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Zehra Z, von Bartheld CS, Agarwal AB, Vasquez-Gross H, Noorani Siddiqui S, Azam M, Qamar R. Exploring WNT2 polymorphisms in comitant strabismus: A genetic association study. Gene 2024; 928:148797. [PMID: 39068999 DOI: 10.1016/j.gene.2024.148797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Strabismus is a complex oculomotor condition characterized by a misalignment of the visual axis. The genetics of strabismus are poorly defined although a few candidate genes have been identified, among which is the WNT2 gene. Our study was designed to assess the association of single nucleotide polymorphisms (SNPs) of WNT2 in Pakistani strabismus patients. METHODS A total of six SNPs, three intronic and three in the 3́ untranslated region, were screened in the current study. Logistic regression was performed using a dominant, recessive and additive model to determine the association of SNPs with strabismus and its clinical subtypes: esotropia and exotropia. Furthermore, haplotype analysis was performed. RESULTS Regression analysis revealed an association of rs2896218, rs3779550, rs2285544 and rs4730775 with strabismus under the dominant model. When analyzed separately, rs2896218 and rs2285544 were found to be associated with both esotropia and exotropia, while rs4730775 was significantly associated only with exotropia under the dominant model. Based on clinical parameters, rs2896218, rs2285544 and rs4730775 were also found to be associated with the group of strabismus patients who were diagnosed at birth, but not in the group of patients who were diagnosed later in life. Haplotype analysis revealed that the haplotype A T T (corresponding to rs2896218, rs3779550 and rs2285544) was significantly more prevalent in the strabismus group. CONCLUSION Overall, the results of the present study suggest an association of WNT2 polymorphisms with strabismus and its subtypes in the Pakistani population, though further studies are needed to elucidate their role in strabismus etiology.
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Affiliation(s)
- Zainab Zehra
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Pakistan
| | | | - Andrea B Agarwal
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center, RRID: SCR_017802, University of Nevada, Reno, USA
| | | | - Maleeha Azam
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Pakistan.
| | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad, Pakistan; Science and Technology Sector, ICESCO, Rabat, Kingdom of Morocco.
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Matsuo T, Hamasaki I, Kamatani Y, Kawaguchi T, Yamaguchi I, Matsuda F, Saito A, Nakazono K, Kamitsuji S. Genome-Wide Association Study with Three Control Cohorts of Japanese Patients with Esotropia and Exotropia of Comitant Strabismus and Idiopathic Superior Oblique Muscle Palsy. Int J Mol Sci 2024; 25:6986. [PMID: 39000095 PMCID: PMC11241339 DOI: 10.3390/ijms25136986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 07/16/2024] Open
Abstract
Esotropia and exotropia in the entity of comitant strabismus are multifactorial diseases with both genetic and environmental backgrounds. Idiopathic superior oblique muscle palsy, as the predominant entity of non-comitant (paralytic) strabismus, also has a genetic background, as evidenced by varying degrees of muscle hypoplasia. A genome-wide association study (GWAS) was conducted of 711 Japanese patients with esotropia (n= 253), exotropia (n = 356), and idiopathic superior oblique muscle palsy (n = 102). The genotypes of single nucleotide polymorphisms (SNPs) were determined by Infinium Asian Screening Array. Three control cohorts from the Japanese population were used: two cohorts from BioBank Japan (BBJ) and the Nagahama Cohort. BBJ (180K) was genotyped by a different array, Illumina Infinium OmniExpressExome or HumanOmniExpress, while BBJ (ASA) and the Nagahama Cohort were genotyped by the same Asian array. After quality control of SNPs and individuals, common SNPs between the case cohort and the control cohort were chosen in the condition of genotyping by different arrays, while all SNPs genotyped by the same array were used for SNP imputation. The SNPs imputed with R-square values ≥ 0.3 were used to compare the case cohort of each entity or the combined entity with the control cohort. In comparison with BBJ (180K), the esotropia group and the exotropia group showed CDCA7 and HLA-F, respectively, as candidate genes at a significant level of p < 5 × 10-8, while the idiopathic superior oblique muscle palsy group showed DAB1 as a candidate gene which is involved in neuronal migration. DAB1 was also detected as a candidate in comparison with BBJ (ASA) and the Nagahama Cohort at a weak level of significance of p < 1 × 10-6. In comparison with BBJ (180K), RARB (retinoic acid receptor-β) was detected as a candidate at a significant level of p < 5 × 10-8 in the combined group of esotropia, exotropia, and idiopathic superior oblique muscle palsy. In conclusion, a series of GWASs with three different control cohorts would be an effective method with which to search for candidate genes for multifactorial diseases such as strabismus.
