Fields of Research

Fluidigm and Next Generation Sequencing

fluidigm next gen

Next generation sequencing promises to revolutionize life science in fields as diverse as human genomics, species discovery, and personalized medicine—any field in which advancement depends on a deeper understanding of genomic variation and transcriptome complexity. Compared to generation I (Sanger) sequencing of the Human Genome Project, generation II technology lowers the cost per base dramatically while producing giga-base results per day. Despite this cost effectiveness, the technology faces barriers to widespread adoption, among them the complexity of sample preparation and quantification.

Fluidigm Access Array™ System for Library Preparation

A proven solution that radically simplifies library preparation and enables massively multiplexed sequencing

The typical library preparation workflow involves an intricate process in which individual target molecules are isolated and then amplified individually. Because of the up-front costs, laboratories typically prepare only one or very few samples at a time for sequencing, and the information gathered from a sample is random, requiring massive oversampling. Sequencing projects encompassing 100s to 1,000s of samples are impractical given these constraints.

The Fluidigm Access Array™ IFC eases the burden of library preparation because it facilitates the amplification and barcoding of 48 samples in parallel, with minimal time and labor and in as few as three hours. Because every sample may be identified by its barcode, all 48 samples can be multiplexed at the sequencing step. This capability dramatically reduces the time and money required for large scale projects, opening new vistas of research. For example, scientists interested in large cohort studies can relatively easily sequence specific genes of interest from hundreds of individuals in a matter of weeks.

Key benefits of the Access Array™ IFC include:

  • High throughput – processes 48 samples per chip
  • Easy to use – requires only 96 liquid transfer steps to process 48 samples
  • Fast – takes just four hours to prepare 48 samples

fluidigm next gen sequencing

Fluidigm SlingShot™ Kit for Library Quantification

Enabling absolute quantification of amplified sequences

While simple in theory, next generation sequencing can be very challenging because of the lack of an easy and reliable method to quantify the concentration of molecules within sequencing libraries. With bead based methods, over-saturation leads to the hybridizing of multiple sequences on the same bead, making the sequences indistinguishable. Under-saturated libraries fail sequencing because the majority of the beads are “blank” and thus give no information. (See graphic.) Non bead-based methods suffer from the similar complications. In either case, the researcher is forced to rerun the samples, at significant additional cost and time.

Library of Unknown Concentration

The SlingShot™ kit from Fluidigm is the first product to easily determine the optimal sample concentration—before samples advance to sequencing. With SlingShot, digital PCR is used to easily determine the absolute quantity of target sequences, thus improving sequencing results generally and enabling the sequencing of previously undetectable samples.

Key benefits of the SlingShot™ kit include:

  • Small sample requirements – a 1,000 fold reduction in input volumes
  • Easy-to-use – only 3 liquid handling steps per library
  • Time efficient – eliminates titration steps at the sequencing stage

Resources

Publications

  • Pushkarev, D., Neff, N.F., Quake, S.R. 2009 Aug 10. Single-molecule sequencing of an individual human genome. Nat Biotechnol. [Epub ahead of print] [Editor's Note: The SlingShot™ Kit from Fluidigm was used in this project to quantitiate samples for sequencing] Access Article
  • Weinstein, J.A., Jiang, N., White, R.A. 3rd, Fisher, D.S., Quake, S.R. 2009 May 8. High-throughput sequencing of the zebrafish antibody repertoire. Science. 324(5928):807-10. [Editor's Note: The SlingShot™ Kit from Fluidigm was used in this project to quantitiate samples for sequencing] Download pdf

Research Poster

  • Implementation of Fluidigm’s SlingShot™ Absolute Quantitation Product offers the dual advantage of replacing the costly and time-consuming titration step as well as recovery of sub-optimal DNA Samples for Roche 454 Next Generation Sequencing - Download poster (pdf)

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