Skip to main content
NCBI home page
JAMA Network logoLink to JAMA Network
. 2023 Dec 1;6(12):e2345821. doi: 10.1001/jamanetworkopen.2023.45821

Whole-Exome Sequencing Among School-Aged Children With High Myopia

Xiangyi Yu 1,2, Jian Yuan 1,2, Zhen Ji Chen 1,2,3, Kai Li 4, Yinghao Yao 3, Shilai Xing 1,2,5, Zhengbo Xue 1,2, Yue Zhang 1, Hui Peng 1, Gang An 5, Xiaoguang Yu 5, Jia Qu 1,2,3,4,✉, Jianzhong Su 1,2,3,4,✉, for the Myopia Associated Genetics and Intervention Consortiums
PMCID: PMC10692858  PMID: 38039006

This cohort study evaluates risk variants in a large high-myopia cohort and the implications of genetic testing of schoolchildren with high myopia.

Key Points

Question

Is genetic testing necessary in the diagnosis of high myopia?

Findings

This cohort study of whole-exome sequencing (WES) on 6215 schoolchildren with high myopia (HM) identified a total of 271 potential pathogenic variants in 75 HM candidate genes in 15.52% students. Subgroup analysis stratified by age and degree of refractive error revealed that the involved variants yield ranging from 7.66% in the common HM group, 8.70% in the ultra myopia group, 11.90% in the extreme myopia group to 22.86% in primary school students with extreme myopia.

Meaning

This study revealed the genetic factor of high myopia, and is expected to guide future research and clinical diagnosis of HM.

Abstract

Importance

High myopia (HM) is one of the leading causes of visual impairment worldwide. Genetic factors are known to play an important role in the development of HM.

Objective

To identify risk variants in a large HM cohort and to examine the implications of genetic testing of schoolchildren with HM.

Design, Setting, and Participants

This cohort study retrospectively reviewed whole-exome sequencing (WES) results in 6215 schoolchildren with HM who underwent genetic testing between September 2019 and July 2020 in Wenzhou City, China. HM is defined as a spherical equivalent refraction (SER) of −6.00 diopters (D) or less. The study setting was a genetic testing laboratory and a multicenter school census. Data were analyzed from July 2021 to June 2022.

Main Outcomes and Measures

The frequency and distribution of positive germline variants, the percentage of individuals with HM in both eyes, and subsequent variant yield for common high myopia (CHM; −8.00 D ≤ SER ≤ −6.00 D), ultra myopia (UM; −10.00 D ≤ SER < −8.00 D), and extreme myopia (EM; SER < −10.00 D).

Results

Of the 6215 schoolchildren with HM, 3278 (52.74%) were male. Their mean (SD) age was 14.87 (2.02) years, including 355 students in primary school, 1970 in junior high school, and 3890 in senior high school. The mean (SD) SER was −7.51 (−1.36) D for the right eye and −7.46 (−1.34) D for the left eye. Among schoolchildren with HM, genetic testing yielded 271 potential pathogenic variants in 75 HM candidate genes in 964 diagnoses (15.52%). A total of 36 known variants were found in 490 HM participants (7.88%) and 235 protein-truncating variants (PTVs) in 506 participants (8.14%). Involved variant yield was significantly positively associated with SER (Cochran-Armitage test for trend Z = 2.5492; P = .01), which ranged from 7.66% in the CHM group, 8.70% in the UM group, to 11.90% in the EM group. We also found that primary school students with EM had the highest variant yield of PTVs (8 of 35 students [22.86%]), which was 1.77 and 4.78 times that of the UM and CHM, respectively.

Conclusions and Relevance

In this cohort study of WES for HM, several potential pathogenic variants were identified in a substantial number of schoolchildren with HM. The high variation frequency in younger students with EM can provide clues for genetic screening and clinical examinations of HM to promote long-term follow-up assessment.

Introduction

Myopia, the most common cause of visual impairment, is a global public health concern due to its increasing prevalence.1,2 High myopia (HM) is generally defined as myopia with a spherical equivalent refractive (SER) error of less than or equal to −6.0 diopters (D). HM is a leading cause of impaired vision due to its association with increased risk of serious ocular complications, most notably retinal degeneration3,4 or even detachment.5,6 The prevalence of HM was reported to be 2% to 5% in American, Western European, and Australian populations7 compared with 4.5% to 38% in East Asian populations.8,9,10,11 A recent study predicted that visual impairment among preschool children will increase by 26% by 2060 with uncorrected refractive error comprising 69% of cases.12 Similar to many other common diseases, HM is a multifactorial disorder, involving interactions between genetic and environmental factors.13,14 Twin and family studies have demonstrated a high heritability for HM, which was estimated to be approximately 90%.15,16

In several early linkage studies and candidate gene studies for myopia, up to 50 loci and genes were identified before the genome-wide association studies (GWAS) era,17,18,19,20,21,22,23,24 but these could not be replicated in other related studies. In a GWAS performed using myopia as a dichotomous outcome or refractive error as a quantitative trait, a series of significant common genetic variants were identified in several loci,25,26 such as 11q24.1,27 5p15,28 4q25,29 13q12,30 21q22,31 15q14,32 and 15q25.33 However, these loci account for only a limited fraction of the heritability for refractive error likely because of small effects not detected due to insufficient statistical power and causal variants, especially those of low allele frequency, not well captured by conventional GWAS. Compared with single-nucleotide variant (SNV) arrays, whole-exome sequencing (WES) offers additional opportunities to investigate rare coding variants that are not well tagged by array SNVs or imputation. Recently, WES has revealed variations in a few genes reported to be associated with HM, including CCDC111,34 NDUFAF7,35 P4HA2,36,37 SCO2,38 UNC5D,39 BSG,40 ARR3,41,42 LOXL3,43,44 SLC39A5,45,46 LRPAP1,47 CTSH,47 CPSF1,48 TNFRSF21,49 DZIP1, XYLT1,50 and ZNF644.51,52 On the other hand, HM has also been identified as a symptom of various forms of retinal dystrophies and systemic syndromes caused by several known genes, including COL2A1,53 COL11A1,54 COL9A1,55 and COL9A256 responsible for Stickler syndrome (OMIM Nos. 108300, 604841, 614134, 614284) and FBN157 for Marfan syndrome (OMIM No. 154700). Variants in these genes were detected in a few cases, with screening of additional HM cohorts expected to uncover more variants. WES studies in HM have made significant advancements by identifying new candidate genes for HM and highlighting the critical role of genetic factors in the development of this condition.58 For instance, a WES study involving 27 families has uncovered 201 candidate variants associated with HM.59 Additionally, our previous study has shown that population-based WES can discover functional risk alleles and provide important clues to elucidate the cause of HM.60 Therefore, large-scale genetic screening for school-aged children with HM could provide further insight into the intersecting contributions of biology and the environment.