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Affiliation(s)
- Toshihiko Matsuo
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama City 700-8558, Japan
- Department of Ophthalmology, Okayama University Hospital, Okayama City 700-8558, Japan
| | - Ichiro Hamasaki
- Department of Ophthalmology, Okayama University Hospital, Okayama City 700-8558, Japan
| | - Yoichiro Kamatani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan;
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (F.M.)
| | - Izumi Yamaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (F.M.)
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan (F.M.)
| | - Akira Saito
- StaGen Co., Ltd., Tokyo 111-0051, Japan (S.K.)
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Jin K, Aboobakar IF, Whitman MC, Oke I. Mental Health Conditions Associated With Strabismus in a Diverse Cohort of US Adults. JAMA Ophthalmol 2024; 142:472-475. [PMID: 38573646 PMCID: PMC11099685 DOI: 10.1001/jamaophthalmol.2024.0540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/03/2024] [Indexed: 04/05/2024]
Abstract
Importance Greater understanding of the association between strabismus and mental health conditions across sociodemographic backgrounds may inform strategies to improve mental well-being in this population. Objective To describe the association of strabismus with mental health conditions in a diverse cohort of US adults. Design, Setting, and Participants This cross-sectional study used data from the National Institutes of Health's All of Us Research Program, an ongoing program launched in 2015. The study included 3646 adults (aged ≥18 years) with strabismus and 3646 propensity score-matched controls. Statistical analysis was conducted from September 12, 2023, to January 29, 2024. Main Outcomes and Measures Adults with strabismus were propensity score matched on age, gender, race and ethnicity, income, educational level, and insurance status in a 1:1 ratio with adults without strabismus. The prevalences of anxiety, depression, substance use and addiction, bipolar disorder, and schizophrenia spectrum disorder among adults with strabismus were compared with controls. Logistic regression was used to evaluate the association of mental health conditions with sociodemographic factors in each group. Results This study included 3646 adults with strabismus (median age, 67 years [IQR, 53-76 years]; 2017 women [55%]) and 3646 propensity score-matched controls (median age, 67 years [IQR, 53-76 years]; 2017 women [55%]). Individuals with strabismus had higher prevalences of anxiety (1153 [32%] vs 519 [14%]; difference, 17%; 95% CI, 15%-19%; P < .001), depression (1189 [33%] vs 514 [14%]; difference, 19%; 95% CI, 17%-20%; P < .001), substance use and addiction (116 [3%] vs 51 [1%]; difference, 2%; 95% CI, 1%-3%; P < .001), bipolar disorder (253 [7%] vs 101 [3%]; difference, 4%; 95% CI, 3%-5%; P < .001), and schizophrenia spectrum disorder (103 [3%] vs 36 [1%]; difference, 2%; 95% CI, 1%-3%; P < .001) compared with individuals without strabismus. Among adults with strabismus, higher odds of mental health conditions were associated with younger age (odds ratio [OR], 1.11 per 10-year decrease; 95% CI, 1.06-1.16 per 10-year decrease), female gender (OR, 1.62; 95% CI, 1.41-1.85), Black or African American race and ethnicity (OR, 1.22; 95% CI, 1.01-1.48), low income (OR, 3.06; 95% CI, 2.56-3.67), and high school education or less (OR, 1.58; 95% CI, 1.34-1.85). Conclusions and Relevance In a diverse and nationwide cohort, adults with strabismus were more likely to have mental health conditions compared with adults without strabismus. Further investigation into the risk factors for poor mental health among adults with strabismus across sociodemographic backgrounds may offer novel opportunities for interventions to improve mental well-being in this population.
