Whole-genome sequencing determines the order of the nucleotides (A, C, G, T) in the entire genome that makes up an organism. The goal of whole-genome sequencing is, typically, to look for genetic aberrations (eg, single nucleotide variants, deletions, insertions and copy number variants). Because the entire genome is being sequenced, changes in the noncoding sections of DNA within genes, called introns, can also be determined. Under normal conditions, introns are removed by RNA splicing during a post-transcriptional process, and alterations in these regions can be important to whether the DNA is transcribed into RNA or potentially result in a truncated, non-functional protein.
An alternative approach is to sequence only the exomes, called whole-exome sequencing. Exomes are the part of the genome formed by exons, or coding regions, which when transcribed and translated become expressed into proteins. Exomes compose only about 2% of the whole genome. Because the genome is so much larger, exomes are able to be sequenced at a much greater depth (number of times a given nucleotide is sequenced) for lower cost. This greater depth provides more confidence in low frequency alterations. Sequencing depth can become even greater for lower cost by using a targeted or “hot-spot” sequencing panel, which has a select number of specific genes, or coding regions within genes that are known to harbor mutations that contribute to pathogenesis of disease, and may include clinically-actionable genes of interest (eg, diagnostic, theranostic, etc.). These are often used in clinical care to provide greater confidence as well as keep the cost down and provide better opportunity for insurance reimbursement. However, whole-exome sequencing and targeted panels only see part of the story as they focus on reduced areas of the genome. Consequently, for some research projects or genetics testing, whole-genome sequencing may be advantageous.
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