In this study, we performed WES on 6215 school-aged children with HM from the Myopia Associated Genetics and Intervention Consortium (MAGIC) cohort to identify variants in known HM-associated genes and potentially contributory variants in HM genes. This study applied genetic testing to a larger population than previous reports. To our knowledge, this whole-exome germline genetic testing is the largest in a population with HM, highlighting the potential of genetic testing to improve diagnosis and management and to allow the definition of specific care pathways.

Methods

Study Design and Participants

The present study was approved by the ethics committee of the Wenzhou Medical University Affiliated Eye Hospital. Written informed consent conforming to the tenets of the Declaration of Helsinki and following the Guidance of Sample Collection of Human Genetic Diseases by the Ministry of Public Health of China was obtained from all participating individuals or their guardians before the study. The study adhered to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline for cohort studies. A list of abbreviations used in the study is available in the eAppendix in Supplement 1.

As part of our ongoing efforts within MAGIC,60 a genetic analysis of refraction-confirmed myopia was conducted among schoolchildren in 10 districts in Wenzhou City, Zhejiang Province, China (eTable 1 in Supplement 2). MAGIC is a large-scale genomic consortium integrating myopia cohorts and sequencing data from different centers. Over the past several years, MAGIC has recruited approximately 10 000 Chinese schoolchildren with HM aged 6 to 18 years. For this cohort study, we developed a semiautomated vision examination and an information-entry pipeline, online eyesight status information management system,61 which involves manual inspection of automated refractometry data, automatic data import, and collaboration between clinicians and a statistician (eFigure 1 in Supplement 1). Certified technicians were trained at the Wenzhou Medical University Affiliated Eye Hospital with respect to standard procedures for determining visual acuity (VA) and autorefraction testing. Each school in the district was equipped with an autorefractometer (GoldEye RM-9000) and electronic logarithmic visual chart (GoldEye CM-1900C) by the Wenzhou Municipal Government to assess the prevalence of myopia. VA was evaluated using an E-type standard logarithmic visual chart at a distance of 5 m. Due to the large sample size, performing the criterion standard of cycloplegic refraction to diagnose myopia was not applicable. All students underwent noncycloplegic refraction testing using an automated refractometer, followed by complement subjective refraction testing for validation using an E-type standard logarithmic visual chart.62 Students who required corrective lenses were examined with and without eyeglasses, and naked eye refraction data were used to calculate the spherical equivalent.

Outcomes

In this case-only cohort study, high myopia was defined as a VA of less than 1.0, and SER of both eyes was defined as sphere + (cylinder / 2) of −6.00 D or less. From September 2019 to July 2020, a total of 6215 school-agedchildren with HM in both eyes, including 355 primary school students (grades 1-6 in Chinese education system), 1970 junior high school students (grades 7-9), and 3890 senior high school students (grades 10-12) (eTable 1 in Supplement 2). Previous studies have reported that extreme myopia (EM) was associated with an increased risk of various ocular pathologic complications compared with common HM.63 Additionally, some substantial evidence suggested that EM is primarily associated with genetic factors rather than being solely caused by behavioral or environmental factors.64 Therefore, exploring the diagnostic utility across the different grades of HM among school ages is important for early diagnosis and efficient interventions in schoolchildren with HM. To this end, we further divided the participants into the 3 groups: common HM group (CHM, −8.00 D ≤ SER ≤ −6.00 D), ultra myopia group (UM, −10.00 D ≤ SER < −8.00 D), and EM group (SER < −10.00 D).65

Whole-Exome Sequencing

A total of 6215 HM samples were sequenced on Illumina NovaSeq 6000 sequencers at Berry Genomics using the Twist Human Core Exome Kit. All samples were joint called together and were aligned to the consensus human genome sequence build GRCh37/hg19, and BAM files were processed using BWA66 and Sambamba 0.6.6.67 Genotype calling was performed using the Genome Analysis Toolkit’s (GATK) HaplotypeCaller.68

Variant Interpretation

Variants were prefiltered so that only those passing the GATK VQSR (variant quality score recalibration) metric and those located outside of low-complexity regions remained. Low-certainty variant positions with a genotype depth (DP) less than 10 and genotype quality (GQ) less than 20 and heterozygous genotype calls with an allele balance of more than 0.8 or less than 0.2 were ignored. The annotation of variants was performed with Ensembl’s Variant Effect Predictor (VEP) version 99 for human genome assembly GRCh37.69 We used the VEP70 CADD, LOFTEE,71 and SpliceAI plugins to generate additional bioinformatic estimations of variant deleteriousness. Potentially pathogenic protein-truncating variants (PTVs) were classified as frameshift variant, splice acceptor variant, splice donor variant, stop gained, or start lost variants. Variant filtering included the following steps: (1) the present analysis focuses on rare variants with presumed large effect sizes. Therefore, we excluded variants that had minor allele frequencies (MAF) higher than 0.005 from 3 external exome sequence databases (1000 Genomes; National Heart, Lung, and Blood Institute Exome Sequencing Project; and gnomAD) and our MAGIC cohort. (2) We excluded variants not consistent with hereditary patterns, which were only 1-hit heterozygous variants in autosomal recessive (AR) genes and homozygous variants in autosomal dominant (AD) genes. Annotation of pathogenic (P), likely pathogenic (LP), variants of uncertain significance (VUS), benign (B), and likely benign (LB) for potentially pathogenic PTVs were performed by using ANNOtate VARiation software version 2020June,72 and pathogenicity was assigned according to 2015 American College of Medical Genetics (ACMG) criteria using InterVar,73 which is a computational implementation of expert panel recommendations for clinical interpretation of genetic variants (ACMG 2015 criteria).74

A total of 75 genes were included in this study (eTable 2 in Supplement 2), including 16 nonsyndromic HM genes, 27 genes of eye syndromes associated with HM, and 32 genes of systemic syndromes associated with HM (hereafter, we refer to this gene list as HM genes). All HM genes were extracted from OMIM,75 IMI-Myopia Genetics Report,76 and PubMed for articles published up to December 2022 using genetic relevant keywords (for example, gene, genetic, mutation, or variant) and “high myopia.” Variants from 75 genes were selected from the WES data set of the school-aged population with HM.

