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Exome sequencing identifies ZNF644 mutations in high myopia.

Shi Y, Li Y, Zhang D, Zhang H, Li Y, Lu F, Liu X, He F, Gong B, Cai L, Li R, Liao S, Ma S, Lin H, Cheng J, Zheng H, Shan Y, Chen B, Hu J, Jin X, Zhao P, Chen Y, Zhang Y, Lin Y, Li X, Fan Y, Yang H, Wang J, Yang Z - PLoS Genet. (2011)

Bottom Line: Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders.A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family.The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE).

View Article: PubMed Central - PubMed

Affiliation: The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.

ABSTRACT
Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

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Fundus photographs and optical coherence tomography (OCT) of high myopia patients from the sporadic cases.A. The fundus of the patient JS047001 (Table 5) showing tigroid or tessellated features, conus, and CNV (choroid neovascularization). Optical Coherence Tomography (OCT) examination of this patient showed continuity of retinal pigment epithelial layer and broken photoreceptor layer (E). B. The fundus of the patient JS103001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaries extending into the macular region and Fuchs spot. OCT examination of this patient showed discontinuity and irregular apophysis of the reflective pigment epithelial layer (F). C. The fundus of the patient JS104001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaris. OCT examination of this patient showed foveal thinning and atrophies of the retinal neuroepithelial layer (G). D. Normal fundus photograph and OCT examination of a normal Control (H).
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pgen-1002084-g004: Fundus photographs and optical coherence tomography (OCT) of high myopia patients from the sporadic cases.A. The fundus of the patient JS047001 (Table 5) showing tigroid or tessellated features, conus, and CNV (choroid neovascularization). Optical Coherence Tomography (OCT) examination of this patient showed continuity of retinal pigment epithelial layer and broken photoreceptor layer (E). B. The fundus of the patient JS103001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaries extending into the macular region and Fuchs spot. OCT examination of this patient showed discontinuity and irregular apophysis of the reflective pigment epithelial layer (F). C. The fundus of the patient JS104001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaris. OCT examination of this patient showed foveal thinning and atrophies of the retinal neuroepithelial layer (G). D. Normal fundus photograph and OCT examination of a normal Control (H).

Mentions: We further carried out direct PCR sequencing of the ZNF644 exons in an additional 300 unrelated (based on their self-identified geographical ancestry), sporadic high myopia patients. The 300 patients had refractive errors ranging from −6.0 to −29.0 DS for both eyes and an axial eye globe length from 26 to 33 mm for both eyes (Table 4). Some of these individuals also showed severe retinal pathological changes in the fundus appearance, an abnormal RPE, and photoreceptor layer alterations at the time of the OCT examination (Figure 4, Table 5). In the 300 sporadic patients, we identified a total of 8 variants when we sequenced the ZNF644 exons, and five out of these 8 variants (present in 11 unrelated individuals) were absent in all the 600 controls. Among these five mutations identified from the sporadic cases, three were in exon 3 (I587V, R680G and C699Y) and two were in the 3′ untranslated region (UTR) (+12 C>G and +592 G>A) (Figure 3, Table 5). The remaining three out of the 8 variants were found in both cases and controls, two (T404T and V444V) were synonymous changes which may not affect the biological function of ZNF644 and one was located in the 3′UTR (+1015 C>G). The P-value for the 17 potentially functional variants in 301 patients with high myopia (One mutation identified in one member of the high myopia family 951 plus the 6 mutations identified in the 16 unrelated patients from the 300 sporadic cases) compared with these variants being seen in 600 controls (3 in 600 controls) was 2.28×10−6 by Fisher's exact test. This data suggests that there are multiple rare variants in ZNF644 associated with high myopia.


Exome sequencing identifies ZNF644 mutations in high myopia.

Shi Y, Li Y, Zhang D, Zhang H, Li Y, Lu F, Liu X, He F, Gong B, Cai L, Li R, Liao S, Ma S, Lin H, Cheng J, Zheng H, Shan Y, Chen B, Hu J, Jin X, Zhao P, Chen Y, Zhang Y, Lin Y, Li X, Fan Y, Yang H, Wang J, Yang Z - PLoS Genet. (2011)

Fundus photographs and optical coherence tomography (OCT) of high myopia patients from the sporadic cases.A. The fundus of the patient JS047001 (Table 5) showing tigroid or tessellated features, conus, and CNV (choroid neovascularization). Optical Coherence Tomography (OCT) examination of this patient showed continuity of retinal pigment epithelial layer and broken photoreceptor layer (E). B. The fundus of the patient JS103001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaries extending into the macular region and Fuchs spot. OCT examination of this patient showed discontinuity and irregular apophysis of the reflective pigment epithelial layer (F). C. The fundus of the patient JS104001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaris. OCT examination of this patient showed foveal thinning and atrophies of the retinal neuroepithelial layer (G). D. Normal fundus photograph and OCT examination of a normal Control (H).
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pgen-1002084-g004: Fundus photographs and optical coherence tomography (OCT) of high myopia patients from the sporadic cases.A. The fundus of the patient JS047001 (Table 5) showing tigroid or tessellated features, conus, and CNV (choroid neovascularization). Optical Coherence Tomography (OCT) examination of this patient showed continuity of retinal pigment epithelial layer and broken photoreceptor layer (E). B. The fundus of the patient JS103001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaries extending into the macular region and Fuchs spot. OCT examination of this patient showed discontinuity and irregular apophysis of the reflective pigment epithelial layer (F). C. The fundus of the patient JS104001 (Table 5) showing tigroid or tessellated features, numerous areas of atrophy of the pigment epithelium, and choriocapillaris. OCT examination of this patient showed foveal thinning and atrophies of the retinal neuroepithelial layer (G). D. Normal fundus photograph and OCT examination of a normal Control (H).
Mentions: We further carried out direct PCR sequencing of the ZNF644 exons in an additional 300 unrelated (based on their self-identified geographical ancestry), sporadic high myopia patients. The 300 patients had refractive errors ranging from −6.0 to −29.0 DS for both eyes and an axial eye globe length from 26 to 33 mm for both eyes (Table 4). Some of these individuals also showed severe retinal pathological changes in the fundus appearance, an abnormal RPE, and photoreceptor layer alterations at the time of the OCT examination (Figure 4, Table 5). In the 300 sporadic patients, we identified a total of 8 variants when we sequenced the ZNF644 exons, and five out of these 8 variants (present in 11 unrelated individuals) were absent in all the 600 controls. Among these five mutations identified from the sporadic cases, three were in exon 3 (I587V, R680G and C699Y) and two were in the 3′ untranslated region (UTR) (+12 C>G and +592 G>A) (Figure 3, Table 5). The remaining three out of the 8 variants were found in both cases and controls, two (T404T and V444V) were synonymous changes which may not affect the biological function of ZNF644 and one was located in the 3′UTR (+1015 C>G). The P-value for the 17 potentially functional variants in 301 patients with high myopia (One mutation identified in one member of the high myopia family 951 plus the 6 mutations identified in the 16 unrelated patients from the 300 sporadic cases) compared with these variants being seen in 600 controls (3 in 600 controls) was 2.28×10−6 by Fisher's exact test. This data suggests that there are multiple rare variants in ZNF644 associated with high myopia.

Bottom Line: Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders.A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family.The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE).

View Article: PubMed Central - PubMed

Affiliation: The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.

ABSTRACT
Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644) was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A) in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE). Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

Show MeSH
Related in: MedlinePlus