User:
Vanessa Hayes, Children's Cancer Institute Australia for Medical Research, Sydney
Project:
SNP discovery and validation in blood samples collected on filter paper and stored for years, looking for prostate cancer markers
Problem:
When Hayes began the project in 2005, accuracy rates using the Sequenom hME instrument, one of the few instruments that genotyped on the scale she needed, were lower than accuracy rates for other medium through-put technologies used in her laboratory. "The heterozygous calls were preferentially called as homozygous," she says, 99% of the time. Adding to the challenge, the DNA for this project, collected in field studies on dried paper, was at a premium.
Solution:
Hayes compared her results with those obtained with other chemistries, suspecting that Sequenom's chemistry - at the time, homogenous MassEXTEND - wasn't compatible with the dried blood DNA. Indeed, two fluorescence-based chemistries, TaqMan and Plexor (run on the ABI 7900 HT instrument), ...
