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

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...

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Autores principales: Miller, Danny E., Lee, Lin, Galey, Miranda, Kandhaya-Pillai, Renuka, Tischkowitz, Marc, Amalnath, Deepak, Vithlani, Avadh, Yokote, Koutaro, Kato, Hisaya, Maezawa, Yoshiro, Takada-Watanabe, Aki, Takemoto, Minoru, Martin, George M., Eichler, Evan E., Hisama, Fuki M., Oshima, Junko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BMJ Publishing Group 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9613861/
https://www.ncbi.nlm.nih.gov/pubmed/35534204
http://dx.doi.org/10.1136/jmedgenet-2022-108485
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author Miller, Danny E.
Lee, Lin
Galey, Miranda
Kandhaya-Pillai, Renuka
Tischkowitz, Marc
Amalnath, Deepak
Vithlani, Avadh
Yokote, Koutaro
Kato, Hisaya
Maezawa, Yoshiro
Takada-Watanabe, Aki
Takemoto, Minoru
Martin, George M.
Eichler, Evan E.
Hisama, Fuki M.
Oshima, Junko
author_facet Miller, Danny E.
Lee, Lin
Galey, Miranda
Kandhaya-Pillai, Renuka
Tischkowitz, Marc
Amalnath, Deepak
Vithlani, Avadh
Yokote, Koutaro
Kato, Hisaya
Maezawa, Yoshiro
Takada-Watanabe, Aki
Takemoto, Minoru
Martin, George M.
Eichler, Evan E.
Hisama, Fuki M.
Oshima, Junko
author_sort Miller, Danny E.
collection PubMed
description 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.
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spelling pubmed-96138612022-10-29 Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases Miller, Danny E. Lee, Lin Galey, Miranda Kandhaya-Pillai, Renuka Tischkowitz, Marc Amalnath, Deepak Vithlani, Avadh Yokote, Koutaro Kato, Hisaya Maezawa, Yoshiro Takada-Watanabe, Aki Takemoto, Minoru Martin, George M. Eichler, Evan E. Hisama, Fuki M. Oshima, Junko J Med Genet Diagnostics 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. BMJ Publishing Group 2022-11 2022-05-09 /pmc/articles/PMC9613861/ /pubmed/35534204 http://dx.doi.org/10.1136/jmedgenet-2022-108485 Text en © Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.
spellingShingle Diagnostics
Miller, Danny E.
Lee, Lin
Galey, Miranda
Kandhaya-Pillai, Renuka
Tischkowitz, Marc
Amalnath, Deepak
Vithlani, Avadh
Yokote, Koutaro
Kato, Hisaya
Maezawa, Yoshiro
Takada-Watanabe, Aki
Takemoto, Minoru
Martin, George M.
Eichler, Evan E.
Hisama, Fuki M.
Oshima, Junko
Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title_full Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title_fullStr Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title_full_unstemmed Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title_short Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases
title_sort targeted long-read sequencing identifies missing pathogenic variants in unsolved werner syndrome cases
topic Diagnostics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9613861/
https://www.ncbi.nlm.nih.gov/pubmed/35534204
http://dx.doi.org/10.1136/jmedgenet-2022-108485
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