GeneChip

GeneChip is a line of DNA microarray products developed by Affymetrix (now part of Thermo Fisher Scientific) for high-density oligonucleotide probes arranged on a solid surface. GeneChip arrays are used to measure gene expression, genotype single nucleotide polymorphisms (SNPs), and other genetic features. Each GeneChip contains thousands to millions of short oligonucleotide probes designed to hybridize with target sequences from a biological sample. Probes are synthesized directly on the chip surface using photolithography, enabling standardized, reproducible arrays with defined probe sequences.

Typical workflow involves extracting RNA or other nucleic acids, producing labeled target material (such as cRNA or cDNA), and hybridizing it to the chip under controlled conditions. After washing to remove non-specific binding, the array is scanned with a laser to capture fluorescence at each probe location. The resulting signals are processed with software to summarize probe-level measurements into gene-level expression or genotype calls, followed by statistical analysis to identify differential expression or associations.

Applications include transcriptional profiling, genotyping, and pharmacogenomics, with various formats such as expression, exon, and genotyping arrays. The platforms support downstream data analysis and integration with bioinformatics workflows, though analysis methods have evolved from early MAS5.0 to more robust normalization approaches.

Originating in the 1990s, GeneChip technology helped establish microarrays as a standard tool in genomics. The brand and product line were incorporated into Thermo Fisher Scientific after the Affymetrix acquisition, and the GeneChip name remains in use for several array formats and companion instruments.