Targeted resequencing is the comparative analysis of selected regions in a genome to identify genetic variants when compared to a reference. Increasingly targeted resequencing experiments are used in basic and clinical research as scientists look for causative variants for rare and complex diseases within populations.

Open Slide Format and Barcoding Capability Enlarge Image
Figure 1. In-solution hybridization method for exome capture enables multiplexing prior to capture.

The accuracy and throughput of the 5500xl Genetic Analyzer make it uniquely suited to targeted resequencing.

  • Pay-per-lane Sequencing—two fully configurable FlowChips, each with 6 independent lanes enable you to run one, a few, or all lanes and pay for reagents only for active lanes
  • Accuracy—ultra-deep sequencing capability combined with superior accuracy using Exact Call Chemistry (ECC) enables accurate detection of variants present in a sample with a frequency as low as 1%
  • Multiplexing—barcoding allows you to multiplex up to 96 samples per lane, or 1,152 samples per run, making it easier for you to dial in the level you need
  • Coverage—ultra–high-throughput translates to increased coverage per sample for confident variant detection in pooled or heterogenous samples
  • Flexibility—libraries can be generated from a variety of enrichment methods including PCR, array-based hybridization, and in-solution hybridization

The TargetSeq™ Exome Enrichment System Provides Efficient Targeted Sequencing

  • Targeted—focused, high-density probe design
  • Economical—precapture sample multiplexing
  • Platform-optimized—superior performance on 5500 Series Genetic Analyzers and SOLiD® Systems
  • Integrated—streamlined data analysis with LifeScope™ Genomic Analysis Software

Exome sequencing is best performed using the TargetSeq™ Exome Enrichment System kits, which are based on an in-solution hybridization method for exome capture. The kits are optimally designed to seamlessly integrate into the 5500 Series Genetic Analysis Systems workflow.

Learn more

Step-by-Step Guide to Targeted Resequencing Products

Decide on important experimental considerations: what type of variation you want to detect, in how many genes (or target regions), and how many samples?

Learn More:

Enrich your DNA using one of the following methods: PCR, long-range PCR, array hybridization, in-solution hybridization, or chromosome sorting. After enrichment, consider multiplexing strategies if you have multiple samples to process.

SequalPrep™ Long PCR kit and Normalization plate

Complete long PCR enrichment and amplicon normalization system that provides a highly efficient enrichment solution to meet NGS re-sequencing throughput capabilities.

Learn More:

Learn More:

User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub.

The tools you need for each step in the targeted sequencing data analysis workflow:

 
Data Analysis Step Applied Biosystems Software 3rd-Party Software***
1. Align reads to reference in color space
  • ICS
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
2. Generate quality metrics and perform mate pair rescue
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
3. Generate sequencing and alignment statistics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
4. Identify Polymorphisms
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
5. Translate color space to base space  
6. Visualize in context of annotation
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
7. Convert to SRF for publishing    
*** Need XSQ --> csfasta/qual converter

Learn more

Validate results using our BigDye® Direct Cycle Sequencing Kit, for Sanger sequencing on our capillary electrophoresis-based DNA sequencers.

BigDye® Direct Cycle Sequencing Kit

Application Notes

Posters

Publications

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.