Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases.

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. 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. 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. 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. © Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.

Citation

Danny E Miller, Lin Lee, Miranda Galey, Renuka Kandhaya-Pillai, Marc Tischkowitz, Deepak Amalnath, Avadh Vithlani, Koutaro Yokote, Hisaya Kato, Yoshiro Maezawa, Aki Takada-Watanabe, Minoru Takemoto, George M Martin, Evan E Eichler, Fuki M Hisama, Junko Oshima. Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases. Journal of medical genetics. 2022 May 09

PMID: 35534204

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