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Exome

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Not to be confused with exosome.

The exome is composed of all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing. This includes untranslated regions of messenger RNA (mRNA), and coding regions. Exome sequencing has proven to be an efficient method of determining the genetic basis of more than two dozen Mendelian or single gene disorders.[1]

Statistics

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Distinction between genome, exome, and transcriptome. The exome consists of all of the exons within the genome. In contrast, the trascriptome varies between cell types (e.g. neurons vs cardiac cells), only involving a portion of the exons that are actually transcribed into mRNA.

The human exome consists of roughly 233,785 exons, about 80% of which are less than 200 base pairs in length, constituting a total of about 1.1% of the total genome, or about 30 megabases of DNA.[2][3][4] Though composing a very small fraction of the genome, mutations in the exome are thought to harbor 85% of mutations that have a large effect on disease.[5]

Definition

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See also: List of human protein-coding genes 1, List of human protein-coding genes 2, List of human protein-coding genes 3, and List of human protein-coding genes 4

It is important to note that the exome is distinct from the transcriptome, which is all of the transcribed RNA within a cell type. While the exome is constant from cell-type to cell-type, the transcriptome changes based on the structure and function of the cells. As a result, the entirety of the exome is not translated into protein in every cell. Different cell types only transcribe portions of the exome, and only the coding regions of the exons are eventually translated into proteins.

Next-generation sequencing

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Next-generation sequencing (NGS) allows for the rapid sequencing of large amounts of DNA, significantly advancing the study of genetics, and replacing older methods such as Sanger sequencing. This technology is starting to become more common in healthcare and research not only because it is a reliable method of determining genetic variations, but also because it is cost effective and allows researchers to sequence entire genomes in anywhere between days to weeks. This compares to former methods which may have taken months. Next-gen sequencing includes both whole-exome sequencing and whole-genome sequencing.[6]

Whole-exome sequencing

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Sequencing an individual's exome instead of their entire genome has been proposed to be a more cost-effective and efficient way to diagnose rare genetic disorders.[7][8] It has also been found to be more effective than other methods such as karyotyping and microarrays.[9] This distinction is largely due to the fact that phenotypes of genetic disorders are a result of mutated exons. In addition, since the exome only comprises 1.5% of the total genome, this process is more cost efficient and fast as it involves sequencing around 40 million bases rather than the 3 billion base pairs that make up the genome.[10]

Whole-genome sequencing

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On the other hand, whole genome sequencing has been found to capture a more comprehensive view of variants in the DNA compared to whole-exome sequencing. Especially for single nucleotide variants, whole genome sequencing is more powerful and more sensitive than whole-exome sequencing in detecting potentially disease-causing mutations within the exome.[11] One must also keep in mind that non-coding regions can be involved in the regulation of the exons that make up the exome, and so whole-exome sequencing may not be complete in showing all the sequences at play in forming the exome.

Ethical considerations

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With either form of sequencing, whole-exome sequencing or whole genome sequencing, some have argued that such practices should be done under the consideration of medical ethics. While physicians strive to preserve patient autonomy, sequencing deliberately asks laboratories to look at genetic variants that may be completely unrelated to the patient's condition at hand and have the potential of revealing findings that were not intentionally sought. In addition, such testing have been suggested to have imply forms of discrimination against particular groups for having certain genes, creating the potential for stigmas or negative attitudes towards that group as a result.[12]

Diseases and diagnoses

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Rare mutations that affect the function of essential proteins constitute the majority of Mendelian diseases. In addition, the overwhelming majority of disease-causing mutations in Mendelian loci can be found within the coding region.[5] With the goal of finding methods to best detect harmful mutations and successfully diagnose patients, researchers are looking to the exome for clues to aid in this process.

Whole-exome sequencing is a recent technology that has led to the discovery of various genetic disorders and increased the rate of diagnoses of patients with rare genetic disorders. Overall, whole-exome sequencing has allowed healthcare providers to diagnose 30–50% of patients who were thought to have rare Mendelian disorders.[citation needed] It has been suggested that whole-exome sequencing in clinical settings has many unexplored advantages. Not only can the exome increase our understanding of genetic patterns, but under clinical settings, it has the potential to the change in management of patients with rare and previously unknown disorders, allowing physicians to develop more targeted and personalized interventions.[13]

For example, Bartter Syndrome, also known as salt-wasting nephropathy, is a hereditary disease of the kidney characterized by hypotension (low blood pressure), hypokalemia (low potassium), and alkalosis (high blood pH) leading to muscle fatigue and varying levels of fatality.[14] It is an example of a rare disease, affecting fewer than one per million people, whose patients have been positively impacted by whole-exome sequencing. Thanks to this method, patients who formerly did not exhibit the classical mutations associated with Bartter Syndrome were formally diagnosed with it after the discovery that the disease has mutations outside of the loci of interest.[5] They were thus able to gain more targeted and productive treatment for the disease.

