Cancer genotyping can be used to identify a predetermined genetic aberration, such as somatic mutations, copy number variations, gene expression changes, and/or DNA methylation.

Cancer Genotyping of Specific Genes or Variants

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Research Interest

 

Applications

 

Challenges

  • Identify tumor specific genomic alterations
  • Detect the presence of cancer cells based on genomic mutation profiles
 
  • Cancer somatic or germline mutation profiling
 
  • Identify cancer driver mutations
  • Accurate and affordable to detect low frequency mutations
  • Low input and low quality DNA
 

Thermo Fischer Scientific Solutions

Ion PGM Sequencer

 

QuantStudio 12k Flex Real-Time PCR System

 

3500 Genetic Analyzer

Somatic Mutation Detection

TaqMan Mutation Detection Technology—Offering Superior Sensitivity for Your Cancer Biomarker Research
TaqMan Mutation Detection Assays detect somatic mutations in genes that are associated with cancer. These research use only assays are powered by competitive allele-specific TaqMan PCR technology, also known as castPCR technology. The castPCR technology is highly specific and sensitive, and it can detect rare amounts of mutated DNA in a sample that contains large amounts of normal, wild type DNA. These assays are compatible with different sample types, such as cell lines, FFPE tissue samples, and fresh frozen tissue samples.

  • High specificity—mutant allele detection is based on an allele-specific primer, while the wild-type background is suppressed by an MGB blocker oligonucleotide
  • High sensitivity—assays can detect as low as 0.1% mutant molecules in a background of wild type gDNA as demonstrated in spiking experiments
  • Wide dynamic range and excellent PCR efficiency—assays demonstrate at least 4 logs of dynamic range and an average efficiency of 100 ± 10%
  • Fast, simple workflow—like other TaqMan Assays, typically requires 3 hours from sample to results, with minimum hands-on time
  • Our current assay set covers 285 assays to key mutation targets in 23 cancer genes

Learn more about TaqMan Mutation Detection Assays powered by castPCR Technology

Application note:Accurate and sensitive mutation detection

Video: TaqMan and castPCR for somatic mutation detection in cancer genes

Germline Mutation Detection

Semiconductor Sequencing and AmpliSeq Target Selection
Ion AmpliSeq technology provides 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. Recommended for human genes or gene panels, allowing detection of both germline and somatic mutations from the same sample.

Learn more about Ion AmpliSeq Panels


Capillary Electrophoresis Sequencing
Capillary electrophoresis is the gold standard for DNA sequencing and fragment analysis. Its utility is proven through decades of results. Recommended for germline mutation detection of genes, small to mid-size gene fragments, and sequence verification.

Learn more about Capillary Electrophoresis Sequencing 


Real-Time PCR
With 4.5 million predesigned TaqMan SNP Assays available and a robust custom design pipeline, genotyping with TaqMan Assays is an ideal method for validating and screening a low to medium number of SNP markers and a high number of samples. With a choice of Applied Biosystems 48-, 96-, 384 or greater than 384-well real-time PCR instrumentation or the OpenArray Real-Time PCR platform, you can select the workflow that best fits your genotyping project needs.

Learn more  about SNP Genotyping Analysis Using TaqMan Assays

For Research Use Only. Not for use in diagnostic procedures.