Targeted Sequencing for Cancer Mutation Detection

Most of cancers result from accumulation of multiple genetic alterations that lead to dysfunction of cancer-associated genes. These genetic alterations are important diagnostic, prognostic, and predictive biologic markers. Next generation sequencing technologies permit deep sequencing of hundreds of cancer genes concurrently. Targeted next generation sequencing utilizes multiplex PCR with ion semiconductor sequencing to sequence a panel of key cancer gene mutations including many clinically actionable mutations. This analysis may provide important individual information regarding tumor development and progression, and a more reliable prediction of personalized cancer therapies.

Methods Predominantly Used to Target and Extract Specific Genomic DNA Regions

There are two methods predominantly used to target and extract specific genomic DNA regions for sequencing: in-solution hybridization-based pullout and PCR-based amplification.

PCR-Based Amplification

The PCR-based amplification method employs specific primers to amplify genomic regions (amplicons). It requires only 10 ng of input DNA, so it is ideal for low-input DNA samples and challenging and fragmented DNA samples such as FFPE tissues. Based on this method, Ion AmpliSeq™ Target Selection Technology permits up to 1,536 primers to be pooled in a single tube for custom-designed assays and as high as 3,000 primers per tube for ready-to-use primer pools. This ultra-high level of multiplexing resolves the technical challenge of manual PCR optimization.

In-Solution Hybridization-Based

The in-solution hybridization-based pullout method uses specific probes that hybridize to the target genomic regions and allow them to be captured. This method is ideal for surveying large regions such as exomes, genomic regions from GWAS studies, or large sets of genes implicated in complex disease states. This method can be used for structural variation detection. Based on this method, Ion TargetSeq™ Custom Enrichment Kit enables practical selection of large genomic regions (20 kb to 80 Mb), making it ideal for sequencing custom gene panels on semiconductor sequencing platforms.

Research Interest

 

Applications

 

Challenges

  • Rapidly identify mutation profile of my tumor samples
  • Routinely screen samples for a specific set of mutations
  • Deep sequencing in established hotspot regions
 
  • Targeted sequencing—gene panels with NGS
 
  • Cost-effectively identify multiple mutations per sample
  • Accurately and affordably detect low-frequency mutations
  • Low input and low quality DNA
 

Life Technologies Solution

Capture large targeted regions of the genome

 

Target small regions of the genome

 

Remove analysis barriers for labs doing routine assays

 
Ion PGM™ Sequencer

Ampliseq™ Target Selection Technology
Ion AmpliSeq™ technology delivers simple and fast library construction for affordable targeted sequencing of specific human genes or genomic regions. Based on ultrahigh-multiplex PCR, Ion AmpliSeq™ technology requires as little as 10 ng of input DNA to target sets of genes, making sequencing of FFPE samples routine on Ion PGM™ Systems.		   Ion Reporter™ Software
A suite of bioinformatics tools streamlines and simplifies analysis, annotation, reporting, and archiving of semiconductor sequencing data. Designed specifically for researchers performing repeated analysis of sequencing assays, Ion Reporter™ Software helps you interpret DNA variants faster and more easily.
 
Targeted Resequencing
Fast and simple workflows optimized for all major target enrichment providers. The Ion TargetSeq™ Custom Enrichment Kit is a fully customizable approach that uses in-solution hybridization to capture targeted regions of the genome.		   Ion PGM™ Sequencer
The Ion Personal Genome Machine™ (PGM™) Sequencer delivers the fastest run times, at the most affordable price, of any next-generation sequencer. High accuracy, and long reads put the Ion PGM™ Sequencer in a class of its own and makes next-generation sequencing more accessible to scientists around the world.

All products referenced are for Research Uses Only and are not intended for human or animal therapeutic or diagnostic uses.

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