Statistical Analysis

Involved variants yield was calculated as the percentage of patients with positive genetic test results among school-aged children with HM in each stratified group. Involved variants yield was also stratified by grade (primary, junior, and high school), SER (CHM, UM, and EM), and eyeballs (right and left). As a negative control compared with PTVs, variation rates for rare synonymous variants (MAF < 0.005 in in-house and external exome sequence databases) were computed among stratified groups. The significance of differences between each continuous groups (eg, CHM, UM, and EM) was assessed using the Cochran-Armitage test, and that of differences between categorical variables was assessed using the χ2 test. The threshold of multiple testing was set as P < .01 (.05 / 4 testings), which was calculated as the 5% type I error rate divided by the number of testings (right eye, left eye, PTV, and synonymous variants). R software version 3.6.1 (R Project for Statistical Computing) was used for analyses. Data were analyzed from July 2021 to June 2022.

Results

Cohort Information

Of the 6215 schoolchildren with HM, 3278 (52.74%) were male. Their mean (SD) age was 14.87 (2.02) years, and 355 participants (5.71%) were primary school students (aged ≤11 years); 1970 (31.70%) were junior school students (aged 12-14 years), and 3890 (62.59%) were high school students (aged ≥15 years). The mean (SD) SER was −7.51 (−1.36) D for the right eye and −7.46 (−1.34) D for the left eye. Detailed demographic information is presented in eTable 1 in Supplement 2.

Variational Spectrums Revealed for Known HM-Related Genes

Through the analysis of the exome sequencing data of 6215 individuals with HM, a total of 271 potential pathogenic variants in 59 of 75 candidate genes were identified in 964 (15.52%) schoolchildren with HM, including 36 known variants in 490 participants (7.88%) and 235 newly identified PTVs in 506 participants. Of 271 variants, 237 P/LP variants, 32 VUS, and 2 B variants were identified using ACMG guidelines (eTable 3 in Supplement 2). Among 36 previously reported variants in 490 participants, 9 variants in 6 HM genes were identified in 34 participants (0.55%), 10 variants in 8 eye syndrome genes were detected in 125 participants (2.01%), and 17 variants in 9 systemic syndrome genes were found in 337 participants (5.42%) (eTable 4, eTable 5, and eTable 6 in Supplement 2). The most frequently varied genes were COL18A1 (c.4318G>A and c.3523_3524del), accounting for 49.18% of the diagnoses, respectively (241 of 490 participants) (Figure 1A).

Figure 1. Distribution of Varied Genes in the 409 Schoolchildren With Known Variants and 506 Schoolchildren With Protein-Truncating Variants (PTV) Who Received a Probable Molecular Diagnosis After Whole-Exome Sequencing Genetic Testing.

Figure 1.

Open in a new tab

Genes without known variants and rare PTVs are not shown. HM indicates high myopia.

A total of 235 potentially P PTVs were identified in 506 of 6215 individuals (8.14%) with HM. Among them, 39 PTVs in HM genes were identified in 63 of 6215 participants (1.01%), 75 PTVs of eye syndrome genes in 132 of 6215 participants (2.12%) and 121 PTVs of systemic syndrome genes in 327 of 6215 participants (5.26%) (eTable 7, eTable 8, and eTable 9 in Supplement 2). Of the 57 genes with PTVs, variants in BBS4 were the most common, accounting for 12.06% of individuals (61 of 506 participants) with PTVs (Figure 1B). Of the 235 potentially P variants, 171 were only found once (ie, in a single student), whereas 64 occurred in 2 or more unrelated students, suggesting substantial genetic heterogeneity in HM loci. Variant types included frameshift (85 of 235 participants), splice acceptor (19 of 235 participants), splice donor (35 of 235 participants), stop gained (93 of 235 participants) and start lost (3 of 235 participants) variants (Figure 2A). We identified 19 PTVs within CEP290 and 14 PTVs in LTBP2 (Figure 2B). These P pathogenic PTVs in HM-related genes have not been observed in public exome sequence databases. They included 14 heterozygous variants in 6 genes (COL11A1, COL2A1, FBN1, LRP2, UNC5D, and ZNF644) and 2 homozygous variants in OPN1LW and RPGR genes (Table). The most common variant in our study was a missense variant (NC_000021:c.4318G>A; p.Asp1440Asn) in COL18A1, which was detected in 3.86% (240 of 6215 participants) of our cohort.

Figure 2. Rare Pathogenic Variants Identified in High Myopia (HM) Candidate Genes.

Figure 2.

Open in a new tab

A, Pathogenic variant types in HM candidate genes detected in schoolchildren with HM. B, Number of protein-truncating variants (PTV) identified in HM candidate genes. Bar plot shows the frequency of PTV in nonsydromic HM genes, eye syndrome genes and systemic syndrome genes. Genes without rare PTVs are not shown.

Table. Overview of PTVs in HM Candidate Genes.

Variant Gene Consequences Transcript cDNA change Residue change LOFTEE MAF Status Sample ID
chr1_91405539 ZNF644 Stop gained ENST00000370440 c.1372C>T p.Arg458Ter HC 8.05 × 10−05 HET 19BY19988
chr1_91447871 ZNF644 Frameshift variant ENST00000370440 c.38_39del p.Lys13IlefsTer2 HC 8.05 × 10−05 HET 19BY16965
chr1_103449692 COL11A1 Splice donor variant ENST00000370096 c.2208 + 2T>C NA HC 8.05 × 10−05 HET 19BY08582
chr1_103491076 COL11A1 Splice donor variant ENST00000370096 c.897 + 696G>A NA HC 8.05 × 10−05 HET 19BY06615
chr2_170002290 LRP2 Stop gained ENST00000263816 c.12955C>T p.Arg4319Ter HC 8.05 × 10−05 HET 19BY04713
chr2_170034316 LRP2 Frameshift variant ENST00000263816 c.10389dup p.Ile3464HisfsTer33 HC 8.05 × 10−05 HET 19BY04553
chr2_170044720 LRP2 Stop gained ENST00000263816 c.9088C>T p.Gln3030Ter HC 8.05 × 10−05 HET 19BY07153
chr2_170063503 LRP2 Stop gained ENST00000263816 c.6727C>T p.Arg2243Ter HC 8.05 × 10−05 HET 19BY11969
chr8_35093311 UNC5D Frameshift variant ENST00000404895 c.1426G>T p.Glu476Ter HC 8.05 × 10−05 HET 19BY02740
chr12_48370913 COL2A1 Stop gained ENST00000380518 c.3299C>G p.Ser1100Ter HC 8.05 × 10−05 HET 19BY04616
chr12_48380199 COL2A1 Stop gained ENST00000380518 c.1447G>T p.Gly483Ter HC 8.05 × 10−05 HET 19BY06672
chr12_48383582 COL2A1 Stop gained ENST00000380518 c.1030C>T p.Arg344Ter HC 8.05 × 10−05 HET 19BY04804
chr15_48829865 FBN1 Stop gained ENST00000316623 c.679C>T p.Gln227Ter HC 8.05 × 10−05 HET 19BY12499
chr15_48829882 FBN1 Frameshift variant ENST00000316623 c.661del p.Cys221ValfsTer109 HC 8.05 × 10−05 HET 19BY06899
chrX_153416181 OPN1LW Frameshift variant ENST00000369951 c.168del p.Ser57ValfsTer4 HC 1.61 × 10−04 HOM 19BY20410
chrX_38176655 RPGR Frameshift variant ENST00000378505 c.532del p.Ser178ValfsTer9 HC 1.61 × 10−04 HOM 19BY06620
Open in a new tab

