Fluidigm announces universal sample prep workflow for single-cell DNA sequencing

Fluidigm CorporationDec 24 2013

Fluidigm Corporation (NASDAQ:FLDM) today announced a universal sample prep workflow for single-cell DNA sequencing that runs on its C₁^TM Single-Cell Auto Prep System. This workflow streamlines targeted, whole exome and whole genome sequencing in heterogeneous cell populations and enables researchers to discover and screen somatic mutations, such as SNP, small indels, and translocations.

Somatic mutations are non-inherited, random mutations that are accumulated over time and may play an important role in the origin and progression of complex diseases, such as aging, cancer, immunity, and neurodegenerative disorders.

"Somatic mutations are often masked in sequencing of bulk tissue, leaving researchers with the risk of missing important, causal variants that elucidate disease mechanisms. Understanding somatic mutations can help identify more effective therapies," said Gajus Worthington, Fluidigm president and chief executive officer. "The C₁ DNA Sequencing workflow is the first to fully automate cell handling, imaging, staining, and whole genome amplification, all at a single-cell level. It enables researchers with a comprehensive suite of single-cell sequencing applications they can use to identify and screen novel DNA variants from heterogeneous samples at unprecedented resolution and speed," he added.

"Human leukemia, such as Acute Myeloid Leukemia (AML), is a genetically heterogeneous disease caused by the accumulation of somatic mutations in hematopoietic stem/progenitor cells. These mutations change the normal mechanisms of self-renewal, proliferation, and differentiation of cells in the blood and are highly variable between AML patients," said Paresh Vyas, MD/PhD and Hematologist at the MRC Molecular Hematology Unit, University of Oxford and Oxford Biomedical Research Centre. "We can use the C₁ DNA Sequencing workflow to detect genetic changes that identify clonal structures to more accurately classify tumors. This will lead to better understanding of prognosis including risk of recurrence and possibly even overall survival," Vyas explained.

From discovery of disease factors to validating the most effective treatment, researchers can now use the C₁ Single-Cell DNA Sequencing workflow for:

• Single-Cell Targeted Resequencing to screen for known mutations or identify signatures that may identify disease susceptibility, progress, or therapeutic efficacy. The C₁ workflow is compatible with the Fluidigm Access Array ^TM System and D3 Assay Design service (Fluidigm's customized primer design service for targeted resequencing, gene expression, and genotyping);
• Single-Cell Exome Sequencing to discover functionally relevant mutations in protein coding regions of the genome; and
• Single-Cell Whole Genome Sequencing for its comprehensive approach, allowing the discovery of all possible somatic mutations in both functional and regulatory regions of the genome.

The new workflow consists of the C₁ Integrated Fluidic Circuits, C₁ Reagent kit, and validated scripts, and also leverages the GE illustra GenomiPhi V2 DNA Amplification Kit for whole genome amplification. The C₁ DNA Sequencing workflow will be further enhanced by Fluidigm's SINGuLAR ^TM Analysis Toolset 3.0, which will include new features to filter, visualize, and rapidly identify biologically relevant variants. The toolset can also be used to create custom variant groups to fit the specific needs of any clinical researcher.

This workflow allows researchers to:

• Isolate and prepare sequencing-ready libraries directly from individual cells;
• Achieve uniform chromosomal coverage (>94%) with low allelic bias;
• Yield enough amplicon from an individual cell for two subsequent sequencing runs and quality control;
• Process, sequence, and analyze 96 single cells in parallel in under 24 hours, with less than six hours of hands-on time; and
• Use the new D3^TM Assay Design Service to create custom panels to interrogate up to 480 genomic targets per cell.

The targeted sequencing workflow is currently available for early access customers. The whole genome and whole exome applications is expected to be released in early 2014.