Wenmin Sun

Exome sequencing of 47 chinese families with cone-rod dystrophy: mutations in 25 known causative genes.

Objective The goal of this study was to identify mutations in 25 known causative genes in 47 unrelated Chinese families with cone-rod dystrophy (CORD). Methods Forty-seven probands from unrelated families with CORD were recruited. Genomic DNA prepared from leukocytes was analyzed by whole exome sequencing. Variants in the 25 genes were selected and then validated by Sanger sequencing. Results Fourteen potential pathogenic mutations, including nine novel and five known, were identified in 10 of the 47 families (21.28%). Homozygous, compound heterozygous, and hemizygous mutations were detected in three, four, or three families, respectively. The 14 mutations in the 10 families were distributed among CNGB3 (three families), PDE6C (two families), ABCA4 (one family), RPGRIP1 (one family), RPGR (two families), and CACNA1F (one family). Conclusions This study provides a brief view on mutation spectrum of the 25 genes in a Chinese cohort with CORD. Identification of novel mutations enriched our understanding of variations in these genes and their associated phenotypes. To our knowledge, this is the first systemic exome-sequencing analysis of all of the 25 CORD-associated genes.

Replication Study Supports CTNND2 as a Susceptibility Gene for High Myopia

PURPOSE The CTNND2 gene is located in the linkage interval of high myopia locus MYP16 and two single-nucleotide polymorphisms (SNPs; rs6885224 and rs12716080) in CTNND2 were recently shown to associate with high myopia. This study evaluated such associations in an independent case-control series. METHODS A total of 2773 unrelated individuals were enrolled in this study, including 1203 subjects with high myopia (spherical refraction at each meridian ≤ -6.00 D), 615 subjects with moderate myopia (-6.00 D < spherical refraction ≤ -4.00 D), and 955 controls (-0.50 D to +1.00 D, spherical equivalent). Genomic DNA was prepared from venous leukocytes. SNPs rs6885224 and rs12716080 in CTNND2 were determined by Sanger sequencing. Allele and genotype frequencies of the SNPs were compared between cases and controls by χ² test (α = 0.05). RESULTS One SNP, rs6885224, in CTNND2 showed significant differences in genotype and allele frequencies between high myopia and controls (genotype P = 2.17E×10(-5), allele P = 5.29E×10(-6), odds ratio [OR] = 0.69, 95% confidence interval [CI] = 0.591-0.812), as well as between moderate myopia and controls (genotype P = 0.009, allele P = 0.005, OR = 0.765, 95% CI = 0.633-0.924). rs12716080 showed no statistical difference between myopias and controls. CONCLUSIONS These results confirmed the strong association between CTNND2 polymorphism and myopia. The minor allele C of rs6885224 was protective against myopia in this study but was a risk allele in a previous study.

Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing.

PURPOSE To evaluate variants in the LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 genes in 298 unrelated patients with early-onset high myopia (eoHM). METHODS Genomic DNA from 298 patients with eoHM was analyzed by whole exome sequencing. Variants in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 genes were selected and analyzed with bioinformatics. Potential candidate variants were confirmed by Sanger sequencing and then validated in available family members and 192 healthy controls. RESULTS A total of nine variants predicted to affect the functional residues were detected. The LRPAP1 gene showed a homozygous frameshift mutation (c.199delC, p.Q67Sfs*8) in a consanguineous family. The ZNF644 gene showed five heterozygous missense mutations (c.1106A>T, p.K369M; c.1648G>A, p.A550T; c.2014A>G, p.S672G; c.2048G>C, p.R683T, and c.2551G>C, p.D851H) in five families, but the c.1106A>T, (p.K369M) and c.1648G>A, (p.A550T) in ZNF644 did not co-segregated with high myopia in the families and should be excluded as causative mutations. The SLC39A5 gene showed a heterozygous missense variant (c.1238G>C, p.G413A) in a sporadic individual. The SCO2 gene showed two heterozygous missense variants (c.334C>T, p.R112W and c.358C>T, p.R120W) in two families. None of the variants was detected in 192 healthy controls and all were predicted to be damaging by both Polyphen-2 and SIFT, except for the previously reported p.S672G mutation in ZNF644, which was predicted to be damaging by SIFT but benign by Polyphen-2. No homozygous or compound heterozygous variants were found in CTSH and LEPREL1. CONCLUSIONS Our results provide additional evidence to support the idea that mutation in LRPAP1 is associated with high myopia. Further studies are expected to evaluate the pathogenicity of the variants in CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2.

Exome sequencing of 18 Chinese families with congenital cataracts: a new sight of the NHS gene.

Purpose The aim of this study was to investigate the mutation spectrum and frequency of 34 known genes in 18 Chinese families with congenital cataracts. Methods Genomic DNA and clinical data was collected from 18 families with congenital cataracts. Variations in 34 cataract-associated genes were screened by whole exome sequencing and then validated by Sanger sequencing. Results Eleven candidate variants in seven of the 34 genes were detected by exome sequencing and then confirmed by Sanger sequencing, including two variants predicted to be benign and the other pathogenic mutations. The nine mutations were present in 9 of the 18 (50%) families with congenital cataracts. Of the four families with mutations in the X-linked NHS gene, no other abnormalities were recorded except for cataract, in which a pseudo-dominant inheritance form was suggested, as female carriers also had different forms of cataracts. Conclusion This study expands the mutation spectrum and frequency of genes responsible for congenital cataract. Mutation in NHS is a common cause of nonsyndromic congenital cataract with pseudo-autosomal dominant inheritance. Combined with our previous studies, a genetic basis could be identified in 67.6% of families with congenital cataracts in our case series, in which mutations in genes encoding crystallins, genes encoding connexins, and NHS are responsible for 29.4%, 14.7%, and 11.8% of families, respectively. Our results suggest that mutations in NHS are the common cause of congenital cataract, both syndromic and nonsyndromic.

