RNA, the link from phenotype to genotype
Researchers interested in understanding phenotypic differences often employ comparative techniques including genome wide SNP studies, exome SNP studies, genome methylation studies, large genomic deletions/rearrangements detection studies, or microRNA marker studies to better understand the genomic basis of observed differences. While these approaches offer researchers a set of powerful tools, it can be a challenge to establish a direct cause/effect association between the genomic and phenotypic differences. The assay may not have captured the source of the variation, too many potential candidates were found, or worse, genomic differences end up falsely associated with the phenotype.
RNA sequencing (RNA-seq), and differential expression analysis provide researchers with an intermediate step between the observed phenotype and genomic differences. Identifying relative differences in gene expression between controls and samples of interest is instructive in both identifying what type of further genetic studies should be pursued as well as narrowing the scope to a subset of genes or pathways implicated by RNA-seq.