Abbreviations: cDNA, complementary DNA; HC, high confidence; HET, heterozygous; HOM, homozygous; MAF, minor allele frequency; NA, not applicable.

Variant Yield by Severity of Myopia

Next, we quantified the involved variants yield (defined as the percentage of cases) to HM attributable to PTVs in well-characterized HM genes. The analysis revealed that the proportion of participants with PTVs varied across HM conditions and grade groups. The involved variants yield showed a positive association with SER, ranging from 7.66% in the CHM group, 8.70% in the UM group to 11.90% in the EM group, with a statistically significant increasing trend (Cochran-Armitage test for trend Z = 2.5492; P = .01, Figure 3A). The trend was also seen in the independent cohorts of people with HM in either the left or the right eye alone (eFigure 2 in Supplement 3). Notably, high SER was significantly associated with a higher involved variants yield in the primary students (Cochran-Armitage test for trend Z = 3.8848; P < .001) but not in other grades (Cochran-Armitage test for trend Z = 1.299; P = .19 for junior high school, and Cochran-Armitage test for trend Z = 1.0135; P = .31 for senior high school) (Figure 3B). The primary students referred for EM had the highest yield (8 of 35 individuals [22.86%]), which was 1.77 and 4.78 times higher than the UM (12.90%; χ21 = 0.52803; P = .16) and CHM (4.78%; χ21 = 12.318; P < .001), respectively. This trend was consistent across groups divided by the SER of either eye (eFigure 3 in Supplement 3). However, as the negative control, the trend was not statistically significant for synonymous variants (eFigure 4 in Supplement 3).

Figure 3. Proportion of Schoolchildren With High Myopia (HM) Carrying Protein-Truncating Variants in the Overall Study Population and Grade Relevant Subgroups.

Figure 3.

Open in a new tab

Spherical refraction ranges are as follows: high myopia, −8 D to −6 D; ultra myopia (UM), −10 D to −8 D; extreme myopia (EM), less than −10 D. Participants were divided into 3 subgroups according to grade when they received genetic testing.

Discussion

In this study, we tested the historic utility of WES in 6215 school-aged students with HM. The association of HM with ocular and systemic diseases has been investigated in several previous studies. For example, Marr et al77 found that 56% of children with HM had simple symptoms of HM, 25% had ocular abnormalities, and 19% had systemic disorders. Another study found variants in genes known to be involved in retinal disease in about a quarter of the participants with early-onset HM.78,79 Therefore, 75 genes were included in the present study, including 16 nonsyndromic HM genes, 27 genes of eye syndromes, and 32 genes of systemic syndromes associated with HM, such as Stickler syndrome, Marfan syndrome, and Knobloch syndrome.

Systematic analysis of variants in the 75 candidate genes showed that genetic testing had a total involved variants yield of 15.52%, including 36 known variants in 490 participants and 235 PTVs in 506 participants. The discovery of variants previously obtained in other studies demonstrated the efficiency of a genetic approach to find pathogenic variants in our cohort. In our cohort, 36 known variants were found in a total of 490 patients (7.88%), including a stop-gain variant (NM_004312:c.298C>T; p.Arg100Ter) in ARR341 found in 1 patient. ARR3 is associated with early-onset HM in a unique X-linked female-limited inheritance.80 The most common variant in our study was a missense variant (NC_000021:c.4318G>A; p.Asp1440Asn) in COL18A1, which was detected in 3.86% (240 of 6215 participants) of our cohort. Variants in COL18A1 have been identified in patients with Knobloch syndrome, an inherited disorder characterized by HM, retinal detachment, and occipital defects.81,82

PTVs result in reduced or abolished protein function and are thus considered to be the most deleterious variants.83 PTVs in HM candidate genes were detected in 506 patients (8.14%), including ZNF644. This is a zinc finger transcription factor expressed in the retina and RPE, which has been suggested to play a role in the development of HM because variants in ZNF644 have been found in patients with HM.51,52 In the present study, we found 2 PTVs in ZNF644 (c.1372C>T and c.38_39del), which have not been recorded in the gnomAD.84 We also found 3 previously unreported stop-gained variants (c.3299C>G, c.1447G>T, and c.1030C>T) and 3 splice-donor variants (c.2208 + 2T>C, c.898-972G>A, and c.897 + 696G>A) in COL11A1. Stickler syndrome is caused by variants of 2 genes,85 and is clinically characterized by HM, which is the most common cause of inherited retinal detachment.86 These results suggested that WES could find potential pathogenic variants and provide new genetic evidence for HM candidate genes in our study.

With the increase in the number of high-throughput sequencing projects generating vast amounts of data and the innovation of more statistical methods, the occurrence and development of HM can be systematically explored. On the one hand, our research showed the potential of large-scale WES in identifying new variants of high myopia. On the other hand, a detailed spherical refraction and grade (age)–stratified study implied the pattern of efficiency of genetic testing in schoolchildren with HM. In our study, the detection rate of PTVs increased with the severity of myopia, specific to the primary school group. Although the diagnostic efficacy of WES in the prevention of HM needs to be further evaluated, more severe myopia presentation with more positive genetic test results was found in younger children, suggesting the importance of genetic testing for early diagnosis and prevention of myopia. Early identification of positive variants may encourage more frequent assessment of high myopia progression and screening of at-risk family members, which can improve behavioral intervention and clinical management for schoolchildren with HM. Taken together, these findings emphasize the potential value of genetic testing in resolving clinical diagnostic challenges in HM.

