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48.770 Digital Array |
12.765 Digital Array |
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BioMark System |
EP1 System |
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| CNV Resolution Using the Digital Array | ||
The digital array enables a new level of sensitivity and flexibility in detecting copy number variations by employing the power of digital PCR. The Fluidigm Digital Array is the first commercially available digital PCR platform with a completely optimized workflow, ready-to-use software and high density resolution.
The digital array allows simultaneous quantification of both the gene of interest and a reference gene by using a different fluorescent dye for each assay. The ratio of the signal is the relative copy number of the gene of interest in the sample.
| The Fluidigm® 48.770 Digital Array at a Glance | |
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| Parameter | Specification |
| Samples: | 48 |
| Partitions per sample: | 770 |
| Input volume per well: | 4 µl |
| Liquid-transfer steps: | 48 |
| Reactions per chip: | 36,960 |
| Experiment tracking: | Chip-specific barcodes |
| Chip setup and valve control: | IFC Controller MX |
| Detection: | BioMark™ System or EP1 Reader |
| The Fluidigm® 12.765 Digital Array at a Glance | |
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| Parameter | Specification |
| Samples: | 12 |
| Partitions per sample: | 765 |
| Input volume per well: | 8 µl |
| Liquid-transfer steps: | 12 |
| Reactions per chip: | 9,180 |
| Experiment tracking: | Chip-specific barcodes |
| Chip setup and valve control: | IFC Controller MX |
| Detection: | BioMark™ System or EP1 Reader |
The BioMark™ Digital PCR Analysis Software is used to analyze the number of reaction chambers that are positive for the gene or genes of interest. The software is flexible and interactive, enabling viewing of results as 765 real-time amplification curves and as heat maps of threshold cycles for each panel. Data for two different PCR assays within the same panel can be displayed separately or as a single color-coded composite, which is useful for analyzing copy number variation using a reference gene. The software also displays data as numeric tables (not shown).
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| Image of end-point positive signal for RNase P | Image of end-point positive signal for CYP2D6 | Software-composed image of end-point positive signal for both genes |
Shown above are end-point images from an experiment to assay five DNA samples for copy number variation of the CYP2D6 gene (FAM TaqMan® assay). The RNase P gene (VIC TaqMan® assay) was used as the reference gene. Genomic DNA for each sample was premixed with primer/probes for both genes. Each of the mixtures was divided into two parts and loaded into side-by-side panels of a digital array. (One of the two replicates was preamplified.) The two bottom panels of the digital array were used as a no template control. The software-generated composite uses color coding (yellow for the VIC and red for the FAM) to show chambers with positive signals for either or both genes.
| Relative Copy Numbers of the CYP2D6 Gene | |||
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| DNA Samples | Ratio (CYP2D6/Rnase P) | # of CYP2D6 per Genome | Allelic Status |
| NA12155 | 0.52 | 1 | Deletion |
| NA12872 | 0.87 | 2 | Normal |
| NA07357 | 0.98 | 2 | Normal |
| NA12873 | 0.52 | 1 | Deletion |
| NA11994 | 1.49 | 3 | Duplication |
Absolute quantification of both genes was used to determine the ratio of the CYP2D6 gene to the RNase P gene for each sample. Thus, the digital array may be used as a tool to quickly and reliably determine the variation in gene copy number between samples.
Overviews
Presentation
September 1 – 3, 2008
Stem Cell Europe Conference 2008; Amsterdam, Netherlands
Poster 1045
BioMark Dynamic Arrays for Single-Cell Gene Expression Analysis
Presented by: Kenneth J. Livak, PhD; Senior Scientific Fellow
View pdf of poster
Listen to the audio presentation by Dr. Livak
November 10 - 13, 2008
qPCR Symposium; Millbrae, CA
Poster
96.96 Dynamic Arrays for Rapid, Accurate Real-Time Gene Expression Analysis
Presented by: Sandra Spurgeon, PhD; Senior Scientist
View pdf of poster
Listen to the audio presentation by Dr. Spurgeon
Poster
Efficient Drug Metabolism Studies Using the BioMarkT System
Presented by: Alain Mir, PhD; Senior Scientist
Product Data Sheet
The Fluidigm 48.770 Digital Array delivers high-throughput digital PCR* - the most powerful technique for individual molecule quantification.
Product Data Sheet
The Fluidigm 12.765 Digital Array harnesses the power of digital PCR*—setting a new standard for PCR sensitivity.
* Digital PCR is a technique to quantify the amount of DNA in a sample by counting amplifications from single molecules.
Application Note
The Study Of Copy Number Variations (CNVs) Using the 12.765 Digital Array.
Application Note
Enabling Loss of Heterozygosity Studies Using Fluidigm Digital Arrays
Application Note
Efficient Drug Metabolism Studies using the Fluidigm System
Product Data Sheet
The BioMark system streamlines workflow for applications demanding sensitivity and dynamic range, at extremely high throughput.
Product Data Sheet
The BioMark™ System Software Suite offers the perfect combination of instrument management, data analysis, and data management tools, as well as an easy-to-use software interface.
Product Data Sheet
The EP1 Reader opens the door to the power of integrated fluidic circuits (IFCs) for high-throughput SNP genotyping and digital PCR.
Product Data Sheet
The Fluidigm® System Software Suite offers the perfect combination of instrument management, data analysis, and data management tools, as well as an easy-to-use software interface.
Product Data Sheet
The Fluidigm Stand-Alone Thermal Cycler (STC) provides an ideal solution for end-point PCR assays on Fluidigm integrated fluidic circuits (IFCs).
Product Data Sheet
The Fluidigm IFC Controller MX allows the simple setup of high-density reactions within the integrated fluidic circuit (IFC) chips.
BioMark™ Bibliography
Gene Expression, Genotyping, Digital PCR - BioMark related journal publications.
