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Regardless of DNA sequencing approach, it is estimated that the diagnostic rate using exome or genome sequencing is plateauing between 35% and 50% (Taylor et al.
It is possible that this test will not find a reason for your or your childs signs and symptoms. About three out of four patients tested (75 percent) do not receive a diagnosis from WES. WES is not a perfect test. Our current understanding of the human exome is limited.
As the name suggests, Trio-exome sequencing analyses genetic data from 3 people, including the baby, its mother, and the father. It is a powerful tool to identify variations in DNA that are known to cause specific inherited genetic conditions.
The biggest limitation of whole exome sequencing (WES) is that it does not target 100% of the genes in the genome. Instead it focuses only on exons or coding proteins, which make up 1 2% of the entire genome. As a result, disease-causing variants in the missed exons go undetected.
Exome sequencing is limited in detecting the following types of mutations (this list might not be exhaustive): large rearrangements. copy number variation mutations (large deletions/duplications) mitochondrial genome mutations.
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Disadvantages of whole exome sequencing: Detection of CNVs (copy number variants) not as reliable as exome sequencing. Difficult to detect large structural variants. Does not detect variants in non-coding regions.
WES is not validated for the detection of structural variations (SVs), including copy number variants (CNVs), inversions, and translocations. WES has low sensitivity for structural variations, so detection is limited1.
Research has shown that exome sequencing could detect genetic mutations related to birth defects and developmental delays. So, patients who have a family history of disease or are searching for a diagnosis to explain symptoms may be able to avoid unnecessary diagnostic tests by undergoing exome sequencing.
Three pathogenic loss-of-function heterozygous variants were identified by exome trio sequencing, each linked to different genetic conditions: SIN3A (WitteveenKolk syndrome), FLG (dermatitis), and EDAR (ectodermal dysplasia). Together, these three genetic alterations could explain the patients overall phenotype.
On average, we capture and sequence 99.4% of the exome with a quality enabling reliable variant calls. Coverage also refers to how many times each nucleotide is being sequenced.

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