NimbleGen Sequence Capture technology is a revolutionary process for the enrichment of selected genomic regions from full complexity human genomic DNA in a single step. Sequence Capture was developed to eliminate the necessity of setting up thousands of PCR reactions, instead allowing for parallel enrichment
of target regions in a single experiment.
Roche NimbleGen created, further refined, and optimized large-scale genomic enrichment technology. Our company is at the forefront of targeted sequencing, driving the innovation of Sequence Capture technologies including custom capture. Capitalizing on the efficiencies inherent with parallel enrichment, researchers can now design economical, higher throughput, and time-saving next-generation sequencing experiments. In combination with high throughput sequencing (short- or long-read), Sequence Capture has made targeted sequencing possible and accessible to more life science researchers. Two options are available for targeted enrichment of genomic regions:
- SeqCap EZ Library is a solution-based capture method that enables enrichment of the whole exome or customer regions of interest in a single test tube. An automated solution for SeqCap EZ Library using the Caliper Sciclone NGS workstation is now available. With the Sciclone NGS workstation you can process up to 288 samples per week.
- Sequence Capture Arrays enable researchers to target custom regions of interest in the human genome.
Roche NimbleGen offers two types of capture methods: SeqCap EZ Library, a solution-based method and Sequence Capture Arrays, an array-based capture method.
Sequence Capture Protocols
- Genomic DNA: SeqCap EZ Oligo pool or an array is made against target regions in the genome.
- Library Preparation: Standard shot-gun sequencing library is made from genomic DNA.
- Hybridization: The sequencing library is hybridized to the SeqCap EZ Oligo pool or to the Sequence Capture array.
Steps 4 and 5 are different for each protocol:
SeqCap EZ Library, biotinylated DNA oligos in solution
- Bead Capture: Streptavidin beads are used to pull down the complex of capture oligos and genomic DNA
fragments.
- Washing: Unbound fragments are removed by washing.
Sequence Capture, capture probes synthesized on array:
- Washing: Unbound fragments are removed by washing.
- Target Fragment Elution: The enriched fragment pool is eluted and recovered from the array.
- Amplification: Enriched fragment pool is amplified by PCR.
- Enrichment QC: The success of enrichment is measured by qPCR at control loci.
- Sequencing-Ready DNA: The end product is a sequencing library enriched for target regions, ready for high throughput
sequencing.
Delivering better coverage with less sequencing
- Achieve greater coverage and uniformity using our 2.1 million optimized DNA oligonucleotides
- Save on sequencing time and cost
Optimized and scalable workflow
- Optimized protocols for next-generation sequencing platforms (short- and long-read)
- A truly scalable in-solution workflow using SeqCap EZ Library, with the ability to process up to 96 samples in a microplate
- Optimized scripts written with the Caliper Sciclone NGS workstation for scalability of up to 288 samples per week
Increased confidence with experimental controls
- Measure success of enrichment using built-in control probes prior to sequencing
Flexibility in designing your experiments
- Optimized design gives you the option to study small or large, contiguous or non-contiguous genomic regions
- The only platform capable of capturing up to 50 Mb customized target regions
- Choose an array-based or solution-based experiment to fit your requirements
Optimized Design for Improved Capture Performance
Probe selection plays a critical role in the performance of enrichment technologies. The most commonly used method is a standard tiling design, where probes are laid out at even spacing across the target regions. However, real world sequencing data have shown that a standard tiling design does not always give the best performance, especially for exonic regions where simple tiling tends to result in bias in coverage profiles between different exons.
Roche NimbleGen has developed a probe selection algorithm based on our extensive collection of sequencing data on multiple capture designs. The result is an empirically optimized design algorithm that improves capture uniformity (see Table 1 below) over standard tiling methods and gives better coverage of target regions.
| 1000 Genomes Exon Capture Array* |
Standard Tiling Design |
Sequence Capture Algorithm |
| Targets Covered by Sequence |
97.5% |
98.3% |
| Bases with 5X Minimum Coverage |
70.0% |
90.1% |
| Bases with 10X Minimum Coverage |
50.5% |
75.0% |
| * 1000 genes, ~3 Mb target sequence, 1 Genome Sequencer FLX run/sample |
Table 1. NimbleGen Sequence Capture design algorithm increases effective sequence coverage. Both designs used similar amount of sequencing, however the Sequence Capture design algorithm produces a higher percentage of bases with ≥ 10X coverage compared to the standard tiling design. Experimental data courtesy of Dr. Richard Gibbs, Baylor College of Medicine. |
| Technology |
Description |
Product |
| SeqCap EZ Library |
Solution-based targeted enrichment for short-read and long-read sequencing platforms. |
|
| Sequence Capture Arrays |
Array-based targeted enrichment with NimbleGen 2.1M and 385K arrays. |
|
SeqCap EZ Library Documents
Brochures and Sales Flyers
User Guides
Downloads
Application & Technical Notes
Sequence Capture Array Documents
Brochures and Sales Flyers
User Guides
Downloads
Technical Notes & Reprints
For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.
