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Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy

Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypot...

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Autores principales: Wieben, Eric D., Aleff, Ross A., Basu, Shubham, Sarangi, Vivekananda, Bowman, Brett, McLaughlin, Ian J., Mills, John R., Butz, Malinda L., Highsmith, Edward W., Ida, Cristiane M., Ekholm, Jenny M., Baratz, Keith H., Fautsch, Michael P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611681/
https://www.ncbi.nlm.nih.gov/pubmed/31276570
http://dx.doi.org/10.1371/journal.pone.0219446
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author Wieben, Eric D.
Aleff, Ross A.
Basu, Shubham
Sarangi, Vivekananda
Bowman, Brett
McLaughlin, Ian J.
Mills, John R.
Butz, Malinda L.
Highsmith, Edward W.
Ida, Cristiane M.
Ekholm, Jenny M.
Baratz, Keith H.
Fautsch, Michael P.
author_facet Wieben, Eric D.
Aleff, Ross A.
Basu, Shubham
Sarangi, Vivekananda
Bowman, Brett
McLaughlin, Ian J.
Mills, John R.
Butz, Malinda L.
Highsmith, Edward W.
Ida, Cristiane M.
Ekholm, Jenny M.
Baratz, Keith H.
Fautsch, Michael P.
author_sort Wieben, Eric D.
collection PubMed
description Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and a new target-enrichment sequence analysis tool developed by Pacific Biosciences to interrogate the sequence structure of expanded repeats. The sequencing was successful in identifying a previously described interruption within an unexpanded allele and provided sequence data on expanded alleles greater than 2000 bases in length. The data revealed considerable heterogeneity in the size distribution of expanded repeats within each patient. Detailed analysis of the long sequence reads did not reveal any instances of interruptions to the expanded CAG repeats, but did reveal novel variants within the AGG repeats that flank the CAG repeats in two of the five samples from clinically unaffected patients with expansions. This first examination of the sequence structure of CAG repeats in CTG18.1 suggests that factors other than interruptions to the repeat structure account for the absence of disease in some elderly patients with repeat expansions in the TCF4 gene.
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spelling pubmed-66116812019-07-12 Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy Wieben, Eric D. Aleff, Ross A. Basu, Shubham Sarangi, Vivekananda Bowman, Brett McLaughlin, Ian J. Mills, John R. Butz, Malinda L. Highsmith, Edward W. Ida, Cristiane M. Ekholm, Jenny M. Baratz, Keith H. Fautsch, Michael P. PLoS One Research Article Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and a new target-enrichment sequence analysis tool developed by Pacific Biosciences to interrogate the sequence structure of expanded repeats. The sequencing was successful in identifying a previously described interruption within an unexpanded allele and provided sequence data on expanded alleles greater than 2000 bases in length. The data revealed considerable heterogeneity in the size distribution of expanded repeats within each patient. Detailed analysis of the long sequence reads did not reveal any instances of interruptions to the expanded CAG repeats, but did reveal novel variants within the AGG repeats that flank the CAG repeats in two of the five samples from clinically unaffected patients with expansions. This first examination of the sequence structure of CAG repeats in CTG18.1 suggests that factors other than interruptions to the repeat structure account for the absence of disease in some elderly patients with repeat expansions in the TCF4 gene. Public Library of Science 2019-07-05 /pmc/articles/PMC6611681/ /pubmed/31276570 http://dx.doi.org/10.1371/journal.pone.0219446 Text en © 2019 Wieben et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Wieben, Eric D.
Aleff, Ross A.
Basu, Shubham
Sarangi, Vivekananda
Bowman, Brett
McLaughlin, Ian J.
Mills, John R.
Butz, Malinda L.
Highsmith, Edward W.
Ida, Cristiane M.
Ekholm, Jenny M.
Baratz, Keith H.
Fautsch, Michael P.
Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title_full Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title_fullStr Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title_full_unstemmed Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title_short Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy
title_sort amplification-free long-read sequencing of tcf4 expanded trinucleotide repeats in fuchs endothelial corneal dystrophy
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611681/
https://www.ncbi.nlm.nih.gov/pubmed/31276570
http://dx.doi.org/10.1371/journal.pone.0219446
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