ABCA4 gene screening by next-generation sequencing in a British cohort

Kaoru Fujinami, Jana Zernant, Ravinder K. Chana, Genevieve A. Wright, Kazushige Tsunoda, Yoko Ozawa, Kazuo Tsubota, Andrew R. Webster, Anthony T. Moore, Rando Allikmets, Michel Michaelides

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Purpose. We applied a recently reported next-generation sequencing (NGS) strategy for screening the ABCA4 gene in a British cohort with ABCA4-associated disease and report novel mutations. Methods. We identified 79 patients with a clinical diagnosis of ABCA4-associated disease who had a single variant identified by the ABCA4 microarray. Comprehensive phenotypic data were obtained, and the NGS strategy was applied to identify the second allele by means of sequencing the entire coding region and adjacent intronic sequences of the ABCA4 gene. Identified variants were confirmed by Sanger sequencing and assessed for pathogenicity by in silico analysis. Results. Of the 42 variants detected by prescreening with the microarray, in silico analysis suggested that 34, found in 66 subjects, were disease-causing and 8, found in 13 subjects, were benign variants. We detected 42 variants by NGS, of which 39 were classified as disease-causing. Of these 39 variants, 31 were novel, including 16 missense, 7 splice-site-altering, 4 nonsense, 1 in-frame deletion, and 3 frameshift variants. Two or more disease-causing variants were confirmed in 37 (47%) of 79 patients, one disease-causing variant in 36 (46%) subjects, and no disease-causing variant in 6 (7%) individuals. Conclusions. Application of the NGS platform for ABCA4 screening enabled detection of the second disease-associated allele in approximately half of the patients in a British cohort where one mutation had been detected with the arrayed primer extension (APEX) array. The time- and cost-efficient NGS strategy is useful in screening large cohorts, which will be increasingly valuable with the advent of ABCA4-directed therapies.

Original languageEnglish
Pages (from-to)6662-6674
Number of pages13
JournalInvestigative Ophthalmology and Visual Science
Volume54
Issue number10
DOIs
Publication statusPublished - 2013

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Genes
Computer Simulation
Alleles
Mutation
Virulence
Costs and Cost Analysis
Therapeutics

Keywords

  • ABCA4
  • Next generation sequencing
  • Stargardt disease

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

Cite this

Fujinami, K., Zernant, J., Chana, R. K., Wright, G. A., Tsunoda, K., Ozawa, Y., ... Michaelides, M. (2013). ABCA4 gene screening by next-generation sequencing in a British cohort. Investigative Ophthalmology and Visual Science, 54(10), 6662-6674. https://doi.org/10.1167/iovs.13-12570

ABCA4 gene screening by next-generation sequencing in a British cohort. / Fujinami, Kaoru; Zernant, Jana; Chana, Ravinder K.; Wright, Genevieve A.; Tsunoda, Kazushige; Ozawa, Yoko; Tsubota, Kazuo; Webster, Andrew R.; Moore, Anthony T.; Allikmets, Rando; Michaelides, Michel.

In: Investigative Ophthalmology and Visual Science, Vol. 54, No. 10, 2013, p. 6662-6674.

Research output: Contribution to journalArticle

Fujinami, K, Zernant, J, Chana, RK, Wright, GA, Tsunoda, K, Ozawa, Y, Tsubota, K, Webster, AR, Moore, AT, Allikmets, R & Michaelides, M 2013, 'ABCA4 gene screening by next-generation sequencing in a British cohort', Investigative Ophthalmology and Visual Science, vol. 54, no. 10, pp. 6662-6674. https://doi.org/10.1167/iovs.13-12570
Fujinami, Kaoru ; Zernant, Jana ; Chana, Ravinder K. ; Wright, Genevieve A. ; Tsunoda, Kazushige ; Ozawa, Yoko ; Tsubota, Kazuo ; Webster, Andrew R. ; Moore, Anthony T. ; Allikmets, Rando ; Michaelides, Michel. / ABCA4 gene screening by next-generation sequencing in a British cohort. In: Investigative Ophthalmology and Visual Science. 2013 ; Vol. 54, No. 10. pp. 6662-6674.
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abstract = "Purpose. We applied a recently reported next-generation sequencing (NGS) strategy for screening the ABCA4 gene in a British cohort with ABCA4-associated disease and report novel mutations. Methods. We identified 79 patients with a clinical diagnosis of ABCA4-associated disease who had a single variant identified by the ABCA4 microarray. Comprehensive phenotypic data were obtained, and the NGS strategy was applied to identify the second allele by means of sequencing the entire coding region and adjacent intronic sequences of the ABCA4 gene. Identified variants were confirmed by Sanger sequencing and assessed for pathogenicity by in silico analysis. Results. Of the 42 variants detected by prescreening with the microarray, in silico analysis suggested that 34, found in 66 subjects, were disease-causing and 8, found in 13 subjects, were benign variants. We detected 42 variants by NGS, of which 39 were classified as disease-causing. Of these 39 variants, 31 were novel, including 16 missense, 7 splice-site-altering, 4 nonsense, 1 in-frame deletion, and 3 frameshift variants. Two or more disease-causing variants were confirmed in 37 (47{\%}) of 79 patients, one disease-causing variant in 36 (46{\%}) subjects, and no disease-causing variant in 6 (7{\%}) individuals. Conclusions. Application of the NGS platform for ABCA4 screening enabled detection of the second disease-associated allele in approximately half of the patients in a British cohort where one mutation had been detected with the arrayed primer extension (APEX) array. The time- and cost-efficient NGS strategy is useful in screening large cohorts, which will be increasingly valuable with the advent of ABCA4-directed therapies.",
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AU - Tsunoda, Kazushige

AU - Ozawa, Yoko

AU - Tsubota, Kazuo

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