Limitations

Although this study was based on grade (age) and spherical equivalent, detailed ocular and systemic examinations, such as eye axis and fundus photography, were not performed. Therefore, additional ocular biological factors should be considered in future research, which could further provide genetic diagnoses across diverse clinical categories, enabling the identification of novel phenotypic extensions. Furthermore, this study lacks follow-up data over several years, and there is a possibility that HM may progress into ultra or extreme myopia in some patients. A clearer conclusion would be reached if the genetic results could be combined with detailed clinical examinations, especially long-term follow-up assessment for schoolchildren with specific variants. Noncycloplegic assessment of refractive error in children overestimates myopia. Cycloplegic autorefraction could be implemented as an efficient approach in the follow-up study. To ensure data reliability, future multiyear follow-up studies are warranted. In addition, WES currently has limited ability to detect genomic imbalances and does not assess variants in noncoding regions of the genome, leaving additional blind spots. Physician knowledge of these technical limitations is important as WES is increasingly being incorporated into clinical practice.

Conclusions

In summary, WES screening can reveal important HM candidate genes at once and allows periodic reevaluation of the sequence data to identify new disease genes. In this study, WES also showed potential diagnostic value for different categories of schoolchildren with HM, yielding the highest contribution rate of pathogenic variants in primary school students. Our study illustrated the ability of genetic testing to identify potentially pathogenic variants in HM and reveal new genes contributing to myopia.

Supplement 1.

eFigure 1. Workflow Chart and Study Profile

eFigure 2. Proportion of HM Cases Carrying Rare PTVs in Overall Study Population

eFigure 3. Proportion of HM Cases Carrying Rare PTVs in Primary School, Junior School, and High School

eFigure 4. Proportion of HM Cases Carrying Rare Synonymous Variants in Primary School, Junior School, and High School

Click here for additional data file. (475.7KB, pdf)
Supplement 2.

eTable 1. Catchment Areas and Schoolchildren Included in the Study

eTable 2. Genes Related to HM According to the OMIM

eTable 3. ACMG Classification of 271 Potential Pathogenic Variants

eTable 4. Demographic and Genetic Characteristics of HM Individual With Known Variations in HM Genes

eTable 5. Demographic and Genetic Characteristics of HM Individual With Known Variations in Eye Syndrome Genes

eTable 6. Demographic and Genetic Characteristics of HM Individual With Known Variations in Systemic Syndrome Genes

eTable 7. All Potential Pathogenic PTVs in HM Genes

eTable 8. All Potential Pathogenic PTVs in Eye Syndrome Genes

eTable 9. All Potential Pathogenic PTVs in Systemic Syndrome Genes

Click here for additional data file. (8.8MB, xlsx)
Supplement 3.

Nonauthor Collaborators

Click here for additional data file. (100.4KB, pdf)
Supplement 4.

Data Sharing Statement

Click here for additional data file. (14.9KB, pdf)

