16 x 24 DNA Hybridization Plate
Above is a picture of the computer representation of a 384 hybridization plate for SNP [single nucleotide polymorphism] genotyping on the Beckman SNPstream platform. Each 16 dot “well” can genotype 12 SNPs in a sample. Fluorescently labeled DNA from a sample hybridizes to DNA-analogs arranged in a grid at the bottom of each well.

The labeling is done during the PCR process, or, more specifically, during a second round of thermal-cycling after an initial PCR when labeled ddNTP, dideoxy nucleotide tri-phosphates that cannot be extended (as opposed to regular dNTPs, deoxynucleotide triphosphates–the As, Gs, Ts and Cs- in regular DNA) are added to a reaction. A pair of lasers excite the fluorescence and the signal is captured by a digital camera.

The hybridization process is similar to that employed by “DNA chips” with the main difference being that this plate records the same 12 loci for 384 samples (or 4608 genotypes per plate minus whatever controls are utilized) while chips generally analyze a single sample for 1000s of SNPs. A 5k chip has roughly the same number of reactions as this plate. The 5k chip is better for wide screening and association studies, while the plate pictured here is better for screening once SNPs of consequence have been identified. The actual method of accessing where hybridization occurred on a chip can be a bit different, but the principle of hybridization to a DNA-analog adhered to glass or silicon or some other material is the real key.

The hybridization plate pictured here is the type that might be employed in screening for a particular SNP associated with a form of cytochrome P450—for example the “poor metabolizer” genotype of CYP2D6..A machine reading of the plate takes about 6 minutes, though preparation of the 384 samples takes a little more than a day. Figuring out what it all means may take much longer.

In my next posting I’ll tell about a recent visit to a DNA lab to observe the processes of extraction, PCR, and analysis. It’s a world apart from my day-to-day office practice, but it’s something I suspect all of us will need to understand to practice medicine in the 21st Century.

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