FocusSeq Technology – Cost-effective, Focused Sequencing of Genomic Regions of Interest

FocusSeq target panel sequencing from Sinuglomics

Identifying genetic variants is an essential component of many research fields, from profiling mutations that increase cancer risk to understanding human ancestral origins to developing targeted therapies. While whole-genome sequencing (WGS) and whole-exome sequencing (WES) can reveal broad-scale genomic differences, a more focused approach that targets specific genomic areas can produce more relevant, precise, and manageable data in a cost-effective way.

Our FocusSeq service is the ideal solution for studying variations in specific genes or other genomic areas of interest. FocusSeq technology is based on the design of targeted next-generation sequencing panels composed of hundreds of PCR targets. The resulting amplicons target specific genomic regions of interest, allowing detection of SNPs and indels faster and more cost-effectively than with whole-genome approaches. FocusSeq yields high-confidence results while also reducing the background noise typical of WGS and other higher throughput methods.

Our service includes the design, optimization, validation, and data analysis of custom panels, incorporating a highly multiplexed PCR-based workflow and amplicon sequencing. Our solution offers high coverage and redundancy, as well as high sensitivity and specificity, with the ability to analyze a few to hundreds of genetic targets. With our optimized protocols for biological samples such as blood, saliva, and frozen tissues, we generate high-confidence data for many areas of application, including cancer and genetic diseases.

At SingulOmics, our custom-designed PCR panels, in combination with our amplicon sequencing and data analysis, have greater proven efficacy in variant detection than conventional sequencing methods. We design targeted panels with high redundancy for each locus of interest, allowing the optimal representation of each region. By focusing on specific genomic areas, our technology can be particularly helpful for detecting low-frequency variants, which can be lost in whole-genome analysis. The FocusSeq solution can be applied to a wide array of samples, including blood, saliva, cell lines, and formalin-fixed paraffin-embedded (FFPE) or frozen tissues. Our methodology ensures highly reliable results and allows us to customize conditions for the specific requirements of each project, from the initial design to final data analysis.

FocusSeq advantages over WGS and WES

  • Higher sensitivity for low-frequency variants
  • Increased sequencing coverage for focused genomic regions at lower cost
  • Faster turnaround time

Applications of FocusSeq

  • Gene expression analysis
  • SNP identification/analysis
  • Disease variant research
  • Tumor profiling
  • Crop trait analysis
  • Genome editing confirmation
  • Identification of low-frequency variants
  • Genetic screening
  • Trait mapping

Why SingulOmics?

  • Extensive experience with targeted sequencing panels
  • Each project is custom-designed to meet individual client’s needs
  • Panels are designed, validated, and tested to guarantee best results
  • Our optimized protocols have been validated and used on thousands of client samples

Service Workflow

Focus Seq targeted sequencing workflow

 

Sample Requirements

We accept samples in the following formats:

  • Frozen cells
    • Amount required: >10,000 cells in cell culture medium (DMEM, EMEM, RPMI 1640, or FBS).
    • Shipping: Frozen cells should be shipped in standard freezing media in 1.5 mL microfuge tubes or cryogenic storage vials. The frozen vials should be shipped on dry ice.
  • Purified genomic DNA
    • Amount required: >500 ng
    • Shipping: Genomic DNA can be shipped in microfuge tubes or 0.2 mL PCR 8-tube strips. For more than 6 samples, PCR strips are preferred. Samples should be shipped on dry ice.
  • PCR products
    • Shipping: PCR products should be shipped in 0.2 mL PCR 8-tube strips. Samples should be shipped on dry ice.
  • Blood and saliva
    • Amount required: blood (1 mL), saliva (2 mL)
    • Shipping: Blood and saliva should be shipped in screw-capped conical tubes. Tubes should be tightly sealed to avoid any leakage and should not be filled to the top. Samples should be shipped at room temperature.
  • Buccal swabs
    • Swab samples should be obtained using a swab specific collection kit. We recommend the Isohelix SK-1S/MS-01 Buccal Swab kit with Isohelix capsules.
    • Shipping: Swab samples should be shipped at room temperature.
  • Frozen tissues
    • Amount required: >50 mg
    • Fresh tissue, immediate after collection, must be "snap" or "flash" frozen on dry ice or in liquid nitrogen
    • If possible, smaller size tissue (approx. 50 mg) is preferred as it can be frozen faster than a larger one.
    • Shipping: Frozen tissues should be shipped on dry ice.
  • FFPE tissue sections
    • Amount required: up to 10 µm thick
    • Shipping: FFPE tissue sections should be shipped at room temperature.

Publications

  1. Miller et al. 2017. Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants. Oncotarget. 8(60): 102033–102045 doi: 10.18632/oncotarget.22116
  2. Delio et al. 2015. Development of a targeted multi-disorder high-throughput sequencing assay for the effective identification of disease-causing variants. PLoS One. 10(7): e0133742 doi: 10.1371/journal.pone.0133742.

Next Steps...

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