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.