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Affiliation(s)
- Kimberly Jin
- University of Massachusetts Chan School of Medicine, Worcester
| | - Inas F. Aboobakar
- Department of Ophthalmology, Massachusetts Eye and Ear and Harvard Medical School, Boston
| | - Mary C. Whitman
- Department of Ophthalmology, Massachusetts Eye and Ear and Harvard Medical School, Boston
- Department of Ophthalmology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Isdin Oke
- Department of Ophthalmology, Massachusetts Eye and Ear and Harvard Medical School, Boston
- Department of Ophthalmology, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
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Martinez Sanchez M, Chan WM, MacKinnon SE, Barry B, Hunter DG, Engle EC, Whitman MC. Presence of Copy Number Variants Associated With Esotropia in Patients With Exotropia. JAMA Ophthalmol 2024; 142:243-247. [PMID: 38358749 PMCID: PMC10870223 DOI: 10.1001/jamaophthalmol.2023.6782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/10/2023] [Indexed: 02/16/2024]
Abstract
Importance Strabismus is a common ocular disorder of childhood. There is a clear genetic component to strabismus, but it is not known if esotropia and exotropia share genetic risk factors. Objective To determine whether genetic duplications associated with esotropia are also associated with exotropia. Design, Setting, and Participants This was a cross-sectional study conducted from November 2005 to December 2023. Individuals with constant or intermittent exotropia of any magnitude or a history of surgery for exotropia were recruited from pediatric ophthalmic practices. Data were analyzed from March to December 2023. Exposure Genetic duplication. Main Outcomes and Measures Presence of genetic duplications at 2p11.2, 4p15.2, and 10q11.22 assessed by digital droplet polymerase chain reaction. Orthoptic measurements and history of strabismus surgery were performed. Results A total of 234 individuals (mean [SD] age, 19.5 [19.0] years; 127 female [54.3%]) were included in this study. The chromosome 2 duplication was present in 1.7% of patients with exotropia (4 of 234; P = .40), a similar proportion to the 1.4% of patients with esotropia (23 of 1614) in whom it was previously reported and higher than the 0.1% of controls (4 of 3922) previously reported (difference, 1.6%; 95% CI, 0%-3.3%; P < .001). The chromosome 4 duplication was present in 3.0% of patients with exotropia (7 of 234; P = .10), a similar proportion to the 1.7% of patients with esotropia (27 of 1614) and higher than the 0.2% of controls (6 of 3922) in whom it was previously reported (difference, 2.8%; 95% CI, 0.6%-5.0%; P < .001). The chromosome 10 duplication was present in 6.0% of patients with exotropia (14 of 234; P = .08), a similar proportion to the 4% of patients with esotropia (64 of 1614) and higher than the 0.4% of controls (18 of 3922) in whom it was previously reported (difference, 5.6%; 95% CI, 2.5%-8.6%; P < .001). Individuals with a duplication had higher mean (SD) magnitude of deviation (31 [13] vs 22 [14] prism diopters [PD]; difference, 9 PD; 95% CI, 1-16 PD; P = .03), were more likely to have constant (vs intermittent) exotropia (70% vs 29%; difference, 41%; 95% CI, 20.8%-61.2%; P < .001), and had a higher rate of exotropia surgery than those without a duplication (58% vs 34%; difference, 24%; 95% CI, 3%-44%; P = .02). Conclusions and Relevance In this cross-sectional study, results suggest that the genetic duplications on chromosomes 2, 4, and 10 were risk factors for exotropia as well as esotropia. These findings support the possibility that esotropia and exotropia have shared genetic risk factors. Whether esotropia or exotropia develops in the presence of these duplications may be influenced by other shared or independent genetic variants or by environmental factors.
