Microarray Benefits & Workflow for Postnatal Genetic Research

Technological advances in genetic analysis have greatly expanded the capabilities of constitutional cytogenetics research 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 postnatal 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. CMA is a widely used genetic analysis tool, recommended by American College of Medical Genetics (ACMG) as a first-tier test for postnatal research of unexplained developmental delay, intellectual disability, congenital anomalies, and autism spectrum disorder. 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 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 study 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)
  • 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 research 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. 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 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 is the recommended first-line test as per the ACMG guidelines. 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 make it easy to obtain consistent and high-quality results.

 

Our complete microarray research 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.