Understanding Microarrays in Genetic Analysis
A microarray is a technology that detects DNA copy number changes and regions of homozygosity to identify unbalanced chromosome abnormalities, including microscopic and submicroscopic aberrations that may be associated with disease. 1
What is a Microarray?
Microarrays are platforms consisting of DNA fragments or oligonucleotides arranged in a specific sequence of rows and columns on a solid support (typically a glass microscope slide). Different types include:
- Comparative genomic hybridization (CGH)-based arrays
- Single-nucleotide polymorphism (SNP)-based arrays
- Combined oligonucleotide plus SNP-based arrays 1
How Microarrays Work
In CGH-based microarrays:
- Patient DNA and reference DNA are labeled with different fluorochromes
- Both are hybridized to probes on the microarray
- A scanner measures differences in fluorochrome intensities
- Data is expressed as log2 ratios (normal copy number = "0")
- Duplications show greater intensity (log2 > 0)
- Deletions show less intensity (log2 < 0) 1
SNP-based arrays use a single color dye compared with an in silico reference and can detect both copy number changes and absence of heterozygosity (AOH). 1
What Microarrays Look For
Microarrays detect:
- Copy number variants (CNVs) - gains and losses of genetic material compared to a reference genome 1
- Unbalanced chromosome abnormalities - including deletions and duplications 1
- Absence of heterozygosity (AOH) - which may indicate loss of heterozygosity (LOH), hemizygosity, or homozygosity (with SNP-array technology) 1
- Genomic instability - including complex genomic aberrations such as chromothripsis 1
In clinical settings, microarrays are used to identify genetic abnormalities associated with:
- Constitutional cytogenetic disorders (developmental disorders, congenital anomalies)
- Neoplastic disorders (hematological malignancies, solid tumors) 1
Advantages of Microarray Analysis
- Can use any sample that yields DNA of sufficient quality
- Provides assessment of the genome at very high resolution
- Uses objective biostatistical algorithms for data interpretation
- Detects copy-number-neutral regions of homozygosity (with SNP-array technology)
- Interfaces digital data with genome browsers and web-based genome databases 1
- Particularly useful when multiple copy number abnormalities need to be tested, replacing multiple FISH analyses 1
- Can detect very small copy number abnormalities of prognostic significance 1
Limitations of Microarray Analysis
- Cannot detect balanced chromosomal rearrangements
- Cannot detect tumor-specific changes when there's a low ratio of tumor cells to normal cells
- Cannot determine chromosomal mechanisms of genetic imbalance (e.g., insertion, tandem duplication)
- Limited ability to detect tetraploidy or other ploidy levels
- Cannot characterize clonal and subclonal populations
- Not designed to detect point mutations, gene expression levels, methylation anomalies, or microRNA anomalies
- Not suitable for minimal residual disease monitoring after treatment 1
Clinical Applications
Microarrays are used in various clinical scenarios:
- As a primary diagnostic tool for detecting chromosomal abnormalities
- As an adjunct to more established testing methods (chromosome analysis, FISH)
- For diagnosis and classification of neoplasms
- For prognostication in certain cancers
- To identify genomic regions requiring further molecular investigation 1
Specific applications in hematological disorders include:
- Chronic myeloid leukemia
- Myelodysplastic syndrome
- Acute leukemia
- Chronic lymphocytic leukemia
- Multiple myeloma
- Lymphoma and other lymphoproliferative disorders 1
Important Considerations in Clinical Use
- Results should be correlated with other established methodologies (chromosome analysis, FISH) at diagnosis
- Parental studies may be needed when abnormalities of unclear clinical significance are detected
- The sensitivity and resolution of genomic regions with clinically relevant genes must be established through validation
- Appropriate follow-up testing may be needed when microarray results are normal but clinical suspicion remains high 1
Microarray technology has revolutionized genetic analysis by enabling simultaneous assessment of thousands of genomic regions, providing crucial information for diagnosis, prognosis, and treatment decisions in various genetic disorders and cancers.