Skip to main content

Molecular Biology

Array Technology

This technology has dramatically scaled up our ability to ask questions of a patient’s DNA or RNA. If a single PCR is like making one phone call to ask one specific question, array technology is like sending out a massive survey to thousands of recipients all at once and getting all the answers back simultaneously. It’s a powerful tool for high-throughput, parallel analysis

At its heart, array technology is a multiplex hybridization assay. The core principle involves immobilizing thousands of known DNA sequences (probes) onto a solid surface in an orderly fashion. A patient’s sample (the target) is then labeled and washed over this surface. By seeing where the patient’s sample sticks, we can learn thousands of things about it in a single experiment

There are two main “flavors” of this technology that you’ll encounter: the classic microarray and the flexible bead array

Microarrays (The “Chip”)

Think of a microarray as a microscopic grid printed onto a glass slide. Each tiny, invisible spot on this grid has a different, known DNA probe chemically attached to it. The location of the spot tells you what the probe is

  • The Setup: A glass slide, often no bigger than a standard microscope slide, is spotted with tens of thousands to millions of unique DNA probes. The x,y coordinate of each spot is meticulously tracked in a database
  • How it Works: The patient’s DNA or RNA (the target) is isolated, fragmented, and labeled with a fluorescent dye. This labeled sample is then incubated with the microarray slide. The patient’s DNA fragments will hybridize, or “stick,” only to the spots containing their complementary probe sequence. After washing away any non-specific binding, the slide is scanned with a laser. The scanner detects the fluorescence at each spot, and the intensity of the light is proportional to the amount of patient DNA that bound there
  • The Result: A computer image of the slide with a grid of glowing dots of varying intensities. Since the identity of the probe at every coordinate is known, the software can quickly generate a massive report of all the sequences present in the patient’s sample

Bead Arrays (The “Liquid Array”)

Bead array technology, most famously represented by Luminex xMAP technology, takes the grid concept and puts it into a liquid format. Instead of a fixed grid on a slide, the probes are attached to microscopic beads (microspheres)

  • The Setup: The system uses up to 500 different sets of tiny beads. Each set is internally dyed with a unique combination of red and infrared fluorophores, giving each bead set a specific spectral “address” or color code. All the beads within one color-coded set are coated with the same specific probe sequence
  • How it Works: The different sets of probe-coated beads are all mixed together in a single tube. The patient’s labeled sample is added to this mixture, and hybridization occurs in suspension. The entire mixture is then drawn into a specialized flow cytometer
  • Detection: As each individual bead flows single-file past two lasers:
    1. The Classification Laser hits the bead and reads its internal color code, identifying which probe is on that bead (e.g., “this is a bead for the CYP2C19 *2 allele”)
    2. The Reporter Laser excites the fluorescent label on the patient’s sample that has bound to the bead’s surface, measuring how much has bound
  • The Result: The instrument can analyze thousands of beads per second, rapidly building a report on the presence and quantity of hundreds of different targets in a single well of a 96-well plate

General Workflow & Clinical Applications

Regardless of the platform, the core applications are similar and highlight the power of multiplexing

  1. Sample Preparation & Labeling Patient DNA/RNA is isolated, sometimes amplified via PCR, and labeled with a fluorescent tag (often biotin, which is then detected by a fluorescent streptavidin conjugate)
  2. Hybridization The labeled sample is incubated with the array (chip or bead mix)
  3. Washing Unbound sample is washed away to reduce background noise
  4. Signal Detection The array is read by a scanner or flow cytometer
  5. Data Analysis Sophisticated software converts the raw signal intensities into a clinical result

Major Clinical Uses

  • Pharmacogenomic (PGx) Testing: This is a perfect application. A single array can simultaneously test for dozens of key SNPs in genes involved in drug metabolism (e.g., CYP2C19, CYP2D6, VKORC1, TPMT), providing a comprehensive drug-response profile for a patient in one test
  • Cytogenomics (Array CGH): Array Comparative Genomic Hybridization is a major diagnostic tool for detecting copy number variations (CNVs)—microdeletions and microduplications that are too small to be seen on a traditional karyotype
    • How it works: The patient’s DNA and a normal reference DNA sample are labeled with two different colored dyes (e.g., patient = green, reference = red). They are mixed and co-hybridized to a microarray containing probes spanning the entire genome
    • Interpretation: If a spot on the array shows a yellow color (equal parts red and green), the patient has a normal copy number at that location. A green color means the patient has more DNA than the reference (a duplication/gain). A red color means the patient has less DNA than the reference (a deletion/loss). This is a primary test for developmental delay and birth defects
  • Gene Expression Profiling: Microarrays can measure the expression levels of thousands of genes at once by analyzing labeled cDNA made from the patient’s mRNA. In oncology, this can help classify tumors into different subtypes (e.g., Oncotype DX for breast cancer), which can predict prognosis and guide treatment decisions
  • Multiplex Pathogen Detection: Arrays can be designed with probes for dozens of different respiratory viruses or bacteria, allowing for a broad infectious disease panel from a single patient swab
  • Multiplex Immunoassays: Bead arrays are especially powerful for non-DNA applications. They can be coated with antigens to detect dozens of different antibodies at once (e.g., HLA antibody screening for transplant patients) or coated with antibodies to measure dozens of different proteins/cytokines from a single drop of blood

Key Terms

  • Array Technology: A high-throughput platform that allows for the simultaneous measurement of thousands of different biological molecules (like DNA, RNA, or protein) by using a grid of immobilized probes
  • Probe: The known, single-stranded molecule (e.g., an oligonucleotide) that is fixed to a specific location on the array surface and is designed to capture a specific target molecule
  • Hybridization: The process by which the labeled target molecules from the patient sample bind to their complementary probes on the array surface
  • Multiplexing: The ability to perform many different tests or assays simultaneously in a single reaction, which is the core advantage of array technology
  • Microarray: An array format where probes are spotted in a high-density grid onto a solid surface, typically a glass slide. The location (x,y coordinate) of a signal identifies the target
  • Bead Array: An array format where probes are attached to microscopic, color-coded beads. A flow cytometry-based instrument identifies the bead by its color and measures the signal on its surface
  • Array CGH (Comparative Genomic Hybridization): A microarray-based technique used to detect copy number variations (gains and losses of DNA) across the genome by comparing a differentially labeled patient sample to a reference sample