After a sequence variant is identified and associated with disease, the association and its biological effects must be confirmed. A variant may have various effects on protein structure, gene expression, and regulation, or it may have no effect. Array- and sequencing-based methods can help to determine exactly how a variant affects disease biology.
Fine mapping of genomic regions of interest can clarify the connection between a SNP and a disease. This can be done through targeted resequencing, or custom genotyping arrays designed by individual researchers or consortia. These approaches enable researchers to magnify regions of interest, avoid irrelevant regions of the genome, and conserve resources.
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By characterizing the downstream effects of variants, researchers can better understand the molecular mechanisms of disease. Genomic variants do not always affect protein structure or function. In fact, many sequence variants regulate gene expression.
RNA Sequencing (RNA-Seq) offers many advantages for assessing how variants affect transcription and protein translation. An unbiased approach to understanding the transcriptome, RNA-Seq quantifies RNA activity and captures subtle gene expression changes.