分野別セミナー

High-density short oligonucleotide microarrays are useful tools for
studying biodiversity, because they can be used to investigate both
nucleotide and expression polymorphisms. However, when different strains
(or species) produce different signal intensities after mRNA
hybridization, it is not easy to determine whether the signal
intensities were affected by nucleotide or expression polymorphisms. To
overcome this difficulty, nucleotide and expression polymorphisms are
currently examined separately.
We have developed SNEP, a new method that allows simultaneous detection
of both nucleotide and expression polymorphisms. SNEP involves a robust
statistical procedure based on the idea that a nucleotide polymorphism
observed at the probe level can be regarded as an outlier, because the
nucleotide polymorphism can reduce the hybridization signal intensity.
To investigate the performance of SNEP, we used three species: barley,
rice and mice. In addition to the publicly available barley data, we
obtained new rice and mouse data from the strains with available genome
sequences. The sensitivity and false positive rate of nucleotide
polymorphism detection were estimated based on the sequence information.
The robustness of expression polymorphism detection against nucleotide
polymorphisms was also investigated.
SNEP performed well regardless of the genome size and showed a better
performance for nucleotide polymorphism detection, when compared with
other previously proposed methods. The R-software ^^ SNEP' is available
at http://www.ism.ac.jp/~fujisawa/SNEP/.