Microarray Benefits and Workflow for Oncology Research

Technological advances in genetic analysis have greatly expanded the capabilities of constitutional and oncology cytogenetics testing in recent years. These advances have led to the emergence of high-resolution, genome-wide methods such as chromosomal microarray analysis (CMA) for advanced study of chromosomal disorders.

Benefits of microarray analysis for oncology research applications

CMA can detect more genetic abnormalities than traditional cytogenetic methods such as karyotyping. It is an ideal platform for copy number variations (CNV) analysis and molecular cytogenetic research. Some arrays also contain probes to detect a targeted panel of sequence variations at a single base (single nucleotide variations, or SNVs). Single nucleotide polymorphism (SNP) is when an SNV is present in at least 1% of the population.

Applied Biosystems CytoScan arrays are hybrid-SNP arrays with more than 99% genotype accuracy. These arrays help boost confidence in breakpoint determination and provide independent confirmation of copy number events throughout the entire genome.

CytoScan arrays apply a reliable genome-wide approach for high-resolution DNA copy number analysis to detect these types of genetic conditions:

  • CNV (from aneuploidies to small CNV > 25 kbp for losses and >50 kbp for gains)
  • Suspected uniparental disomy (UPD), whole genome UPD, cnLOH, or AOH
  • Mosaicism
  • Zygosity
  • Consanguinity
  • Parent of origin (requires parental genomic analysis)
  • Twin-twin or maternal cell contamination
  • Allele-specific changes
  • Sample heterogeneity, clonal diversity
  • Genomic contamination

SNP analyses are also used for:

  • Breakpoint determination
  • Mendelian consistency checking
  • Confirmation of CNV events

Other benefits of our microarray solutions are faster turn-around-time, lower cost, high causal variant coverage, and low variants of unknown significance (VUS) and secondary findings (SF) burden. Additionally, CytoScan arrays enable analysis of various sample types including blood, bone marrow, buccal swabs, saliva, fresh and frozen tissues, cultured and uncultured cells, amniocytes, and products of conception (POC). DNA from these sample types is extracted, amplified, processed, analyzed, and interpreted using our advanced cytogenetic analysis software: Chromosome Analysis Suite (ChAS) software.

 

Key features of ChAS software to help make data analysis simpler and more intuitive:

  • Analyze copy number, mosaicism, and loss of heterozygosity (LOH) segment data at different levels of resolution
  • Customize and load your own annotations and regions for focused analysis
  • Store, query, and display historic sample data and annotations for streamlined analysis
  • Application programming interfaces (APIs) to push and pull segment coordinates in and out of ChAS software

Workflow

CMA can detect more genetic abnormalities than traditional cytogenetic methods such as karyotyping. It is an ideal platform for copy number variations (CNV) analysis and molecular cytogenetic research. Thermo Fisher Scientific offers microarray solutions powered with robust workflows that help make it easy to obtain consistent and high-quality results.

 

Our complete microarray platform, the CytoScan Cytogenetics Suite, includes hybrid-SNP arrays, automated and manual target preparation options, fully kitted reagents, the GeneChip System 3000 instrument for array processing, and ChAS software for data interpretation and reporting. These tools support labs to generate accurate, high-quality data and maximize operational time.

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