to RefSeq sequences represented more than one third of mapped reads [89, and personal communication from R.D. Mayfield]. Moreover, RNA-seq reveals sequence variations (such as single nucleotide polymorphisms, SNPs) within the transcripts. In the future, it would be interesting to determine whether ethanol differentially regulates the expression of SNP variants, in particular for SNPs previously shown by genome-wide association studies to confer vulnerability to or protection against alcoholism [2]. Finally, reads spanning exon junctions also inform about alternative splicing patterns. RNA-seq can therefore be used to assess whether ethanol alters expression of specific splice variants of individual genes, as was previously shown for Kcnma1 [86]. Accordingly, preliminary evidence for differential splice behavior of 125 genes emerged from transcriptome sequencing in the prefrontal cortex of alcoholics [89, and personal communication from R.D. Mayfield].
