Xiaoyun Jia

Novel locus for X linked recessive high myopia maps to Xq23–q25 but outside MYP1

Background: High myopia is a common genetic variation in most cases, affecting 1–2% of people, and is the fourth most common disorder causing blindness worldwide. Six autosomal dominant loci and one X-linked recessive locus have been reported, but no genes responsible for high myopia have been identified. Objective: To report a Chinese family in which six males presented with high myopia consistent with an X linked recessive trait. Results: Affected individuals shared three common features: high myopia, reduced visual acuity, and fundal changes of high myopia. Protan and deutan were observed in the family, but they did not co-segregate with the high myopia phenotype. X-chromosome-wide linkage analysis mapped the high myopia locus to a 25 cM (14.9 Mb) region on Xq23–q25 between DXS1210 and DXS8057, with maximum two point lod scores at θ = 0 of 2.75 and 2.29 for DXS1001 and DXS8059, respectively. Conclusions: This new myopia locus is outside the linked region of the first high myopia locus (MYP1). Refinement of the linkage region with additional families and screening candidate genes for mutation may lead to the identification of the defect gene.

Detection of Variants in 15 Genes in 87 Unrelated Chinese Patients with Leber Congenital Amaurosis

Background Leber congenital amaurosis (LCA) is the earliest onset and most severe form of hereditary retinal dystrophy. So far, full spectrum of variations in the 15 genes known to cause LCA has not been systemically evaluated in East Asians. Therefore, we performed comprehensive detection of variants in these 15 genes in 87 unrelated Han Chinese patients with LCA. Methodology/Principal Findings The 51 most frequently mutated exons and introns in the 15 genes were selected for an initial scan using cycle sequencing. All the remaining exons in 11 of the 15 genes were subsequently sequenced. Fifty-three different variants were identified in 44 of the 87 patients (50.6%), involving 78 of the 88 alleles (11 homozygous and 56 heterozygous variants). Of the 53 variants, 35 (66%) were novel pathogenic mutations. In these Chinese patients, variants in GUCY2D are the most common cause of LCA (16.1% cases), followed by CRB1 (11.5%), RPGRIP1 (8%), RPE65 (5.7%), SPATA7 (4.6%), CEP290 (4.6%), CRX (3.4%), LCA5 (2.3%), MERTK (2.3%), AIPL1 (1.1%), and RDH12 (1.1%). This differs from the variation spectrum described in other populations. An initial scan of 55 of 215 PCR amplicons, including 214 exons and 1 intron, detected 83.3% (65/78) of the mutant alleles ultimately found in these 87 patients. In addition, sequencing only 9 exons would detect over 50% of the identified variants and require less than 5% of the labor and cost of comprehensive sequencing for all exons. Conclusions/Significance Our results suggest that specific difference in the variation spectrum found in LCA patients from the Han Chinese and other populations are related by ethnicity. Sequencing exons in order of decreasing risk is a cost-effective way to identify causative mutations responsible for LCA, especially in the context of genetic counseling for individual patients in a clinical setting.

Molecular epidemiology of mtDNA mutations in 903 Chinese families suspected with Leber hereditary optic neuropathy

AbstractWe report the molecular epidemiology of three primary mutations in mitochondrial DNA (mtDNA) responsible for Leber hereditary optic neuropathy (LHON) based on analysis of probands suspected with LHON from 903 Chinese families. Most of them had optic neuropathy of unknown cause, and only 128 had a family history of optic neuropathy. Mutations in the mtDNA were detected in 346 probands. Of the 346 cases, 340 were homoplasmic and only six were heteroplasmic; 284 were male and 62 were female; 120 had a family history and 226 were sporadic. G11778A, T14484C and G3460A mutations were detected in 312 (90.2%), 30, and four families, respectively. The majority (226/346, 65.3%) of all LHON cases in Chinese are sporadic. These 226 probands (29.2%) were identified from 775 probands with sporadic optic neuropathy. Affected male-to-female ratio was 4.6:1 for all probands but was 2.2:1 for family members. Average age at onset was 18.5 years, ranging from 4.5 to 47 years old.