References

  • 1.Resnikoff S, Pascolini D, Mariotti SP, Pokharel GP. Global magnitude of visual impairment caused by uncorrected refractive errors in 2004. Bull World Health Organ. 2008;86(1):63-70. doi: 10.2471/BLT.07.041210 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Resnikoff S, Jonas JB, Friedman D, et al. Myopia–a 21st century public health issue. Invest Ophthalmol Vis Sci. 2019;60(3):Mi-Mii. doi: 10.1167/iovs.18-25983 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Chen H, Wen F, Li H, et al. The types and severity of high myopic maculopathy in Chinese patients. Ophthalmic Physiol Opt. 2012;32(1):60-67. doi: 10.1111/j.1475-1313.2011.00861.x [DOI] [PubMed] [Google Scholar]
  • 4.Ripandelli G, Rossi T, Scarinci F, Scassa C, Parisi V, Stirpe M. Macular vitreoretinal interface abnormalities in highly myopic eyes with posterior staphyloma: 5-year follow-up. Retina. 2012;32(8):1531-1538. doi: 10.1097/IAE.0b013e318255062c [DOI] [PubMed] [Google Scholar]
  • 5.Baba T, Ohno-Matsui K, Futagami S, et al. Prevalence and characteristics of foveal retinal detachment without macular hole in high myopia. Am J Ophthalmol. 2003;135(3):338-342. doi: 10.1016/S0002-9394(02)01937-2 [DOI] [PubMed] [Google Scholar]
  • 6.Benhamou N, Massin P, Haouchine B, Erginay A, Gaudric A. Macular retinoschisis in highly myopic eyes. Am J Ophthalmol. 2002;133(6):794-800. doi: 10.1016/S0002-9394(02)01394-6 [DOI] [PubMed] [Google Scholar]
  • 7.Kempen JH, Mitchell P, Lee KE, et al. The prevalence of refractive errors among adults in the United States, Western Europe, and Australia. Archives of ophthalmology. 2004;122(4):495-505. doi: 10.1001/archopht.122.4.495 [DOI] [PubMed] [Google Scholar]
  • 8.Xu L, Ma Y, Yuan J, et al. ; Myopic Epidemiology and Intervention Study . COVID-19 quarantine reveals that behavioral changes have an effect on myopia progression. Ophthalmology. 2021;128(11):1652-1654. doi: 10.1016/j.ophtha.2021.04.001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Lin LLK, Shih YF, Hsiao CK, Chen CJ. Prevalence of myopia in Taiwanese schoolchildren: 1983 to 2000. Ann Acad Med Singap. 2004;33(1):27-33. doi: 10.47102/annals-acadmedsg.V33N1p27 [DOI] [PubMed] [Google Scholar]
  • 10.Jung SK, Lee JH, Kakizaki H, Jee D. Prevalence of myopia and its association with body stature and educational level in 19-year-old male conscripts in seoul, South Korea. Invest Ophthalmol Vis Sci. 2012;53(9):5579-5583. doi: 10.1167/iovs.12-10106 [DOI] [PubMed] [Google Scholar]
  • 11.Wang TJ, Chiang TH, Wang TH, Lin LL, Shih YF. Changes of the ocular refraction among freshmen in National Taiwan University between 1988 and 2005. Eye (Lond). 2009;23(5):1168-1169. doi: 10.1038/eye.2008.184 [DOI] [PubMed] [Google Scholar]
  • 12.Varma R, Tarczy-Hornoch K, Jiang X. Visual impairment in preschool children in the United States: demographic and geographic variations from 2015 to 2060. JAMA Ophthalmol. 2017;135(6):610-616. doi: 10.1001/jamaophthalmol.2017.1021 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Wojciechowski R. Nature and nurture: the complex genetics of myopia and refractive error. Clin Genet. 2011;79(4):301-320. doi: 10.1111/j.1399-0004.2010.01592.x [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Young TL, Metlapally R, Shay AE. Complex trait genetics of refractive error. Arch Ophthalmol. 2007;125(1):38-48. doi: 10.1001/archopht.125.1.38 [DOI] [PubMed] [Google Scholar]
  • 15.Lopes MC, Andrew T, Carbonaro F, Spector TD, Hammond CJ. Estimating heritability and shared environmental effects for refractive error in twin and family studies. Invest Ophthalmol Vis Sci. 2009;50(1):126-131. doi: 10.1167/iovs.08-2385 [DOI] [PubMed] [Google Scholar]
  • 16.Guggenheim JA, Kirov G, Hodson SA. The heritability of high myopia: a reanalysis of Goldschmidt’s data. J Med Genet. 2000;37(3):227-231. doi: 10.1136/jmg.37.3.227 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Baird PN, Schäche M, Dirani M. The GEnes in Myopia (GEM) study in understanding the aetiology of refractive errors. Prog Retin Eye Res. 2010;29(6):520-542. doi: 10.1016/j.preteyeres.2010.05.004 [DOI] [PubMed] [Google Scholar]
  • 18.Hornbeak DM, Young TL. Myopia genetics: a review of current research and emerging trends. Curr Opin Ophthalmol. 2009;20(5):356-362. doi: 10.1097/ICU.0b013e32832f8040 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Hawthorne FA, Young TL. Genetic contributions to myopic refractive error: insights from human studies and supporting evidence from animal models. Exp Eye Res. 2013;114:141-149. doi: 10.1016/j.exer.2012.12.015 [DOI] [PubMed] [Google Scholar]
  • 20.Mutti DO, Cooper ME, O’Brien S, et al. Candidate gene and locus analysis of myopia. Mol Vis. 2007;13:1012-1019. [PMC free article] [PubMed] [Google Scholar]
  • 21.Lam DSC, Lee WS, Leung YF, et al. TGFbeta-induced factor: a candidate gene for high myopia. Invest Ophthalmol Vis Sci. 2003;44(3):1012-1015. doi: 10.1167/iovs.02-0058 [DOI] [PubMed] [Google Scholar]
  • 22.Veerappan S, Pertile KK, Islam AF, et al. Role of the hepatocyte growth factor gene in refractive error. Ophthalmology. 2010;117(2):239-245.e1-2. doi: 10.1016/j.ophtha.2009.07.002 [DOI] [PubMed] [Google Scholar]
  • 23.Metlapally R, Ki CS, Li YJ, et al. Genetic association of insulin-like growth factor-1 polymorphisms with high-grade myopia in an international family cohort. Invest Ophthalmol Vis Sci. 2010;51(9):4476-4479. doi: 10.1167/iovs.09-4912 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Wojciechowski R, Yee SS, Simpson CL, Bailey-Wilson JE, Stambolian D. Matrix metalloproteinases and educational attainment in refractive error: evidence of gene-environment interactions in the Age-Related Eye Disease Study. Ophthalmology. 2013;120(2):298-305. doi: 10.1016/j.ophtha.2012.07.078 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Hysi PG, Choquet H, Khawaja AP, et al. ; Consortium for Refractive Error and Myopia; UK Eye and Vision Consortium; 23andMe Inc. . Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia. Nat Genet. 2020;52(4):401-407. doi: 10.1038/s41588-020-0599-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Tedja MS, Wojciechowski R, Hysi PG, et al. ; CREAM Consortium; 23andMe Research Team; UK Biobank Eye and Vision Consortium . Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error. Nat Genet. 2018;50(6):834-848. doi: 10.1038/s41588-018-0127-7 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Nakanishi H, Yamada R, Gotoh N, et al. A genome-wide association analysis identified a novel susceptible locus for pathological myopia at 11q24.1. PLoS Genet. 2009;5(9):e1000660. doi: 10.1371/journal.pgen.1000660 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Li YJ, Goh L, Khor CC, et al. Genome-wide association studies reveal genetic variants in CTNND2 for high myopia in Singapore Chinese. Ophthalmology. 2011;118(2):368-375. doi: 10.1016/j.ophtha.2010.06.016 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Li Z, Qu J, Xu X, et al. A genome-wide association study reveals association between common variants in an intergenic region of 4q25 and high-grade myopia in the Chinese Han population. Hum Mol Genet. 2011;20(14):2861-2868. doi: 10.1093/hmg/ddr169 [DOI] [PubMed] [Google Scholar]
  • 30.Shi Y, Qu J, Zhang D, et al. Genetic variants at 13q12.12 are associated with high myopia in the Han Chinese population. Am J Hum Genet. 2011;88(6):805-813. doi: 10.1016/j.ajhg.2011.04.022 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Nishizaki R, Ota M, Inoko H, et al. New susceptibility locus for high myopia is linked to the uromodulin-like 1 (UMODL1) gene region on chromosome 21q22.3. Eye (Lond). 2009;23(1):222-229. doi: 10.1038/eye.2008.152 [DOI] [PubMed] [Google Scholar]
  • 32.Solouki AM, Verhoeven VJ, van Duijn CM, et al. A genome-wide association study identifies a susceptibility locus for refractive errors and myopia at 15q14. Nat Genet. 2010;42(10):897-901. doi: 10.1038/ng.663 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Hysi PG, Young TL, Mackey DA, et al. A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25. Nat Genet. 2010;42(10):902-905. doi: 10.1038/ng.664 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Zhao F, Wu J, Xue A, et al. Exome sequencing reveals CCDC111 mutation associated with high myopia. Hum Genet. 2013;132(8):913-921. doi: 10.1007/s00439-013-1303-6 [DOI] [PubMed] [Google Scholar]
  • 35.Wang B, Liu Y, Chen S, et al. A novel potentially causative variant of NDUFAF7 revealed by mutation screening in a Chinese family with pathologic myopia. Invest Ophthalmol Vis Sci. 2017;58(10):4182-4192. doi: 10.1167/iovs.16-20941 [DOI] [PubMed] [Google Scholar]
  • 36.Napolitano F, Di Iorio V, Testa F, et al. Autosomal-dominant myopia associated to a novel P4HA2 missense variant and defective collagen hydroxylation. Clin Genet. 2018;93(5):982-991. doi: 10.1111/cge.13217 [DOI] [PubMed] [Google Scholar]
  • 37.Guo H, Tong P, Liu Y, et al. Mutations of P4HA2 encoding prolyl 4-hydroxylase 2 are associated with nonsyndromic high myopia. Genet Med. 2015;17(4):300-306. doi: 10.1038/gim.2015.28 [DOI] [PubMed] [Google Scholar]
  • 38.Tran-Viet KN, Powell C, Barathi VA, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. Am J Hum Genet. 2013;92(5):820-826. doi: 10.1016/j.ajhg.2013.04.005 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Feng L, Zhou D, Zhang Z, He L, Liu Y, Yang Y. Exome sequencing identifies a novel UNC5D mutation in a severe myopic anisometropia family: a case report. Medicine (Baltimore). 2017;96(24):e7138. doi: 10.1097/MD.0000000000007138 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Jin ZB, Wu J, Huang XF, et al. Trio-based exome sequencing arrests de novo mutations in early-onset high myopia. Proc Natl Acad Sci U S A. 2017;114(16):4219-4224. doi: 10.1073/pnas.1615970114 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Xiao X, Li S, Jia X, Guo X, Zhang Q. X-linked heterozygous mutations in ARR3 cause female-limited early onset high myopia. Mol Vis. 2016;22:1257-1266. [PMC free article] [PubMed] [Google Scholar]
