PCR

BioMark HD high-throughput real-time PCR system

The Biomark HD system is a high-throughput real-time PCR system developed by Fluidigm. The system relies on microfluidic valve technology for sample and reagents handling. The key benefits of the system include high-throughput (10s of thousand PCR reactions per day possible), low reagent consumption (nanoliter reaction chambers), reproducible results from populations of cells down to a single cell. In addition to real-time PCR the system enables digital PCR measurements and the generation of multiplexed amplicon libraries for NGS applications.

The system consists of a real-time PCR instrument (the Biomark HD Reader), Dynamic or Digital array Integrated Fluidic Circuits (IFCs) and the IFC controllers.

PCR Equipment Genomics Basel

Fluidigm BioMark HD PCR system
The IFC controllers are designed to prime and load Dynamic and Digital array IFCs. From left to right: MX, HX, AX (pre-PCR), AX (post-PCR). Open IFC controller HX with 96.96 Dynamic array.

Array formats which are supported by our setup

Dynamic Array IFCs allow for high-throughput gene expression analysis of 48 or 96 (48/96) target genes in 48/96 cDNA samples or testing of 48/96 SNPs in 48/96 patient samples. You can choose eg. between TaqMan probes and EvaGreen as method of detection.

48.48 Dynamic Array IFC
96.96 Dynamic Array IFC

Digital Array IFCs: Digital PCR enables absolute quantification of molecules in a sample. This technology can be used for determining the absolute count of mRNAs in a given sample, analysis of copy number variations (CNV) and detection of low frequency mutatio.

12.765 Digital Array IFC
48.770 Digital Array IFC

Access Array IFCs enable the generation of multiplexed amplicon libraries for targeted sequencing on the Illumina or Roche NGS systems. In the format of 48x48 2,304 PCR reactions are assembled each containing one of 48 primer pairs and one of 48 DNA (patient) samples. After the PCR reaction the 48 amplicons of a single sample are pooled and harvested out of the Access Array IFC. Each sample (patient) contains a unique barcode/index so that all 48 patient samples can be combined, sequenced and afterwards de-multiplexed.

QX100 ddPCR

Droplet Digital PCR (ddPCR ) provides an absolute quantification of target DNA molecules with high accuracy and sensitivity. ddPCR is considered the 3rd generation of PCR technology. ddPCR applications include measurement of copy number variation, rare variant detection, mutation detection, and gene expression analysis.

BioRad QX100 ddPCR system

QX100 droplet reader and accessory PCR system for intermediate end point PCR step. The reader enables detection of FAM, VIC and HEX probes. BioRad QX100 droplet generator and accessory sealer (left).
Image shows the uniformity of the generated droplets. Green droplets contain PCR amplicons whereas dark droplets are negative.

Further information

external page Introductory video to the system on YouTube.

Publications with information to QX100 Droplet Digital PCR:

external page Evaluation of a Droplet Digital Polymerase Chain Reaction Format for DNA Copy Number Quantification

external page High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number