Targeted Genomic Sequencing Service

Targeted genomic sequencing is an innovative technique that allows the sequencing of specific regions of interest. BaseClear uses Roche Nimblegen SeqCap Choice capture technology together with Illumina sequencing, allowing you to sequence the genomic regions of your choice for a fraction of the cost of whole-genome sequencing.

This approach allows researchers to focus specifically on their genomic regions of interest, instead of sequencing a complete genome. Targeted genomic sequencing provides an efficient and cost-effective way to perform experiments that focus on specific loci, thereby also simplifying the data analysis. This can be accomplished via the SeqCap Choice capture technology of Roche Nimblegen, in combination with Illumina HiSeq 2000 sequencing.

Sequence Capture protocol TThe Sequence Capture was developed to eliminate the necessity of setting up thousands of PCR reactions, instead allowing for parallel enrichment of target regions in one single experiment. First, a custom-made SeqCap Choice oligo pool is prepared based on the target genomic regions determined by the researcher (stage1). Then, a standard shot-gun library is made from genomic DNA (stage 2), and hybridized to the SeqCap Choice oligo pool (stage 3). Streptavidin beads are used to pull down the complexes of capture oligos and genomic DNA fragments (stage 4). Unbound fragments are removed by washing (stage 5). The enriched fragment pool is amplified by PCR (stage 6). Subsequently, the success of the enrichment is checked by qPCR at control loci (stage 7). Finally, the end product is a sequencing library enriched for target regions, which will be sequenced by high throughput sequencing.  The combination of SeqCap Choice with next generation sequencing results in high performance custom data. The enrichment results in a significant reduction of sequencing, leading to a better coverage with less sequencing.

Certified Service Provider (CSPro)
From early in 2011, BaseClear is Certified Service Provider for Roche Nimblegen. This certification enables BaseClear to offer customers a complete set of DNA target enrichment services. Targeted genomic enrichment options open new possibilities for custom-made experiments.

Approach

Our product specialist will work with you to determine which sample preparation and run type is best to perform.

Starting material

• 20 ug genomic DNA (minimal concentration 200 ng/ul).

Enrichment and sequencing

• Enrichment with a custom-made Roche Nimblegen SeqCap EZ Choice oligo pool, capture capabilities from 100 kb up to 50 Mb. 
• Sequencing with the Illumina HiSeq 2000

Output and further bioinformatics options

• Output data amount on request based to target size and needed coverage.
• The raw sequencing data will be provided in either fasta or scarf format.
• Are you interested in further downstream analysis such as SNP detection or reference alignment? If so, please take a look at BaseClear’s additional NGS analysis services or contact our Bioinformatics Product specialists for further details.
• The bioinformatics strategy will be determined in close collaboration between the customer and the bioinformatics and Genome Analysis product specialists.