  • 42.Gu L, Cong P, Ning Q, Jiang B, Wang J, Cui H. The causal mutation in ARR3 gene for high myopia and progressive color vision defect. Sci Rep. 2023;13(1):8986. doi: 10.1038/s41598-023-36141-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Li J, Gao B, Xiao X, et al. Exome sequencing identified null mutations in LOXL3 associated with early-onset high myopia. Mol Vis. 2016;22:161-167. [PMC free article] [PubMed] [Google Scholar]
  • 44.Jiang Y, Zhou L, Wang Y, et al. The genetic confirmation and clinical characterization of LOXL3-associated MYP28: a common type of recessive extreme high myopia. Invest Ophthalmol Vis Sci. 2023;64(3):14-14. doi: 10.1167/iovs.64.3.24 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 45.Guo H, Jin X, Zhu T, et al. SLC39A5 mutations interfering with the BMP/TGF-β pathway in non-syndromic high myopia. J Med Genet. 2014;51(8):518-525. doi: 10.1136/jmedgenet-2014-102351 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Dong S, Tian Q, Zhu T, et al. SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis. J Cell Mol Med. 2021;25(17):8432-8441. doi: 10.1111/jcmm.16803 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Aldahmesh MA, Khan AO, Alkuraya H, et al. Mutations in LRPAP1 are associated with severe myopia in humans. Am J Hum Genet. 2013;93(2):313-320. doi: 10.1016/j.ajhg.2013.06.002 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Ouyang J, Sun W, Xiao X, et al. CPSF1 mutations are associated with early-onset high myopia and involved in retinal ganglion cell axon projection. Hum Mol Genet. 2019;28(12):1959-1970. doi: 10.1093/hmg/ddz029 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Pan H, Wu S, Wang J, et al. TNFRSF21 mutations cause high myopia. J Med Genet. 2019;56(10):671-677. doi: 10.1136/jmedgenet-2018-105684 [DOI] [PubMed] [Google Scholar]
  • 50.Lee JK, Kim H, Park YM, Kim DH, Lim HT. Mutations in DZIP1 and XYLT1 are associated with nonsyndromic early onset high myopia in the Korean population. Ophthalmic Genet. 2017;38(4):395-397. doi: 10.1080/13816810.2016.1232415 [DOI] [PubMed] [Google Scholar]
  • 51.Jiang D, Li J, Xiao X, et al. Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing. Invest Ophthalmol Vis Sci. 2014;56(1):339-345. doi: 10.1167/iovs.14-14850 [DOI] [PubMed] [Google Scholar]
  • 52.Shi Y, Li Y, Zhang D, et al. Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet. 2011;7(6):e1002084. doi: 10.1371/journal.pgen.1002084 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 53.Ahmad NN, McDonald-McGinn DM, Zackai EH, et al. A second mutation in the type II procollagen gene (COL2AI) causing stickler syndrome (arthro-ophthalmopathy) is also a premature termination codon. Am J Hum Genet. 1993;52(1):39-45. [PMC free article] [PubMed] [Google Scholar]
  • 54.Annunen S, Körkkö J, Czarny M, et al. Splicing mutations of 54-bp exons in the COL11A1 gene cause Marshall syndrome, but other mutations cause overlapping Marshall/Stickler phenotypes. Am J Hum Genet. 1999;65(4):974-983. doi: 10.1086/302585 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 55.Van Camp G, Snoeckx RL, Hilgert N, et al. A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene. Am J Hum Genet. 2006;79(3):449-457. doi: 10.1086/506478 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 56.Baker S, Booth C, Fillman C, et al. A loss of function mutation in the COL9A2 gene causes autosomal recessive Stickler syndrome. Am J Med Genet A. 2011;155A(7):1668-1672. doi: 10.1002/ajmg.a.34071 [DOI] [PubMed] [Google Scholar]
  • 57.Dietz HC, McIntosh I, Sakai LY, et al. Four novel FBN1 mutations: significance for mutant transcript level and EGF-like domain calcium binding in the pathogenesis of Marfan syndrome. Genomics. 1993;17(2):468-475. doi: 10.1006/geno.1993.1349 [DOI] [PubMed] [Google Scholar]
  • 58.Haarman AEG, Thiadens AAHJ, van Tienhoven M, et al. Whole exome sequencing of known eye genes reveals genetic causes for high myopia. Hum Mol Genet. 2022;31(19):3290-3298. doi: 10.1093/hmg/ddac113 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 59.Liu Y, Zhang JJ, Piao SY, et al. Whole-exome sequencing in a cohort of high myopia patients in Northwest China. Front Cell Dev Biol. 2021;9:645501. doi: 10.3389/fcell.2021.645501 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Su J, Yuan J, Xu L, et al. ; Myopia Associated Genetics and Intervention Consortium . Sequencing of 19,219 exomes identifies a low-frequency variant in FKBP5 promoter predisposing to high myopia in a Han Chinese population. Cell Rep. 2023;42(5):112510. doi: 10.1016/j.celrep.2023.112510 [DOI] [PubMed] [Google Scholar]
  • 61.Xu L, Zhuang Y, Zhang G, et al. Design, methodology, and baseline of whole city-million scale children and adolescents myopia survey (CAMS) in Wenzhou, China. Eye Vis (Lond). 2021;8(1):31. doi: 10.1186/s40662-021-00255-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 62.Sankaridurg P, He X, Naduvilath T, et al. Comparison of noncycloplegic and cycloplegic autorefraction in categorizing refractive error data in children. Acta Ophthalmol. 2017;95(7):e633-e640. doi: 10.1111/aos.13569 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 63.Devarajan K, Sim R, Chua J, et al. Optical coherence tomography angiography for the assessment of choroidal vasculature in high myopia. Br J Ophthalmol. 2020;104(7):917-923. doi: 10.1136/bjophthalmol-2019-314769 [DOI] [PubMed] [Google Scholar]
  • 64.Zhao F, Zhang D, Zhou Q, et al. Scleral HIF-1α is a prominent regulatory candidate for genetic and environmental interactions in human myopia pathogenesis. EBioMedicine. 2020;57:102878. doi: 10.1016/j.ebiom.2020.102878 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 65.Gupta P, Cheung CY, Saw SM, et al. Peripapillary choroidal thickness in young Asians with high myopia. Invest Ophthalmol Vis Sci. 2015;56(3):1475-1481. doi: 10.1167/iovs.14-15742 [DOI] [PubMed] [Google Scholar]
  • 66.Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754-1760. doi: 10.1093/bioinformatics/btp324 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 67.Sambamba: process your BAM data faster. Accessed November 6, 2023. https://lomereiter.github.io/sambamba/
  • 68.Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43(1):11.10.1-11.10.33. doi: 10.1002/0471250953.bi1110s43 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 69.Aken BL, Ayling S, Barrell D, et al. The Ensembl gene annotation system. Database (Oxford). 2016;2016:baw093. doi: 10.1093/database/baw093 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 70.McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122. doi: 10.1186/s13059-016-0974-4 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 71.LOFTEE. Accessed November 6, 2023. https://github.com/konradjk/loftee
  • 72.Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10(10):1556-1566. doi: 10.1038/nprot.2015.105 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 73.Li Q, Wang K. InterVar: clinical interpretation of genetic variants by the 2015 ACMG-AMP guidelines. Am J Hum Genet. 2017;100(2):267-280. doi: 10.1016/j.ajhg.2017.01.004 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 74.Richards S, Aziz N, Bale S, et al. ; ACMG Laboratory Quality Assurance Committee . Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424. doi: 10.1038/gim.2015.30 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 75.Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 2015;43(Database issue):D789-D798. doi: 10.1093/nar/gku1205 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 76.Tedja MS, Haarman AEG, Meester-Smoor MA, et al. ; CREAM Consortium . IMI—myopia genetics report. Invest Ophthalmol Vis Sci. 2019;60(3):M89-M105. doi: 10.1167/iovs.18-25965 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 77.Marr JE, Halliwell-Ewen J, Fisher B, Soler L, Ainsworth JR. Associations of high myopia in childhood. Eye (Lond). 2001;15(Pt 1):70-74. doi: 10.1038/eye.2001.17 [DOI] [PubMed] [Google Scholar]
  • 78.Sun W, Huang L, Xu Y, et al. Exome sequencing on 298 probands with early-onset high myopia: approximately one-fourth show potential pathogenic mutations in RetNet genes. Invest Ophthalmol Vis Sci. 2015;56(13):8365-8372. doi: 10.1167/iovs.15-17555 [DOI] [PubMed] [Google Scholar]
  • 79.Ye M, Ma Y, Qin YX, et al. Mutational investigation of 17 causative genes in a cohort of 113 families with nonsyndromic early-onset high myopia in northwestern China. Mol Genet Genomics. 2023;298(3):669-682. doi: 10.1007/s00438-023-02003-7 [DOI] [PubMed] [Google Scholar]
  • 80.van Mazijk R, Haarman AEG, Hoefsloot LH, et al. Early onset X-linked female limited high myopia in three multigenerational families caused by novel mutations in the ARR3 gene. Hum Mutat. 2022;43(3):380-388. doi: 10.1002/humu.24327 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 81.Menzel O, Bekkeheien RC, Reymond A, et al. Knobloch syndrome: novel mutations in COL18A1, evidence for genetic heterogeneity, and a functionally impaired polymorphism in endostatin. Hum Mutat. 2004;23(1):77-84. doi: 10.1002/humu.10284 [DOI] [PubMed] [Google Scholar]
  • 82.Hull S, Arno G, Ku CA, et al. Molecular and clinical findings in patients with Knobloch syndrome. JAMA Ophthalmol. 2016;134(7):753-762. doi: 10.1001/jamaophthalmol.2016.1073 [DOI] [PubMed] [Google Scholar]
  • 83.MacArthur DG, Balasubramanian S, Frankish A, et al. ; 1000 Genomes Project Consortium . A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012;335(6070):823-828. doi: 10.1126/science.1215040 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 84.Karczewski KJ, Francioli LC, Tiao G, et al. ; Genome Aggregation Database Consortium . The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581(7809):434-443. doi: 10.1038/s41586-020-2308-7 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 85.Richards AJ, McNinch A, Martin H, et al. Stickler syndrome and the vitreous phenotype: mutations in COL2A1 and COL11A1. Hum Mutat. 2010;31(6):E1461-E1471. doi: 10.1002/humu.21257 [DOI] [PubMed] [Google Scholar]
  • 86.Snead MP, McNinch AM, Poulson AV, et al. Stickler syndrome, ocular-only variants and a key diagnostic role for the ophthalmologist. Eye (Lond). 2011;25(11):1389-1400. doi: 10.1038/eye.2011.201 [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplement 1.

