Zernant Jana, Xie Yajing Angela, Ayuso Carmen, Riveiro-Alvarez Rosa, Lopez-Martinez Miguel-Angel, Simonelli Francesca, Testa Francesco, Gorin Michael B, Strom Samuel P, Bertelsen Mette, Rosenberg Thomas, Boone Philip M, Yuan Bo, Ayyagari Radha, Nagy Peter L, Tsang Stephen H, Gouras Peter, Collison Frederick T, Lupski James R, Fishman Gerald A, Allikmets Rando
Department of Ophthalmology and.
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.
Hum Mol Genet. 2014 Dec 20;23(25):6797-806. doi: 10.1093/hmg/ddu396. Epub 2014 Jul 31.
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.
常染色体隐性遗传性斯特格黄斑营养不良（STGD1，MIM 248200）由ABCA4基因突变引起。对STGD患者的ABCA4进行全序列分析发现，65%-70%的患者存在复合杂合或纯合的疾病相关等位基因，15%-20%的患者仅存在一个突变。本研究旨在通过下一代测序（NGS）、阵列比较基因组杂交（aCGH）筛查、家系分离分析和计算机分析相结合的方法，寻找遗漏的致病ABCA4变异。对114例已知ABCA4外显子突变的STGD患者的整个140 kb ABCA4基因组位点进行测序，平均每个样本发现200个内含子变异。对这些数据进行筛选后得到141个新突变候选基因。在4个样本中检测到2个变异，在3个样本中检测到2个变异，在2个样本中检测到20个变异，其余117个新变异仅被检测到一次。多模式分析提示12个新的可能致病的ABCA4内含子变异，其中一些变异是特定（孤立）种族群体所特有的。在任何患者中均未检测到拷贝数变异（大的缺失和插入），这表明在ABCA4基因座中这是非常罕见的事件。许多变异被排除，因为它们在非人类灵长类动物中不保守，在非洲人群中很常见，因此代表的是祖先变异而非疾病相关变异。ABCA4基因座的序列变异性很大，在欧美裔STGD患者中，非编码序列不存在频繁突变。确定ABCA4基因座中的疾病相关等位基因需要特征明确的大样本队列，并结合多种方法进行广泛分析。