Molecular genetics of cone-rod dystrophy in Chinese patients: New data from 61 probands and mutation overview of 163 probands

Cone-rod dystrophy (CORD) is a common form of inherited retinal degeneration. Previously, we have conducted serial mutational analysis in probands with CORD either by Sanger sequencing or whole exome sequencing (WES). In the current study, variants in all genes from RetNet were selected from the whole exome sequencing data of 108 CORD probands (including 61 probands reported here for the first time) and were analyzed by multistep bioinformatics analysis, followed by Sanger sequencing and segregation validation. Data from the previous studies and new data from this study (163 probands in total) were summarized to provide an overview of the molecular genetics of CORD. The following potentially pathogenic mutations were identified in 93 of the 163 (57.1%) probands: CNGA3 (32.5%), ABCA4 (3.8%), ALMS1 (3.1%), GUCY2D (3.1%), CACNA1F (2.5%), CRX (1.8%), PDE6C (1.8%), CNGB3 (1.8%), GUCA1A (1.2%), UNC119 (0.6%), RPGRIP1 (1.2%), RDH12 (0.6%), KCNV2 (0.6%), C21orf2 (0.6%), CEP290 (0.6%), USH2A (0.6%) and SNRNP200 (0.6%). The 17 genes with mutations included 12 known CORD genes and five genes (ALMS1, RDH12, CEP290, USH2A, and SNRNP200) associated with other forms of retinal degeneration. Mutations in CNGA3 is most common in this cohort. This is a systematic molecular genetic analysis of Chinese patients with CORD.

Exome Sequencing on 298 Probands With Early-Onset High Myopia: Approximately One-Fourth Show Potential Pathogenic Mutations in RetNet Genes

PURPOSE To investigate mutations in 234 genes associated with retinal dystrophies in a cohort of 298 probands with early-onset high myopia using whole exome sequencing. METHODS Genomic DNA from 298 probands with early-onset high myopia was analyzed by whole exome sequencing. Variants from 234 genes were selected and analyzed by multistep bioinformatics analyses. RESULTS Systematic analysis of variants in the 234 genes identified potential pathogenic mutations in 34 of 234 genes in 71 of 298 (23.8%) probands. Of the 71 probands, 44 (62.0%) had mutations in 11 genes responsible for ocular diseases accompanied by high myopia, including COL2A1, COL11A1, PRPH2, FBN1, GNAT1, OPA1, PAX2, GUCY2D, TSPAN12, CACNA1F, and RPGR. Initial clinical records of the 71 patients with mutations did not show recognizable signs of original diseases other than high myopia. CONCLUSIONS Mutations in genes known to be responsible for retinal diseases were found in approximately one-fourth of the probands with early-onset high myopia. The high mutation frequency of RetNet genes in these patients can provide clues for genetic screening and further specific clinical examinations of high myopia to promote long-term follow-up assessment and prompt treatment of some diseases.

Novel GUCA1A mutation identified in a Chinese family with cone-rod dystrophy.

Ten mutations in the guanylate cyclase activator 1A (GUCA1A) have been previously identified and reported in patients with retinal degeneration, including patients from 12 families with cone-rod dystrophy (CORD) and in an isolated patient with retinitis pigmentosa (RP). In this study, the coding exons and adjacent regions of GUCA1A were evaluated in 130 probands with CORD from 130 unrelated Chinese families using Sanger sequencing. A novel heterozygous c.464A>C (p.Glu155Ala) mutation was detected in a proband from a large family. The mutation presented in all nine patients examined in that family, but it was absent in six unaffected family members and 192 normal controls. All the nine patients in that family expressed typical CORD in eight cases and atypical CORD in one case. The results of this study suggested that the GUCA1A mutation only contributes to a small portion of CORD in people of Chinese descent.

Molecular genetics of Leber congenital amaurosis in Chinese: New data from 66 probands and mutation overview of 159 probands.

Leber congenital amaurosis (LCA) is the most severe form of inherited retinal dystrophy. We have previously performed a mutational analysis of the known LCA-associated genes in probands with LCA by both Sanger and whole exome sequencing. In this study, whole exome sequencing was carried out on 66 new probabds with LCA. In conjunction with these data, the present study provides a comprehensive analysis of the spectrum and frequency of all known genes associated with retinal dystrophy in a total of 159 Chinese probands with LCA. The known genes responsible for all forms hereditary retinal dystrophy were included based on information from RetNet. The candidate variants were filtered by bioinformatics analysis and confirmed by Sanger sequencing. Potentially causative mutations were further validated in available family members. Overall, a total of 118 putative pathogenic mutations from 23 genes were identified in 56.6% (90/159) of probands. These mutations were harbored in 13 LCA-associated genes and in ten genes related to other forms of retinal dystrophy. The most frequently mutated gene in probands with LCA was GUCY2D (10.7%, 17/159). A series of mutational analyses suggests that all known genes associated with retinal dystrophy account for 56.6% of Chinese patients with LCA. A comprehensive molecular genetic analysis of Chinese patients with LCA provides an overview of the spectrum and frequency of ethno-specific mutations of all known genes, as well as indications about other unknown genes in the remaining probands who lacked identified mutations.