Introduction
“Whole genome sequencing (WGS) has significant benefits that will help to improve the accuracy of testing for rare diseases. The full capability of WGS remains unknown as it can only be recognized when the full potential of noncoding regions is understood. ”
Molecular diagnostics has had very beneficial effects on improving rare disease diagnosis. More funding towards the research of molecular diagnostics will help to improve rare disease diagnoses for patients. Specifically, research should be focused on genome sequencing, which is one approach used in molecular diagnostics. This technique allows for an assessment of the entire genomic sequence to determine any abnormalities that may be linked to genetic diseases. New advancements in genome sequencing can significantly improve the diagnosis of rare diseases as it can assess more than just Mendelian diseases. Mendelian disease discovery has led to some progress as 20% of human-protein coding disease genes have been definitively associated with one or more human phenotypes. 1 There is a complex relationship between Mendelian conditions and associated genes and phenotypes leading to the current challenges with present clinical diagnostics and discovery methods. 1 Not all rare diseases follow Mendelian conditions, which contributes to the challenge to diagnose them.
Past Research
Past research in molecular diagnostics was focused on chromosomal array (CMA).1 CMA brought an increased resolution of the genome-wide detection of copy number variants, which are the number of copies of a particular gene an individual has. However, CMA is not able to detect all variants. 1 Presently, techniques used in next generation sequencing only target known disease genes. Past debates have been centered around targeted genome sequencing or whether the whole genome should be sequenced.1
Previously, only targeted genome sequencing was agreed upon. Although, most known mutations causing diseases are in exons, there is a research gap in the understanding as to how noncoding sequences contribute to genetic diseases. This is why exome sequencing is the dominant approach used in molecular diagnostics. 2
Current Research and Gaps
Funded centers show a steady trajectory of discovering 263 diseases each year, which is done through targeted genome sequencing. 1 Next generation sequencing allows large sequences of DNA to be sequenced. It has been moving into the clinical diagnosis arena transforming molecular diagnosis. 2 Whole exome sequencing (WES) tests are generally used in molecular genomics in which targeted genome sequencing is used. 3
WES can be used for clinical testing. 3 Exome sequencing can determine Mendelian disorders caused by missense or nonsense variants and disorders that have been reported in the Human Gene Mutation Database. 4 It is also able to determine Mendelian disorders caused by small insertions or deletions within nonrepetitive coding of the DNA. 4 Some limitations of exome sequencing is that the commercial exome-capture reagents made may vary as different vendors target a different number of bases, meaning that different number of variants will be detected when using different kits. 3 Additionally, WES is not able to determine variations outside of exons that can affect gene activity and protein production and also contribute to rare diseases. 1 These types of variations require whole genome sequencing (WGS) to be understood.
WGS has significant benefits that will help to improve the accuracy of testing for rare diseases. The full capability of WGS remains unknown as it can only be recognized when the full potential of noncoding regions is understood. 3 Genome sequencing is significantly more costly than exome sequencing although the benefits include simpler sample preparation and the ability to identify structural variants and chromosome breakpoints in the noncoding regions. 4 Genome sequencing identifies variants outside of the coding region, although most confirmed pathogenic variants lie within the exome. 5 The clinical sensitivity and value of genome sequencing will increase as more noncoding pathogenic variants are discovered. 1 WES and WEG have a dual functionality allowing for the discovery and diagnostics of rare diseases. 3 Although how they determine rare diseases differs which affects the accuracy of molecular testing. The sensitivity of genome sequencing needs to be explored more. Researchers need to have a better understanding of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variations at the locus, and advances of functional annotation of the identified genes. 1 For example, one study shows that WGS led to a diagnostic yield of 85% in the retrospective cohort, revealing that the test has high accuracy. 5 Having more studies that show a high accuracy will allow a more prevalent use of WGS in molecular diagnostics.
How Research Translates into Better Diagnostics
WES and WGS are both used in clinical and research settings, although more research needs to be done in order for WGS to become the dominant approach used in diagnostics. 6 Searching the entire genome instead of just specific exons will include coding and noncoding regions allowing for a more accurate diagnosis. Coding the entire genome will enable scanning of regions that are not part of exons that may contribute to genetic disorders. The main goal of implementing genome sequencing is to maximize the effectiveness of molecular testing and to avoid overwhelming clinicians and patients with irrelevant or uninterpretable information. 7 Improving the effectiveness of molecular testing will allow patients to be diagnosed faster due to a more accurate approach, which will help to reduce the occurence of misdiagnosis. Reducing the occurence of misdiagnoses will help patients to receive their treatment faster.
Jonta Kamara
Works Cited:
1. Posey J. Genome sequencing and implications for rare disorders. Orphanet J Rare Dis. 2019;14(1). doi:10.1186/s13023-019-1127-0
2. National Institute of Health. What are whole exome sequencing and whole genome sequencing?. Genetics Home Reference. https://ghr.nlm.nih.gov/primer/testing/sequencing. Published 2020. Accessed January 16, 2020.
3. Yu Y, Wu B, Wu J, Shen Y. Exome and Whole-Genome Sequencing as Clinical Tests: A Transformative Practice in Molecular Diagnostics. Clin Chem. 2012;58(11):1507-1509. doi:10.1373/clinchem.2012.193128
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4. Wallace S, Bean L. Educational Materials — Genetic Testing: Current Approaches. In: MP A, HH A, ed. Genereviews. Seattle: University of Washington; 2020. https://www.ncbi.nlm.nih.gov/books/NBK279899/. Accessed January 17, 2020.
5. Helman G, Lajoie B, Crawford J et al. Genome sequencing in persistently unsolved white matter disorders. Ann Clin Transl Neurol. 2020;7(1):144-152. doi:10.1002/acn3.50957
6. National Institute of Health. How does genetic testing in a research setting differ from clinical genetic testing?. Genetics Home Reference. https://ghr.nlm.nih.gov/primer/testing/researchtesting. Published 2020. Accessed January 25, 2020.
7. PHG Foundation. Whole Genome Sequencing. Cambridge; 2011. https://www.phgfoundation.org/documents/279_1319536722.pdf. Accessed January 25, 2020.
Cite This Article:
Kamara J. How improvements in molecular diagnostics could save your life. Rare Disease Review. June 2020.