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Affiliation(s)
- Mayra Martinez Sanchez
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Wai-Man Chan
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sarah E. MacKinnon
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brenda Barry
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - David G. Hunter
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth C. Engle
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Mary C. Whitman
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
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Chaomulige, Matsuo T, Sugimoto K, Miyaji M, Hosoya O, Ueda M, Kobayashi R, Horii T, Hatada I. Morphometric Analysis of the Eye by Magnetic Resonance Imaging in MGST2-Gene-Deficient Mice. Biomedicines 2024; 12:370. [PMID: 38397974 PMCID: PMC10887158 DOI: 10.3390/biomedicines12020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Strabismus, a neuro-ophthalmological condition characterized by misalignment of the eyes, is a common ophthalmic disorder affecting both children and adults. In our previous study, we identified the microsomal glutathione S-transferase 2 (MGST2) gene as one of the potential candidates for comitant strabismus susceptibility in a Japanese population. The MGST2 gene belongs to the membrane-associated protein involved in the generation of pro-inflammatory mediators, and it is also found in the protection against oxidative stress by decreasing the reactivity of oxidized lipids. To look for the roles of the MGST2 gene in the development, eye alignment, and overall morphology of the eye as the possible background of strabismus, MGST2 gene knockout (KO) mice were generated by CRISPR/Cas9-mediated gene editing with guide RNAs targeting the MGST2 exon 2. The ocular morphology of the KO mice was analyzed through high-resolution images obtained by a magnetic resonance imaging (MRI) machine for small animals. The morphometric analyses showed that the height, width, and volume of the eyeballs in MGST2 KO homozygous mice were significantly greater than those of wild-type mice, indicating that the eyes of MGST2 KO homozygous mice were significantly enlarged. There were no significant differences in the axis length and axis angle. These morphological changes may potentially contribute to the development of a subgroup of strabismus.
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Affiliation(s)
- Chaomulige
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8558, Japan;
| | - Toshihiko Matsuo
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8558, Japan;
- Department of Ophthalmology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Kohei Sugimoto
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8558, Japan;
| | - Mary Miyaji
- Department of Medical Neurobiology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (M.M.); (O.H.)
| | - Osamu Hosoya
- Department of Medical Neurobiology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; (M.M.); (O.H.)
| | - Masashi Ueda
- Department of Biofunctional Imaging Analysis, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan;
| | - Ryosuke Kobayashi
- Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan; (R.K.); (T.H.); (I.H.)
| | - Takuro Horii
- Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan; (R.K.); (T.H.); (I.H.)
| | - Izuho Hatada
- Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Japan; (R.K.); (T.H.); (I.H.)
- Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Maebashi 371-8511, Japan
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Chen MH, Yan JH. Diffusion tensor imaging of horizontal extraocular muscles in patients with concomitant and paralytic esotropia. Int J Ophthalmol 2023; 16:1350-1355. [PMID: 37602335 PMCID: PMC10398516 DOI: 10.18240/ijo.2023.08.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/21/2023] [Indexed: 08/22/2023] Open
Abstract
AIM To assess metrics of diffusion tensor imagining (DTI) in evaluating microstructural abnormalities of horizontal extraocular muscles (EOM) in esotropia. METHODS Six adult concomitant esotropia patients, 5 unilateral abducent paralysis patients and 2 healthy volunteers were enrolled. Conventional magnetic resonance imaging (MRI) and DTI were performed on all subjects using 3T MR scanner. Fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) of medial and lateral rectus muscles were measured and compared between patients group and control group. RESULTS Medial rectus MD and RD within the adducted eye of concomitant patients was significantly greater than that in unilateral abducent paralysis patients (0.259×10-2 mm2/s vs 0.207×10-2 mm2/s, P=0.014; 0.182×10-2 mm2/s vs 0.152×10-2 mm2/s, P=0.017). Both strabismus patients showed a significantly decreased MD and AD than that obtained in normal controls for lateral rectus muscles (P<0.05). Medial rectus MD of the adducted eye in concomitant strabismus patients was significantly decreased than that in healthy controls (0.259×10-2 mm2/s vs 0.266×10-2 mm2/s, P=0.010). Lateral rectus AD of the adducted eye in concomitant strabismus patients was significantly decreased as compared with that in healthy controls (0.515×10-2 mm2/s vs 0.593×10-2 mm2/s, P=0.013). No statistically significant differences were present between the adducted and fixating eyes in concomitant strabismus patients. CONCLUSION DTI represents a feasible technique to assess tissue characteristics of EOM. The effects of eye position changes on DTI parameters are subtle. Decreased MD and RD could be evidence for remodeling of the medial rectus muscle contracture. Lower medial and lateral recuts MD of concomitant esotropia patients indicates a thinner fibrous structure of the EOM. Lower MD and AD should be general character of esotropia.
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Affiliation(s)
- Ming-Hao Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, Guangdong Province, China
| | - Jian-Hua Yan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, Guangdong Province, China
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Abstract
Strabismus, or misalignment of the eyes, is the most common ocular disorder in the pediatric population, affecting approximately 2%-4% of children. Strabismus leads to the disruption of binocular vision, amblyopia, social and occupational discrimination, and decreased quality of life. Although it has been recognized since ancient times that strabismus runs in families, its inheritance patterns are complex, and its precise genetic mechanisms have not yet been defined. Family, population, and twin studies all support a role of genetics in the development of strabismus. There are multiple forms of strabismus, and it is not known if they have shared genetic mechanisms or are distinct genetic disorders, which complicates studies of strabismus. Studies assuming that strabismus is a Mendelian disorder have found areas of linkage and candidate genes in particular families, but no definitive causal genes. Genome-wide association studies searching for common variation that contributes to strabismus risk have identified two risk loci and three copy number variants in white populations. Causative genes have been identified in congenital cranial dysinnervation disorders, syndromes in which eye movement is limited or paralyzed. The causative genes lead to either improper differentiation of cranial motor neurons or abnormal axon guidance. This article reviews the evidence for a genetic contribution to strabismus and the recent advances that have been made in the genetics of comitant strabismus, the most common form of strabismus.
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Affiliation(s)
- Mayra Martinez Sanchez
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, United States
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Mary C. Whitman
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA, United States
- Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA, United States
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Rahpeyma M, Sabermoghaddam A, Kiarudi MY, Aghabozorgi AS, Pasdar A. Role of Abelson Helper Integration Site 1, Nebulin, and Paired Box 3 Genes in the Development of Nonsyndromic Strabismus in a Series of Iranian Families: Sequence Analysis and Systematic Review of the Genetics of Nonsyndromic Strabismus. J Curr Ophthalmol 2023; 35:216-225. [PMID: 38681684 PMCID: PMC11047811 DOI: 10.4103/joco.joco_53_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 05/01/2024] Open
Abstract
Purpose To look for causative genetic mutations in a series of Iranian families with strabismus. In addition, we systematically reviewed all the published articles regarding the role of genetic variations in primary and nonsyndromic comitant strabismus. Methods Four families with a history of multiple cases of primary and nonsyndromic comitant strabismus were enrolled in this study. Polymerase chain reaction and Sanger sequencing of exons 23, 11, and 3 of the Abelson helper integration site 1 (AHI1), nebulin (NEB), and paired box 3 (PAX3) genes were performed, respectively. One offspring of a consanguineous marriage underwent whole-exome sequencing (WES) to look for possible causative variants. To conduct a systematic review, we thoroughly searched PubMed, Scopus, and ISI Web of Knowledge extracting relevant publications, released by April 2021. Results We examined four Iranian strabismus pedigrees with multiple affected offspring in different generations. Among these 17 participants, 10 family members had strabismus and 7 were healthy. Sanger sequencing did not reveal a causative mutation. Therefore, to further investigate, one affected offspring was chosen for WES. The WES study demonstrated two possible variants in MYO5B and DHODH genes. These genetic variants showed high allele frequency in our population and are thought to be polymorphisms in our series of Iranian families. Conclusions We demonstrated that mutations in AHI1, NEB, and PAX3 genes were not common in a series of Iranian patients with familial strabismus. Moreover, by performing WES, we revealed that two variants of uncertain significance as possible causative variants for strabismus are not related to this disease in our population.
