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Hum Mol Genet. 2014 Dec 20;23(25):6797-806. doi: 10.1093/hmg/ddu396. Epub 2014 Jul 31.

Analysis of the ABCA4 genomic locus in Stargardt disease.

Author information

1
Department of Ophthalmology and.
2
Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain.
3
Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy.
4
Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and.
5
Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
6
Kennedy Center Eye Clinic, Glostrup Hospital, Glostrup, Denmark.
7
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
8
Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA and.
9
Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
10
Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
11
The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA.
12
Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA rla22@columbia.edu.

Abstract

Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of ABCA4 in STGD patients identifies compound heterozygous or homozygous disease-associated alleles in 65-70% of patients and only one mutation in 15-20% of patients. This study was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic variants per sample. Filtering of these data resulted in 141 candidates for new mutations. Two variants were detected in four samples, two in three samples, and 20 variants in two samples, the remaining 117 new variants were detected only once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in STGD patients of European-American descent. Defining disease-associated alleles in the ABCA4 locus requires exceptionally well characterized large cohorts and extensive analyses by a combination of various approaches.

PMID:
25082829
PMCID:
PMC4245042
DOI:
10.1093/hmg/ddu396
[Indexed for MEDLINE]
Free PMC Article

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