Theoretical and Natural Science

- The Open Access Proceedings Series for Conferences


Theoretical and Natural Science

Vol. 32, 06 March 2024


Open Access | Article

Current research progress of whole genome sequencing in practical

Zishan Huang * 1
1 Queen Mary University of London

* Author to whom correspondence should be addressed.

Theoretical and Natural Science, Vol. 32, 76-81
Published 06 March 2024. © 2023 The Author(s). Published by EWA Publishing
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Citation Zishan Huang. Current research progress of whole genome sequencing in practical. TNS (2024) Vol. 32: 76-81. DOI: 10.54254/2753-8818/32/20240802.

Abstract

Gene sequencing, a vital technique nowadays, detects patients’ diseases and helping with diagnosis. Whole genome sequencing (WGS) is one member of this family, which mainly functions in analysing participant’s gene sequences in clinical diagnosis for the purpose of indicating therapeutic interventions. This essay compares WGS and other sequencing methods, such as whole exome sequencing (WES), which comprises both positive and negative sides of this sequencing test for evaluation. And point out the help of WGS in certain diseases. This paper serves as a synopsis of some WGS-related themes as well as potential directions in the future for technical advancement.

Keywords

whole genome sequencing; whole exome sequencing; tuberculosis

References

1. Purushothaman S, Meola M, Egli A. Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. International Journal of Molecular Sciences. 2022 Aug 30;23(17):9834.

2. Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M. Exome Sequencing: Current and Future Perspectives. G3: Genes|Genomes|Genetics. 2015 Jul 2;5(8):1543–50.

3. Quentin T, Vitobello A, Frédéric Tran Mau-Them, Yannis Duffourd, Agnès Fromont, Giroud M, et al. High efficiency and clinical relevance of exome sequencing in the daily practice of neurogenetics. Journal of Medical Genetics. 2021 Mar 5;59(5):445–52.

4. Basel-Salmon L, Orenstein N, Markus-Bustani K, Ruhrman-Shahar N, Kilim Y, Magal N, et al. Improved diagnostics by exome sequencing following raw data reevaluation by clinical geneticists involved in the medical care of the individuals tested. Genetics in Medicine: Official Journal of the American College of Medical Genetics [Internet]. 2019 Jun 1;21(6):1443–51. Available from: https://pubmed.ncbi.nlm.nih.gov/30377382/

5. Kim J, Hu C, Moufawad El Achkar C, Black LE, Douville J, Larson A, et al. Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease. New England Journal of Medicine. 2019 Oct 24;381(17):1644–52.

6. Wortmann SB, Oud MM, Alders M, Coene KLM, van der Crabben SN, Feichtinger RG, et al. How to proceed after “negative” exome: a review on genetic diagnostics, limitations, challenges and emerging new multi‐omics techniques. Journal of Inherited Metabolic Disease. 2022 May 4;

7. Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, et al. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology. 2021 Sep;39(9):1141–50.

8. McPherson A. Whole genome sequencing drives progress in cancer [Internet]. Genomics Education Programme. 2020. Available from: https://www.genomicseducation.hee.nhs.uk/ blog/whole-genome-sequencing-drives-progress-in-cancer

9. Reuter S, Ellington MJ, Cartwright EJP, Köser CU, Török ME, Gouliouris T, et al. Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology. JAMA Internal Medicine [Internet]. 2013 Aug 12;173(15):1397. Available from: https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/1726980

10. Cobain EF, Wu YM, Vats P, Chugh R, Worden F, Smith DC, et al. Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors. JAMA Oncology [Internet]. 2021 Apr 1;7(4):525–33. Available from: https://jamanetwork.com/journals/jamaoncology/ fullarticle/2776760

11. Priestley P, Baber J, Lolkema MP, Steeghs N, de Bruijn E, Shale C, et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature. 2019 Oct 23;575(7781):210–6.

12. Satta G, Lipman M, Smith GP, Arnold C, Kon OM, McHugh TD. Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential? Clinical Microbiology and Infection. 2018 Jun;24(6):604–9.

13. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998 Jun;393(6685):537–44.

14. Zignol M, Cabibbe AM, Dean AS, Glaziou P, Alikhanova N, Ama C, et al. Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study. The Lancet Infectious Diseases. 2018 Jun;18(6):675–83.

15. Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, et al. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology [Internet]. 2019 Jun 17;17(9):533–45. Available from: https://www.nature.com/articles/s41579-019-0214-5

16. Cortés-Ciriano I, Lee JJK, Xi R, Jain D, Jung YL, Yang L, et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics [Internet]. 2020;52(3):331–41. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/ PMC7058534/

17. Chrystoja CC, Diamandis EP. Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities. Clinical Chemistry. 2013 Nov 13;60(5):724–33.

18. Zhao EY, Jones M, Jones SJM. Whole-Genome Sequencing in Cancer. Cold Spring Harbor Perspectives in Medicine. 2018 May 29;9(3):a034579.

19. Coll F, McNerney R, José Afonso Guerra-Assunção, Glynn JR, João Perdigão, Viveiros M, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications. 2014 Sep 1;5(1).

20. Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nature Communications [Internet]. 2015 Dec;6(1). Available from: http://www.nature.com/articles/ncomms10063

21. Metcalf BJ, Chochua S, Gertz RE, Hawkins PA, Ricaldi J, Li Z, et al. Short-read whole genome sequencing for determination of antimicrobial resistance mechanisms and capsular serotypes of current invasive Streptococcus agalactiae recovered in the USA. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases [Internet]. 2017 Aug 1;23(8):574.e7–14. Available from: https://pubmed.ncbi.nlm.nih.gov/28257899/

22. Kwong JC, Lane CR, Romanes F, Gonçalves da Silva A, Easton M, Cronin K, et al. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ. 2018 Jan 3;6:e4210.

23. Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, et al. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends in Microbiology [Internet]. 2018 Dec;26(12):1035–48. Available from: https://www.sciencedirect.com/science/article/pii/S0966842X18301768

24. Samsom KG, Schipper LJ, Roepman P, Bosch LJ, Lalezari F, Klompenhouwer EG, et al. Feasibility of whole-genome sequencing-based tumor diagnostics in routine pathology practice. The Journal of Pathology [Internet]. 2022 Oct 1;258(2):179–88. Available from: https://pubmed.ncbi.nlm.nih.gov/35792649/

Data Availability

The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. Authors who publish this series agree to the following terms:

1. Authors retain copyright and grant the series right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this series.

2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the series's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this series.

3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See Open Access Instruction).

Volume Title
Proceedings of the 2nd International Conference on Modern Medicine and Global Health
ISBN (Print)
978-1-83558-321-0
ISBN (Online)
978-1-83558-322-7
Published Date
06 March 2024
Series
Theoretical and Natural Science
ISSN (Print)
2753-8818
ISSN (Online)
2753-8826
DOI
10.54254/2753-8818/32/20240802
Copyright
06 March 2024
Open Access
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Copyright © 2023 EWA Publishing. Unless Otherwise Stated