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Affiliation(s)
- Maliheh Rahpeyma
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | | | | | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Genetic causal inference between amblyopia and perinatal factors. Sci Rep 2022; 12:18050. [PMID: 36302817 PMCID: PMC9613760 DOI: 10.1038/s41598-022-22121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/10/2022] [Indexed: 01/24/2023] Open
Abstract
Amblyopia is a common visual disorder that causes significant vision problems globally. Most non-ocular risk factors for amblyopia are closely related to the intrauterine environment, and are strongly influenced by parent-origin effects. Parent-origin perinatal factors may have a direct causal inference on amblyopia development; therefore, we investigated the causal association between perinatal factors and amblyopia risk using a one-sample Mendelian Randomization (MR) with data from the UK Biobank Cohort Data (UKBB). Four distinct MR methods were employed to analyze the association between three perinatal factors (birth weight [BW], maternal smoking, and breastfeeding) and amblyopia risk, based on the summary statistics of genome-wide association studies in the European population. The inverse variance weighting method showed an inverse causal association between BW and amblyopia risk (odds ratio, 0.48 [95% CI, 0.29-0.80]; p = 0.004). Maternal smoking and breastfeeding were not causally associated with amblyopia risk. Our findings provided a possible evidence of a significant genetic causal association between low BW and increased amblyopia risk. This evidence may highlight the potential of BW as a predictive factor for visual maldevelopment and the need for careful management of amblyopia risk in patients with low BW.
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Candidate Genes in Testing Strategies for Linkage Analysis and Bioinformatic Sorting of Whole Genome Sequencing Data in Three Small Japanese Families with Idiopathic Superior Oblique Muscle Palsy. Int J Mol Sci 2022; 23:ijms23158626. [PMID: 35955756 PMCID: PMC9369257 DOI: 10.3390/ijms23158626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/24/2022] [Accepted: 07/31/2022] [Indexed: 02/01/2023] Open
Abstract
Idiopathic superior oblique muscle palsy is a major type of paralytic, non-comitant strabismus and presents vertical and cyclo-torsional deviation of one eye against the other eye, with a large vertical fusion range and abnormal head posture such as head tilt. Genetic background is considered to play a role in its development, as patients with idiopathic superior oblique muscle palsy have varying degrees of muscle hypoplasia and, rarely, the complete absence of the muscle, that is, aplasia. In this study, whole genome sequencing was performed, and single nucleotide variations and short insertions/deletions (SNVs/InDels) were annotated in two patients each in three small families (six patients in total) with idiopathic superior oblique muscle palsy, in addition to three normal individuals in one family. At first, linkage analysis was carried out in the three families and SNVs/InDels in chromosomal loci with negative LOD scores were excluded. Next, SNVs/InDels shared by the six patients, but not by the three normal individuals, were chosen. SNVs/InDels were further narrowed down by choosing low-frequency (<1%) or non-registered SNVs/InDels in four databases for the Japanese population, and then by choosing SNVs/InDels with functional influence, leading to one candidate gene, SSTR5-AS1 in chromosome 16. The six patients were heterozygous for 13-nucleotide deletion in SSTR5-AS1, except for one homozygous patient, while the three normal individuals were wild type. Targeted polymerase chain reaction (PCR) and direct sequencing of PCR products confirmed the 13-nucleotide deletion in SSTR5-AS1. In the face of newly-registered SSTR5-AS1 13-nucleotide deletion at a higher frequency in a latest released database for the Japanese population, the skipping of low-frequency and non-registration sorting still resulted in only 13 candidate genes including SSTR5-AS1 as common variants. The skipping of linkage analysis also led to the same set of 13 candidate genes. Different testing strategies that consisted of linkage analysis and simple unintentional bioinformatics could reach candidate genes in three small families with idiopathic superior oblique muscle palsy.