eFigure 1. Workflow Chart and Study Profile

eFigure 2. Proportion of HM Cases Carrying Rare PTVs in Overall Study Population

eFigure 3. Proportion of HM Cases Carrying Rare PTVs in Primary School, Junior School, and High School

eFigure 4. Proportion of HM Cases Carrying Rare Synonymous Variants in Primary School, Junior School, and High School

Click here for additional data file. (475.7KB, pdf)
Supplement 2.

eTable 1. Catchment Areas and Schoolchildren Included in the Study

eTable 2. Genes Related to HM According to the OMIM

eTable 3. ACMG Classification of 271 Potential Pathogenic Variants

eTable 4. Demographic and Genetic Characteristics of HM Individual With Known Variations in HM Genes

eTable 5. Demographic and Genetic Characteristics of HM Individual With Known Variations in Eye Syndrome Genes

eTable 6. Demographic and Genetic Characteristics of HM Individual With Known Variations in Systemic Syndrome Genes

eTable 7. All Potential Pathogenic PTVs in HM Genes

eTable 8. All Potential Pathogenic PTVs in Eye Syndrome Genes

eTable 9. All Potential Pathogenic PTVs in Systemic Syndrome Genes

Click here for additional data file. (8.8MB, xlsx)
Supplement 3.

Nonauthor Collaborators

Click here for additional data file. (100.4KB, pdf)
Supplement 4.

Data Sharing Statement

Click here for additional data file. (14.9KB, pdf)

Articles from JAMA Network Open are provided here courtesy of American Medical Association

RESOURCES