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Article

Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome

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College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
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Department of Psychiatry, Al Jalila Children’s Specialty Hospital, Dubai 7662, United Arab Emirates
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Genetics and Genomic Medicine Centre, NeuroGen Children’s Healthcare, Dhaka 1205, Bangladesh
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Department of Biochemistry and Molecular Biology, Dhaka University, Dhaka 1000, Bangladesh
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Department of Biotechnology, Bharathidasan University, Tiruchirappalli 620024, India
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The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5S 1A1, Canada
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Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S, Canada
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Authors to whom correspondence should be addressed.
Academic Editor: John P. Quinn
Int. J. Mol. Sci. 2021, 22(4), 2060; https://doi.org/10.3390/ijms22042060
Received: 16 December 2020 / Revised: 21 January 2021 / Accepted: 27 January 2021 / Published: 19 February 2021
The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic variants fail to be found in the protein-coding genic regions along chromosomes, we proposed a scalable workflow to characterize the risk factor of SVs impacting non-coding elements of the genome. We applied whole-genome sequencing on an Emirati family having three children with ASD using long and short-read sequencing technology. A series of analytical pipelines were established to identify a set of SVs with high sensitivity and specificity. At 15-fold coverage, we observed that long-read sequencing technology (987 variants) detected a significantly higher number of SVs when compared to variants detected using short-read technology (509 variants) (p-value < 1.1020 × 10−57). Further comparison showed 97.9% of long-read sequencing variants were spanning within the 1–100 kb size range (p-value < 9.080 × 10−67) and impacting over 5000 genes. Moreover, long-read variants detected 604 non-coding RNAs (p-value < 9.02 × 10−9), comprising 58% microRNA, 31.9% lncRNA, and 9.1% snoRNA. Even at low coverage, long-read sequencing has shown to be a reliable technology in detecting SVs impacting complex elements of the genome. View Full-Text
Keywords: long-read sequencing; non-coding RNA; structural variation; whole-genome sequencing (WGS); Oxford Nanopore Technology (ONT) long-read sequencing; non-coding RNA; structural variation; whole-genome sequencing (WGS); Oxford Nanopore Technology (ONT)
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MDPI and ACS Style

Begum, G.; Albanna, A.; Bankapur, A.; Nassir, N.; Tambi, R.; Berdiev, B.K.; Akter, H.; Karuvantevida, N.; Kellam, B.; Alhashmi, D.; Sung, W.W.L.; Thiruvahindrapuram, B.; Alsheikh-Ali, A.; Scherer, S.W.; Uddin, M. Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome. Int. J. Mol. Sci. 2021, 22, 2060. https://doi.org/10.3390/ijms22042060

AMA Style

Begum G, Albanna A, Bankapur A, Nassir N, Tambi R, Berdiev BK, Akter H, Karuvantevida N, Kellam B, Alhashmi D, Sung WWL, Thiruvahindrapuram B, Alsheikh-Ali A, Scherer SW, Uddin M. Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome. International Journal of Molecular Sciences. 2021; 22(4):2060. https://doi.org/10.3390/ijms22042060

Chicago/Turabian Style

Begum, Ghausia; Albanna, Ammar; Bankapur, Asma; Nassir, Nasna; Tambi, Richa; Berdiev, Bakhrom K.; Akter, Hosneara; Karuvantevida, Noushad; Kellam, Barbara; Alhashmi, Deena; Sung, Wilson W.L.; Thiruvahindrapuram, Bhooma; Alsheikh-Ali, Alawi; Scherer, Stephen W.; Uddin, Mohammed. 2021. "Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome" Int. J. Mol. Sci. 22, no. 4: 2060. https://doi.org/10.3390/ijms22042060

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