as the identification of novel transcripts and isoforms, alternative splicing sites, and allele-specific expressions. However, this means higher complexity in terms of bioinformatics and data storage and processing.

To advance the adoption of RNA-Seq, EA teamed up with Golden Helix and created a solution that processes data in a service-based cloud-computing environment. These integrated desktop tools are simplified, scalable, and affordable, notes McPhail.

In the current configuration, raw sequence data are streamed to the cloud, where FASTQ files are generated in a primary analysis pipeline from EA. FASTQ files are aligned and normalized and both isoform and gene detection are performed in a secondary analysis pipeline from EA. When users are ready to interpret this data, Golden Helix provides differential expression workflows optimized for RNA-Seq data.

Golden Helix also services customers with its SNP & Variation Suite software, which incorporates a desktop-based genome browser designed to query and view datasets in the cloud. “We’re excited to bring the complementary capabilities to the broader community,” says McPhail.

To further entice researchers to try RNA-Seq, EA, Golden Helix, and Illumina teamed up to offer three grants for cutting-edge projects aimed at identifying genetic elements involved in human health. EA will perform the sequencing and data analysis, Golden Helix will provide cloud-based storage and tertiary analysis tools, and Illumina will furnish products required for the study.

EA recently partnered with Pacific Biosciences to offer its PacBio RS system. This technology uses single molecule, real-time sequencing to give insights into fundamental underlying biological processes. Initial applications include de novo and hybrid assembly, pathogen identification, and targeted sequencing.

The DNA sequencing platform generates ultra-long read lengths and detects kinetic information not available elsewhere. “The longest sequence reads in our lab are approaching 20,000 bases,” says McPhail.

Over the years, EA also has formed alliances with many government agencies and foundations, including the International Serious Adverse Events Consortium, the Spinal Muscular Atrophy Foundation, the Cure Huntington’s Disease Foundation, and International Neuroscience Network Foundation.

“We participate to help move genomics testing forward to meet our mission of applying genomic data to improve the diagnosis, treatment, and management of complex diseases,” explains McPhail.

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