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

Eric D Wieben, Ross A. Aleff, Shubham Basu, Vivekananda Sarangi, Brett Bowman, Ian J. McLaughlin, John R. Mills, Malinda L. Butz, W Edward Jr. Highsmith, Cristiane M. Ida, Jenny M. Ekholm, Keith Baratz, Michael P Fautsch

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article numbere0219446
JournalPloS one
Volume14
Issue number7
DOIs
StatePublished - Jan 1 2019

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Fuchs' Endothelial Dystrophy
Trinucleotide Repeat Expansion
Trinucleotide Repeats
Amplification
microsatellite repeats
Genes
Sequence Analysis
Alleles
alleles
genes
sequence analysis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

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, W Edward Jr.; Ida, Cristiane M.; Ekholm, Jenny M.; Baratz, Keith; Fautsch, Michael P.

In: PloS one, Vol. 14, No. 7, e0219446, 01.01.2019.

Research output: Contribution to journalArticle

Wieben, ED, Aleff, RA, Basu, S, Sarangi, V, Bowman, B, McLaughlin, IJ, Mills, JR, Butz, ML, Highsmith, WEJ, Ida, CM, Ekholm, JM, Baratz, K & Fautsch, MP 2019, 'Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy', PloS one, vol. 14, no. 7, e0219446. https://doi.org/10.1371/journal.pone.0219446
Wieben, Eric D ; Aleff, Ross A. ; Basu, Shubham ; Sarangi, Vivekananda ; Bowman, Brett ; McLaughlin, Ian J. ; Mills, John R. ; Butz, Malinda L. ; Highsmith, W Edward Jr. ; Ida, Cristiane M. ; Ekholm, Jenny M. ; Baratz, Keith ; Fautsch, Michael P. / Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy. In: PloS one. 2019 ; Vol. 14, No. 7.
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