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NimbleGen

Overview

NimbleGen

NimbleGen Sequence Capture products allow parallel enrichment of many genomic target regions in a single experiment for sequencing with the GS FLX and GS Junior Systems.

Methods

Two formats are available for targeted enrichment of genomic regions:

  1. SeqCap EZ Library is a solution-based capture method that enables enrichment of the whole exome or custom target regions of interest in a single reaction.
    • SeqCap EZ Choice Libraries enable enrichment of custom regions of interest and are offered in two configurations: SeqCap EZ Choice Library can capture up to 7 Mb of target regions with a single design; SeqCap EZ Choice XL Library can capture up to 50Mb of target regions with a single design. Both libraries are available in 6 different reaction sizes.
    • SeqCap EZ Exome Libraries enable enrichment of the human exome: SeqCap EZ Exome LR is optimized for long read sequencing with 454 Sequencing Systems. Focus your research only on the coding region of the genome along with the directly adjacent interonic regions.
  2. Sequence Capture Arrays enable researchers to target custom regions of interest in the human genome using a solid substrate for capture.
    • SeqCap Human Exome 2.1M Array: Focus your research only on the coding region of the genome along with the directly adjacent interonic regions.
    • SeqCap Custom 385K and 2.1M Arrays: Capture up to 50 Mb total regions on a single 2.1M array and up to 5Mb on a single 385K array with high coverage and specificity.

Sequence Capture protocols.


  1. Genomic DNA: An array or SeqCap EZ oligo pool is made against target regions in the genome.
  2. Library Preparation: Standard shot-gun sequencing library is made from genomic DNA.
  3. 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, biotinylated DNA oligos in solution

  1. Bead Capture: Streptavidin beads are used to pull down the complex of capture oligos and genomic DNA fragments.
  2. Washing: Unbound fragments are removed by washing.

Sequence Capture, capture probes synthesized on array:

  1. Washing: Unbound fragments are removed by washing.
  2. Target Fragment Elution: The enriched fragment pool is eluted and recovered from the array.

  1. Amplification: Enriched fragment pool is amplified by PCR.
  2. Enrichment QC: The success of enrichment is measured by qPCR at control loci.
  3. Sequencing-Ready DNA: The end product is a sequencing library enriched for target regions, ready for high throughput sequencing.

Learn more at www.nimblegen.com