Spotlight: Benchmarking

You have options in enrichment methods for targeted sequencing. How does Xdrop® compare to other commercial solutions?

Why targeted sequencing?

With high-throughput sequencing becoming more affordable and widespread, you ask why enrich targets in the first place.

The short answer: simple, robust, detailed scrutiny of a genomic region.

The long answer is that targeting:

  • saves time and cost, especially with large and complex genomes

  • allows for a higher sample throughput and read depth

  • simplifies bioinformatic analysis by reducing sequence diversity

  • mitigates ethical complications in a diagnostics setting

Not all enrichment methods are alike

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On average, other enrichment methods use 10–1000 times more input DNA than Xdrop

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From assay design to sequencing results, alternatives to Xdrop take on average 5 times longer

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Xdrop stands alone in its use of a completely different strategy to capture target fragments of DNA

What are your options?

 

Xdrop VS. OTHER CAPTURE TECHNOLOGIES

FEATURE
Xdrop
Long-range PCR
Highly Multiplexed PCR
Hybridization Capture
REQUIRED DNA INPUT* 1-10 ng 10–250 ng 20-200 ng 50-3000 ng
TOTAL PCR CYCLES INCLUDING LIBRARY PREP No PCR 25-35 20-25 20-25
ESTIMATED PCR-INDUCED ERRORS AND BIAS Low High High Medium
CAPTURES REPETITIVE AND GC-RICH REGIONS Easy Difficult Difficult Difficult
CLOSES GAPS CAPTURING UNKNOWN REGIONS Compatible (up to 100 kb per round) Compatible with small gaps (< 10 kb per round) Not compatible Not compatible
OPTIMAL SEQUENCING PLATFORM Illumina, PacBio, Oxford nanopore Illumina, PacBio, Oxford nanopore Illumina Illumina
TURNAROUND TIME FROM DESIGN TO SEQUENCING RESULTS Short (1 week) Medium-Long** Medium (5-7 weeks) Medium (5-7 weeks)
RELATIVE COST Affordable Affordable Expensive Expensive
*Varies depending on DNA quality **Long turnaround time linked to repeated redesign during the enrichment process, dramatically increasing with target length.

Xdrop® VS. OTHER TECHNOLOGies

REQUIRED DNA INPUT*
  • Xdrop®: 1-10 ng
  • Long-Range PCR: 10-250 ng
  • Highly Multiplexed PCR: 20-200 ng
  • Hybridization capture: 50-3000 ng
  • *Varies depending on DNA quality
    • TOTAL PCR CYCLES FOR INCLUDING LIBRARY PREP
  • Xdrop™: No PCR
  • Long-Range PCR: 25-35
  • Highly Multiplexed PCR: 20-25
  • Hybridization capture: 20-25
    • ESTIMATED PCR-INDUCED ERROR BIAS
  • Xdrop®: Low
  • Long-Range PCR: High
  • Highly Multiplexed PCR: High
  • Hybridization capture: Medium
    • APTURES REPETITIVE AND GC-RICH REGIONS
  • Xdrop®: Easy
  • Long-Range PCR: Difficult
  • Highly Multiplexed PCR: Difficult
  • Hybridization capture: Difficult
    • CLOSES GAPS CAPTURING UNKNOWN REGIONS
  • Xdrop®: Compatible (up to 100 kb per round)
  • Long-Range PCR: Compatible with small gaps (< 10 kb per round)
  • Highly Multiplexed PCR: Not compatible
  • Hybridization capture: Not compatible
    • OPTIMAL SEQUENCING PLATFORM
  • Xdrop®: Illumina, PacBio, Oxford nanopore
  • Long-Range PCR: Illumina, PacBio, Oxford nanopore
  • Highly Multiplexed PCR: Illumina
  • Hybridization capture: Illumina
    • TURNAROUND TIME FROM DESIGN TO SEQUENCING RESULTS
  • Xdrop®: Short (1 week)
  • Long-Range PCR: Medium-Long**
  • Highly Multiplexed PCR: Medium (5-7 weeks)
  • Hybridization capture: Medium (5-7 weeks)
    • RELATIVE COST
  • Xdrop®: Affordable
  • Long-Range PCR: Affordable
  • Highly Multiplexed PCR: Expensive
  • Hybridization capture: Expensive

    • What about non-commercial methods for long DNA targets?

    Targeted Locus Amplification (TLA)
    A technique that leverages cross-linking between adjacent sequences to generate complex DNA libraries. The design and implementation is challenging and time-consuming.

    CRISPR-Cas9 Systems
    Uses RNA-guided engineering nucleases to isolate targeted DNA fragments. Requires a large amount of input DNA and achieves moderate enrichment.

    Region Specific Extraction (RSE)
    Target molecules are captures with a large selection of oligos. The right constellation of oligos can be very difficult to optimize.

    Use the method best suited to your goals

    Xdrop vs. Hybridization Capture  – comparable outcomes, complementary uses

    Our benchmarking study shows that Xdrop is an agile platform that allows you to easily switch from one target to another and explore each in depth, with a very even coverage, easily spanning across repeats and GC-rich regions. Take a look at our data.

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    Download the Technical Note details

    How does Xdrop work?

    Xdrop is a novel microfluidic approach and the only solution on the market that uses Indirect Sequence Capture to enrich long DNA fragments. The differentiating features of Xdrop are the low input DNA amount, the flexibility of new designs, its compatibility with both short and long-read sequencing, and its straightforward and fast workflow.

    10 simple steps to insight

    A world of possibilities

    Learn more about the Xdrop workflow
    Discover the versatility of Xdrop

    Want to Learn More?

    Contact us

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