Wednesday, December 12, 2012

Fun Fact Wednesday – To RT-PCR or Not To RT-PCR

Most labs have access to a thermocyler or PCR machine that can cycle 96 samples in an hour for SNP genotyping.  If you want to genotype a freezer full of samples using allele specific primers, you could analyze about 96 an hour, or 768 in an eight hour day.  If you wanted to collect data more quickly, you could add more and more thermocyclers and have them running in parallel…or you could detect your genotypes on a plate reader.

Method example for GWA study designs
Using water-bath batch cyclers, it is possible for you to cycle hundreds of plates at a time—and with 384-samples per plate, not just 96 samples at a time.  The PHERAstar FS can read a 384-well SNP plate in 28 seconds (two measurements). That means that one hundred and twenty plates an hour can be measured, for eight hours, at 384-samples per plate is 386,000 samples per day—480x more than the original setup.  If you add multiple PHERAstars onto your robotic plate handler, you could genotype about 1.2 million samples a day.  If you switched to 1536-well plates, you could collect genotype data from 2.4 million samples in eight hours! This also does not take into account that the misread rate is much smaller on the PHERAstar FS than on an RT-PCR instrument, further saving time and money. 

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