title: Analysis of the ABCA4 genomic locus in Stargardt disease.
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.
authors.affiliation: Department of Ophthalmology and.
authors.forename: Jana
authors.initials: J
authors.lastname: Zernant
authors.affiliation: Department of Ophthalmology and.
authors.forename: Yajing Angela
authors.initials: YA
authors.lastname: Xie
authors.affiliation: 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.
authors.forename: Carmen
authors.initials: C
authors.lastname: Ayuso
authors.affiliation: 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.
authors.forename: Rosa
authors.initials: R
authors.lastname: Riveiro-Alvarez
authors.affiliation: 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.
authors.forename: Miguel-Angel
authors.initials: MA
authors.lastname: Lopez-Martinez
authors.affiliation: Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Simonelli
authors.affiliation: Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Testa
authors.affiliation: Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Gorin
authors.affiliation: 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.
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Strom
authors.affiliation: Kennedy Center Eye Clinic, Glostrup Hospital, Glostrup, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Bertelsen
authors.affiliation: Kennedy Center Eye Clinic, Glostrup Hospital, Glostrup, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rosenberg
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Philip M
authors.initials: PM
authors.lastname: Boone
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Yuan
authors.affiliation: Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA and.
authors.forename: Radha
authors.initials: R
authors.lastname: Ayyagari
authors.affiliation: Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Nagy
authors.affiliation: Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Tsang
authors.affiliation: Department of Ophthalmology and.
authors.forename: Peter
authors.initials: P
authors.lastname: Gouras
authors.affiliation: The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA.
authors.forename: Frederick T
authors.initials: FT
authors.lastname: Collison
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Lupski
authors.affiliation: The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Fishman
authors.affiliation: Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA rla22@columbia.edu.
authors.forename: Rando
authors.initials: R
authors.lastname: Allikmets
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D000483:Alleles; D044383:Black People; D016022:Case-Control Studies; D055028:Comparative Genomic Hybridization; D005091:Exons; D005260:Female; D015870:Gene Expression; D005808:Genes, Recessive; D056426:Genetic Loci; D014644:Genetic Variation; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D006801:Humans; D007438:Introns; D008268:Macular Degeneration / Q000151:congenital* / Q000208:ethnology / Q000235:genetics / Q000473:pathology; D008297:Male; D009154:Mutation; D010375:Pedigree; D000080362:Stargardt Disease; D044465:White People
chemical_list: C056475:ABCA4 protein, human; D018528:ATP-Binding Cassette Transporters
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