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

The penetrance of Lebers hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P<0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a secondary mutation G13708A. As a result, it is likely that unknown nuclear gene involvement and/or other factors contribute to the strikingly different penetrance of LHON.

High Myopia Is Not Associated with the SNPs in the TGIF, Lumican, TGFB1, and HGF Genes

PURPOSE Four single-nucleotide polymorphisms (SNPs) in the TGIF, lumican, TGFB1, and HGF genes have been declared to be associated with high myopia in Chinese living in southeast China, but none of them has been confirmed by additional studies. This study was conducted to verify the reported positive association results by analysis of subjects from the same region. METHODS DNA was prepared from venous leukocytes of 288 patients with high myopia and 208 control subjects. The four SNPs (rs2229336, rs3759223, rs1982073, and rs3735520) in the four genes were genotyped by restriction fragment length polymorphism (RFLP) analysis. The allele and genotype frequencies of these SNPs from patients and control subjects were compared by chi(2) test. RESULTS Polymorphism at rs2229336 was not detected in all 496 subjects. There were no statistically significant differences between patients and control subjects for the other three SNPs: rs3759223, rs1982073, and rs3735520. CONCLUSIONS The study does not support the association of high myopia with alleles of rs2229336 in TGIF, rs3759223 in lumican, rs1982073 in TGFB1, and rs3735520 in HGF. These results provide a view contrary to those in previous reports. Reasonable criteria as well as replication should be the first priority for genetic association studies to avoid excessive expansion of false-positive results, especially for high myopia.

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.

Mitochondrial DNA Haplogroup Background Affects LHON, but Not Suspected LHON, in Chinese Patients

Recent studies have shown that mtDNA background could affect the clinical expression of Leber hereditary optic neuropathy (LHON). We analyzed the mitochondrial DNA (mtDNA) variation of 304 Chinese patients with m.11778G>A (sample #1) and of 843 suspected LHON patients who lack the three primary mutations (sample #2) to discern mtDNA haplogroup effect on disease onset. Haplogroup frequencies in the patient group was compared to frequencies in the general Han Chinese population (n = 1,689; sample #3). The overall matrilineal composition of the suspected LHON population resembles that of the general Han Chinese population, suggesting no association with mtDNA haplogroup. In contrast, analysis of these LHON patients confirms mtDNA haplogroup effect on LHON. Specifically, the LHON sample significantly differs from the general Han Chinese and suspected LHON populations by harboring an extremely lower frequency of haplogroup R9, in particular of its main sub-haplogroup F (#1 vs. #3, P-value = 1.46×10−17, OR = 0.051, 95% CI: 0.016–0.162; #1 vs. #2, P-value = 4.44×10−17, OR = 0.049, 95% CI: 0.015–0.154; in both cases, adjusted P-value <10−5) and higher frequencies of M7b (#1 vs. #3, adjusted P-value = 0.001 and #1 vs. #2, adjusted P-value = 0.004). Our result shows that mtDNA background affects LHON in Chinese patients with m.11778G>A but not suspected LHON. Haplogroup F has a protective effect against LHON, while M7b is a risk factor.

Confirmation of a genetic locus for X-linked recessive high myopia outside MYP1

AbstractHigh myopia is a severe ocular condition affecting ∼ 100 million people throughout the world. It is a common cause of blindness, and several studies have suggested it is transmitted through Mendelian traits. High myopia is clinically and genetically heterogeneous, with eight loci assigned. Most loci have not been confirmed by additional studies, and genes responsible for high myopia have not been identified. We recently studied a Chinese family with X-linked high myopia and mapped the high myopia locus to Xq25-q27.2. This linked region overlapped with that of MYP13 but was outside MYP1.

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.