Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases.
Martin, George M
Eichler, Evan E
Hisama, Fuki M
J Med Genet
BMJ Publishing Group
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Miller, D. E., Lee, L., Galey, M., Kandhaya-Pillai, R., Tischkowitz, M., Amalnath, D., Vithlani, A., et al. (2022). Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases.. J Med Genet https://doi.org/10.1136/jmedgenet-2022-108485
BACKGROUND: Werner syndrome (WS) is an autosomal recessive progeroid syndrome caused by variants in WRN. The International Registry of Werner Syndrome has identified biallelic pathogenic variants in 179/188 cases of classical WS. In the remaining nine cases, only one heterozygous pathogenic variant has been identified. METHODS: Targeted long-read sequencing (T-LRS) on an Oxford Nanopore platform was used to search for a second pathogenic variant in WRN. Previously, T-LRS was successfully used to identify missing variants and analyse complex rearrangements. RESULTS: We identified a second pathogenic variant in eight of nine unsolved WS cases. In five cases, T-LRS identified intronic splice variants that were confirmed by either RT-PCR or exon trapping to affect splicing; in one case, T-LRS identified a 339 kbp deletion, and in two cases, pathogenic missense variants. Phasing of long reads predicted all newly identified variants were on a different haplotype than the previously known variant. Finally, in one case, RT-PCR previously identified skipping of exon 20; however, T-LRS did not detect a pathogenic DNA sequence variant. CONCLUSION: T-LRS is an effective method for identifying missing pathogenic variants. Although limitations with computational prediction algorithms can hinder the interpretation of variants, T-LRS is particularly effective in identifying intronic variants.
Diagnostics, 1506, nanopore sequencing, genomics, genetic variation
External DOI: https://doi.org/10.1136/jmedgenet-2022-108485
This record's URL: https://www.repository.cam.ac.uk/handle/1810/337011