A Genotyping League of Its Own

Flex-Seq® Ex-L is an ultra-high-throughput targeted genotyping platform for commercial next-generation-sequencing applications. Focusing on scalability paired with data accuracy, reproducibility, and completeness allows Flex-Seq® Ex-L to deliver industry-scale solutions for industry-scale genotyping.

Flex-Seq® Ex-L genotype data matches chip-based genotyping array technology, ensuring consistency between legacy datasets. Genotyping data from other technologies can also be incorporated into Flex-Seq® Ex-L assays and custom/novel genotyping markers can be developed for any species.


Full-service pipeline

  • Tissue/DNA to SNPs

Greater balance & specificity than multiplexed PCR

Target up to 5,000 markers

  • Novel marker panels
  • Legacy data compatible

Used for:

  • Genomic selection & parentage testing
  • Plant and animal breeding
  • Population genetics
  • Pathogen detection and analysis


  • Up to 2-week turnaround time – tissue/DNA to SNPs


  • Up to 98% marker recovery
  • Up to 99% on-target sequencing
  • 99% agreement between technical reps
  • 98% agreement with array technology


  • Update Flex-Seq® Ex-L panels by adding/removing markers for evolving needs
  • Low DNA input


Multiplexed hybridization > PCR

The secret is Ex-L probe technology

  • Higher multiplexing w/ cleaner data than multiplexed PCR
  • Higher marker recovery than multiplexed PCR
  • Greater flexibility to include targets than chip-based arrays

SNPs within a 300bp window may be suitable for haplotyping.  Phased alleles improve breeding selections, especially in polyploid species.

Flex-Seq® Ex-L targets individual regions using two Ex-L probes, often focusing on a single SNP. Probes can be designed to flexibly bind on either side of the SNP, leading to greater ability to recover desired targets. Once both probes bind, the complementary sequence is synthesized between the probes and the target region is amplified from the genomic DNA. The genomic DNA and non-specific binding products are removed. The proprietary Ex-L probes enable high levels of target multiplexing in a single reaction.

Flex-Seq® Ex-L Technology

Flex-Seq® Ex-L Panel Performance

Summary metrics of genotyping results from three Flex-Seq® Ex-L marker panels.

Data Uniformity displays the percentage of markers with >0.2x mean sequence depth (91% – 98%).

Markers Recovered shows the percentage of markers (92% – 98%) with sufficient sequencing depth for accurate genotyping (i.e. 10X per haploid genome).

Sequencing Reads on Target reflects the reaction specificity, with 95 – 99% of all aligned sequencing data mapping to the intended targets.

The combination of high marker recovery, data uniformity and reaction specificity ensures efficiency and overall completeness of genotyping results for any marker panel.

Flex-Seq® Ex-L Results Uniformity

Log transformation of sequencing depth per marker using three different marker panels.
Uniform sequencing depth across all markers enables efficient multiplexed sequencing of thousands of samples.

These efficiencies can be replicated in novel marker panel designs to enable customized targeting of thousands of markers across the genome.

Flex-Seq® Ex-L Results Reliability

Correlation of the percentage of reads generated per marker between technical replicates using three different marker panels.

Flex-Seq® Ex-L demonstrates high levels of consistency in marker recovery and data quantity per marker from independent sample reactions.

High repeatability translates to a more predictable recovery of markers from sample to sample, improving the ease of additional data analysis and completeness of final results.




Number of targeted markers: flexible, fully supported design parameters for specific regions or general strategies


Sample type validation
Marker optimization and fine-tuning


Genomic selection
Parentage assignment
Fingerprinting and more

Get Started Today