Much of the focus of exome sequencing in the context of disease diagnosis has been on protein coding "loss of function" alleles. Research has shown, however, that future advances that allow the study of non-coding regions, within and without the exome, may lead to additional abilities in the diagnoses of rare Mendelian disorders.[15] The exome is the part of the genome composed of exons, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing and contribute to the final protein product encoded by that gene. It consists of all DNA that is transcribed into mature RNA in cells of any type, as distinct from the transcriptome, which is the RNA that has been transcribed only in a specific cell population. The exome of the human genome consists of roughly 180,000 exons constituting about 1% of the total genome, or about 30 megabases of DNA.[16] Though composing a very small fraction of the genome, mutations in the exome are thought to harbor 85% of mutations that have a large effect on disease.[17][18] Exome sequencing has proved to be an efficient strategy to determine the genetic basis of more than two dozen Mendelian or single gene disorders.[19]

See also

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References

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  1. ^ Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J (September 2011). "Exome sequencing as a tool for Mendelian disease gene discovery". Nature Reviews Genetics. 12 (11): 745–55. doi:10.1038/nrg3031. PMID 21946919. S2CID 15615317.
  2. ^ Sakharkar MK, Chow VT, Kangueane P (2004). "Distributions of exons and introns in the human genome". In Silico Biology. 4 (4): 387–93. PMID 15217358.
  3. ^ Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. (February 2001). "The sequence of the human genome". Science. 291 (5507): 1304–51. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995.
  4. ^ Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, et al. (September 2009). "Targeted capture and massively parallel sequencing of 12 human exomes". Nature. 461 (7261): 272–6. Bibcode:2009Natur.461..272N. doi:10.1038/nature08250. PMC 2844771. PMID 19684571.
  5. ^ a b c Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. (November 2009). "Genetic diagnosis by whole exome capture and massively parallel DNA sequencing". Proceedings of the National Academy of Sciences of the United States of America. 106 (45): 19096–101. Bibcode:2009PNAS..10619096C. doi:10.1073/pnas.0910672106. PMC 2768590. PMID 19861545.
  6. ^ "What are whole exome sequencing and whole genome sequencing?". Genetics Home Reference. National Library of Medicine, National Institutes of Health, U.S. Department of Health & Human Services. Retrieved 2019-11-07.
  7. ^ Erjavec SO, Gelfman S, Abdelaziz AR, Lee EY, Monga I, Alkelai A, Ionita-Laza I, Petukhova L, Christiano AM (Feb 2022). "Whole exome sequencing in Alopecia Areata identifies rare variants in KRT82". Nat Commun. 13 (1): 800. Bibcode:2022NatCo..13..800E. doi:10.1038/s41467-022-28343-3. PMC 8831607. PMID 35145093.
  8. ^ Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. (October 2013). "Clinical whole-exome sequencing for the diagnosis of mendelian disorders". The New England Journal of Medicine. 369 (16): 1502–11. doi:10.1056/NEJMoa1306555. PMC 4211433. PMID 24088041.
  9. ^ Edelson PK, Dugoff L, Bromley B (2019-01-01). "Chapter 11 – Genetic Evaluation of Fetal Sonographic Abnormalities". In Norton ME, Kuller JA, Dugoff L (eds.). Perinatal Genetics. Content Repository Only!. pp. 105–124. ISBN 9780323530941.
  10. ^ Nagele P (November 2013). "Exome sequencing: one small step for malignant hyperthermia, one giant step for our specialty—why exome sequencing matters to all of us, not just the experts". Anesthesiology. 119 (5): 1006–8. doi:10.1097/ALN.0b013e3182a8a90c. PMC 3980570. PMID 24195944.
  11. ^ Belkadi A, Bolze A, Itan Y, Cobat A, Vincent QB, Antipenko A, et al. (April 2015). "Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants". Proceedings of the National Academy of Sciences of the United States of America. 112 (17): 5473–8. Bibcode:2015PNAS..112.5473B. doi:10.1073/pnas.1418631112. PMC 4418901. PMID 25827230.
  12. ^ Gaff CL, Macciocca I (2016-01-01). "Chapter 15 – Genomic Perspective of Genetic Counseling". In Kumar D, Antonarakis S (eds.). Medical and Health Genomics. Academic Press. pp. 201–212. doi:10.1016/b978-0-12-420196-5.00015-0. ISBN 9780124201965.
  13. ^ Zhu X, Petrovski S, Xie P, Ruzzo EK, Lu YF, McSweeney KM, et al. (October 2015). "Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios". Genetics in Medicine. 17 (10): 774–81. doi:10.1038/gim.2014.191. PMC 4791490. PMID 25590979.
  14. ^ "Bartter syndrome". Genetics Home Reference. National Library of Medicine, National Institutes of Health, U.S. Department of Health & Human Services. Retrieved 2019-11-19.
  15. ^ Frésard L, Montgomery SB (December 2018). "Diagnosing rare diseases after the exome". Cold Spring Harbor Molecular Case Studies. 4 (6): a003392. doi:10.1101/mcs.a003392. PMC 6318767. PMID 30559314.
  16. ^ Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, et al. (September 2009). "Targeted capture and massively parallel sequencing of 12 human exomes". Nature. 461 (7261): 272–6. Bibcode:2009Natur.461..272N. doi:10.1038/nature08250. PMC 2844771. PMID 19684571.
  17. ^ Suleiman SH, Koko ME, Nasir WH, Elfateh O, Elgizouli UK, Abdallah MO, et al. (2015). "Exome sequencing of a colorectal cancer family reveals shared mutation pattern and predisposition circuitry along tumor pathways". Frontiers in Genetics. 6: 288. doi:10.3389/fgene.2015.00288. PMC 4584935. PMID 26442106.
  18. ^ Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. (November 2009). "Genetic diagnosis by whole exome capture and massively parallel DNA sequencing". Proceedings of the National Academy of Sciences of the United States of America. 106 (45): 19096–101. Bibcode:2009PNAS..10619096C. doi:10.1073/pnas.0910672106. PMC 2768590. PMID 19861545.
  19. ^ Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J (September 2011). "Exome sequencing as a tool for Mendelian disease gene discovery". Nature Reviews Genetics. 12 (11): 745–55. doi:10.1038/nrg3031. PMID 21946919. S2CID 15615317.
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