Updated Instrumentation for Continuous Array Genotyping of Short Insertion/Deletion Polymorphisms

Methods for DNA testing are abundant, with much emphasis placed on short tandem repeat polymorphisms (STRPs) and single nucleotide polymorphisms (SNPs). However, lower cost, higher-throughput genotyping is still needed. Another important polymorphism is the diallelic short insertion/deletion (indel). Our laboratory is using a continuous reel of 384 well arrays on polypropylene tape to genotype indel polymorphisms. The reel of continuous arrays allows lower cost automation, and decreased reaction volumes. The diallelic indel is typed by tagging allele-specific PCR primers with a FAM or JOE molecular beacon uniprimer. Our most recent tape has wells with reaction volumes of 700 nanoliters or less. Commercial equipment for the microtape is not available. A series of instruments to handle the tape was developed in-house. A pipetting instrument was developed to deliver the specific DNA samples or other reagents. A solenoid micro-valve aspirating and jetting unit was developed for dispensing a common reaction mix. The arrays are sealed with commercially available continuous roll seal material prior to polymerase chain reaction (PCR). After PCR the arrays are scanned using an epi-fluorescence detection unit. The detector uses an argon ion laser for excitation and photomultiplier tubes (PMTs) for detection.