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- Title
Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome.
- Authors
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; Quinn, John P.
- Abstract
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.
- Subjects
GENOMES; NON-coding RNA; AUTISM spectrum disorders; GENES; SHOTGUN sequencing; GENETIC disorders
- Publication
International Journal of Molecular Sciences, 2021, Vol 22, Issue 4, p2060
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms22042060