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A Paradigm Shift In Next-Generation Sequencing

OmeSeq Technology

OmeSeq-qRRS (quantitative Reduced Representation Sequencing; patent pending) is a novel library preparation approach for NGS-based genotyping and metagenome profiling that mitigates current challenges and limitations of other NGS-based applications. Due to its unique adapter design and use of isothermal amplification, OmeSeq provides distinct benefits that include unparalleled read quality with high-fidelity base calls across entire read lengths. The cost-effective and quantitative assays are offered in two formats: (1) “OmeSeq-qRRS”, and (2) “OmeSeq-array” or targeted OmeSeq-qRRS (i.e., in solution oligo array). More information on each method is provided below.


Based on dual restriction enzyme digestion and isothermal amplification (ligation-free), a small fraction (scalable density) of the genome/metagenome is sequenced in gene-rich regions. Several unique features of the protocol (see below) distinguish it from other commonly used methods, such as multiplexed-pcr, GBS/ddRAD-Seq, and Capture-Seq.


Considering a large proportion of qRRS-derived fragments/reads tend to be monomorphic, a “targeted OmeSeq-qRRS” uses inexpensive/short adapters and isothermal amplification to capture polymorphic regions. This leads to a decrease in cost of sequencing and significantly reduced computational burden. Adapter probe design/cost is very cost-effective due to a novel multiplexed-adapter synthesis method. OmeSeq-array has no limitation on SNP density; compare to other targeted sequencing approaches that are limited to a few thousand.

Key Features


Library preparation cost is $10 per sample. NGS cost is $1 to $10, depending on plex level and library type (i.e., OmeSeq-qRRS or OmeSeq-array)

Free of Chimeric reads

Adapter design ensures potential chimeric reads are eliminated from library

Quantitative assay

Isothermal amplification and final qPCR enrichment minimizes PCR bias and permits accurate estimation of allelic ratios for dosage-sensitive assays

dsDNA protection during adapter hybridization

The absence of a denaturation step maintains native dsDNA structure and ensures perfect adapter hybridization/matching at high annealing temperatures (65℃)

Flexible/scaling multiplexing

Capable of multiplexing 96 – 9,216 samples. More than 9,216 is possible upon request

Exceptional read quality

Unique adapter design generates high quality base calls across the entire length of reads

Robust for low quality and low concentration DNA

Degraded DNA with fragments no longer than 1-2 kb and concentrations as low as 1 ng/μl have been successfully sequenced

Imputation not required

Uniform sequencing across loci and samples minimizes missing data

Fully automated pipelines developed for downstream analysis

Software has been designed and implemented to complement and account for novel features of OmeSeq (see Bioinformatic Tools)

OmeSeq Workflow

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Potential Applications

Molecular breeding
  • Linkage map construction
  • Marker-assisted selection and genomic selection
  • Genetic diversity analyses
  • Phylogenetic analyses
Metagenomics profiling
  • Strain-level profiling from viruses to eukaryotes
  • Quantification of community members
  • Metagenome-enhanced association analysis and genomic prediction
  • Identification of genetic disorders
  • Disease risk assessment
  • Pathogen/microbe identification

Future Applications

While current applications of OmeSeq can be applied to variant identification and metagenome profiling, the OmeSeq protocol is currently being developed for:

  • Transcriptomic profiling
  • Small RNA profiling
  • Methylome sequencing
  • NGS-based Hierarchical shotgun whole genome sequencing and assembly
    (benefits of BAC-based WGS/assembly without the need for laborious BAC libraries)