The MonsterPlex Technology


Floodlight Genomics uses a series of innovations, collectively known as “MonsterPlex”, to PCR amplify 100’s of genetic targets from small amounts of genomic DNA.  The entire process is single-tube.  Indices (barcodes) are added during amplification and the resulting indexed amplicons are pooled. A sequencing library is then constructed from the pooled amplicons for analysis on a next generation sequencing platform (Ion or Illumina).

Our goal is  >20X sequence coverage per target. The overall cost of a project depends on the size of the multiplex mixtures and the sequencing technology employed. For example, a study using a MiSeq device to process 380bp targets (>10M paired reads in a 2×300 config) will have a per target cost higher than a study that takes advantage of the sequencing capacity of a HiSeq device with 80bp targets (>200M paired reads).

MonsterPlex was specifically designed to assess genetic variation in 1000’s of samples (e.g. parentage panels or large surveys) but can also be valuable for smaller studies involving 100’s of samples.

Special not-for-profit rates are available to University or other not-for-profit projects through the Educational Outreach Program.  Please contact Floodlight Genomics for more details on how this works (  With this program, you only pay for time and reagents/consumables.

MonsterPlex has been blind tested on animals and plants at a commercial scale (e.g. 1000 samples) and demonstrated a low genotype error rate (>98% concordance) even for highly complex target regions containing clustered SNPs and multi-base INDELs. Replication both within and across sequencing platforms has proved similarly robust.

MonsterPlex has been used extensively to amplify targets from mixed samples (e.g. pathogen targets amplified from infected plant tissue) and the opportunities for novel discovery are immense.

Massively multi-plexed, low cost, high sample number, targeted genetic sequencing (amplicon sequencing). Genotyping. CRISPR screening (1 to 50bp INDELs). Tiling-based re-sequencing. Gene expression (gene profiling). PCR-free library prep. Whole-genome sequencing. SNP discovery. RAD and GBS marker conversion. You dream it up, we do it.