Spotlight: Benchmarking

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

Also available as a Service

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

calendarAsset 6xxxhdpi

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

Asset 7xxxhdpi

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

Asset 3xxxhdpi

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.

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 get in touch?

Contact
Bregnerødvej 96
3460 Birkerød
Denmark

info@samplix.com
Phone: (+45) 82 30 45 00

CVR 32 30 93 21

Samplix Cookie policy Samplix Privacy policy

Connect with us