Custom Human Sequence Capture 2.1M Array
 Format: 2.1MSource: UCSC Build: HG18 or HG19 Recommended Storage: Store arrays desiccated at room temperature. |
||||||
| Description | # of Probes | Capture Target Size | Catalog Number | Pack Size | Work- flow |
Ordering* |
| Custom Human Sequence Capture 2.1M Array | 2.1M | Up to 50Mb | 05329841001 | 1 Slide |  |
 |
| * Availability of products varies from country to country. | ||||||
Advantages
Applications
NimbleGen Sequence Capture arrays are suitable for targeted sequencing of any size, from small target regions like 250KB (Figure 1) to large regions as large as 30MB (Table 1). All human designs utilize the empirically optimized Sequence Capture design algorithm to ensure highly uniform capture. For example, a 250KB contiguous region, representing a typical GWAS locus, is captured with high specificity and uniformity (Figure 1). Note that small repetitive regions where no probes were selected can still be covered by sequencing, due to efficient capture from neighboring probes and with the advantage of long reads from the Genome Sequencer FLX Titanium Series (red boxes in Figure 1).
Table 1
| Capture of Large Contiguous Regions using 2.1M Arrays | ||
| Experiment | A | B |
| Total Reads (millions) | 1.2 | 1.3 |
| Total Bases | 347 Mb | 380 Mb |
| % Reads Mapped Uniquely | 87.6 | 86.7 |
| % Bases Mapped Uniquely | 93.1 | 92.6 |
| % Mapped Reads on Target | 79.1 | 70.8 |
| Average/Median Coverage | 10.3/9 | 10.1/8 |
Table 1. The ENCODE pilot regions (~30Mb) are captured using 2.1M arrays and sequenced. The target regions consist of ~ 50 individual contigs of ~ 500kb each
Figure 1
Figure 1. High-Performance Targeted Resequencing in a 250kb Target Region.
Roche offers a seamless workflow combining NimbleGen Sequence Capture Arrays and the high throughput sequencing of the Genome Sequencer FLX System from 454 Life Sciences. This complete solution of kits, arrays and instruments are specifically designed to optimize the workflow, reduce processing time, minimize costs, and enhance data quality. Furthermore, the GS Reference Mapper software from 454 Life Sciences enables researchers to easily identify variants like SNPs and indels from the final data output without complicated bioinformatics infrastructure (Table 2)
Table 2
| 454 Optimized Sequence Capture: Resequencing of HapMap Research Sample | ||
| Experiment | 250 kb - 1 | 1 Mb - 1 |
| Total Reads | 70,190 | 140,374 |
| Total Bases | 27,646,394 | 55,453,593 |
| On-Target Reads | 75.2% | 87.3% |
| Median Coverage | 85 | 49 |
| Target Bases with 1+ Coverage | 98.6% | 96.9% |
| Target Bases with 10+ Coverage | 97.3% | 92.8% |
| Known SNP Detection Rate | 97.4% | 96.5% |
Table 2. Sequence Capture Performance on a 250 kb contiguous region and a 1 Mb contiguous region in the human genome. Data shown are from 1 of the 4 independent experiments for each region. A HapMap sample is used in the study and SNP calls were generated by the GS Reference Mapper software.
An example of discovering causative mutations, the mouse Kit locus (~200KB) from 5 non-complementing Kit mutants is shown in Figure 2. These alleles include one known allele W-41J, and four unknown alleles, W-20J, W-39J, W-40J and W-73J. The known mutation from W-41J was confirmed in this experiment, and the data analysis successfully identified a non-synonymous coding mutation for each of the 4 unknown alleles. (D’Ascenzo et al, Mamm. Genome, 2009, 20:424–436)
Figure 2
Figure 2. Mutation discovery in the mouse KIT Locus using Sequence Capture and 454 Sequencing.
Protocol
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.
For more information on how to get trained and set up with Sequence Capture Arrays, visit our Quick Guide page.
Reagents
NimbleGen Sequence Capture Array Hybridization and Wash Kits contain the components to perform hybridization and wash steps in sequence capture protocols using NimbleGen Sequence Capture Arrays.
| Description | Catalog Number | Pack Size | Kit Capacity | Compatible Applications | Ordering* |
| Sequence Capture Array Hybridization and Wash Kit | 05853257001 | 1 Kit | 8 Arrays | Sequence Capture Arrays | |
| * Availability of products varies from country to country. | |||||
