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.

    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