Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies

@inproceedings{Ramasamy2013ResolvingTP,
  title={Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies},
  author={Adaikalavan Ramasamy and Daniah Trabzuni and Jesse Raphael Gibbs and Allissa Dillman and Dena G. Hernandez and Sampath Arepalli and Robert Walker and Colin Smith and Gigaloluwa Peter Ilori and Andrey A. Shabalin and Yun Li and Andrew Singleton and Mark R Cookson and John Hardy and Mina Ryten and Michael E. Weale},
  booktitle={Nucleic acids research},
  year={2013}
}
Polymorphisms in the target mRNA sequence can greatly affect the binding affinity of microarray probe sequences, leading to false-positive and false-negative expression quantitative trait locus (QTL) signals with any other polymorphisms in linkage disequilibrium. We provide the most complete solution to this problem, by using the latest genome and exome sequence reference data to identify almost all common polymorphisms (frequency >1% in Europeans) in probe sequences for two commonly used… CONTINUE READING