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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12
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Commonly occurring genetic polymorphisms with a major impact on the risk of nonsyndromic strabismus: replication in a sample from Finland. J AAPOS 2022; 26:12.e1-12.e6. [PMID: 34856371 DOI: 10.1016/j.jaapos.2021.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/20/2022]
Abstract
PURPOSE To replicate associations between polymorphisms in the WRB and TSPAN10 genes and strabismus in an independent Finnish cohort and to calculate their population attributable risk. METHODS Polymorphisms in the WRB (rs2244352) and TSPAN10 (rs6420484) genes were investigated in individuals from the FinnGen study group who had one of three categories of strabismus, with clinical diagnoses of (1) "strabismus-all subtypes" (3,515 cases and 173,384 controls), (2) "convergent concomitant strabismus" (ICD-10 code H50.0; 737 cases and 170,976 controls), and (3) "divergent concomitant strabismus" (ICD-10 code H50.1; 1,059 cases and 170,976 controls). RESULTS The WRB polymorphism was associated with "all subtypes" of strabismus (OR = 1.08; P = 0.008) and divergent strabismus (OR = 1.11; P = 0.046) but not with convergent strabismus (P = 0.41). The WRB polymorphism had a population attributable risk of 3.4% for all strabismus subtypes and 4.7% for divergent strabismus. The TSPAN10 polymorphism was associated with all three strabismus phenotypes: "all subtypes" (OR = 1.08; P = 0.002), convergent strabismus (OR = 1.19; P = 0.001) and divergent strabismus (OR = 1.20; P =7.21E-05). The population attributable risk for the TSPAN10 polymorphism was 6.0% for any strabismus, 13.3% for convergent strabismus, and 13.9% for divergent strabismus. CONCLUSIONS Genetic association with strabismus was replicated in a Finnish cohort for two common polymorphisms. Under the assumption that these polymorphisms are independent of other risk factors, they are responsible for up to 20% of isolated cases of strabismus in Finland, similar to estimates in other European populations.
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13
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Wang Y, Chen X, Jiang T, Gu Y, Zhang X, Yuan W, Zhao A, Li R, Wang Z, Hu Z, Liu H. Expanding the phenotypic spectrum of mutations in LRP2: a novel candidate gene of non-syndromic familial comitant strabismus. J Transl Med 2021; 19:495. [PMID: 34872573 PMCID: PMC8647414 DOI: 10.1186/s12967-021-03155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Comitant strabismus (CS) is a heterogeneous disorder that is a major contributing factor to unilateral childhood-onset visual impairment. Studies have confirmed that genetic factors play an important role in the development of CS. The aim of this study was to identify the genetic cause of non-syndromic familial CS. Methods Fourteen unrelated CS families were recruited for the study. Twelve affected and 2 unaffected individuals from a large four-generation family (CS08) were selected to perform whole genome-wide linkage analysis. Parallel whole-exome sequencing (WES) was conducted in the same family (9 patients and 1 unaffected member) and 31 additional CS cases from 13 other unrelated families. Sanger sequencing was used to determine whether any of the remaining variants co-segregated with the disease phenotype in the corresponding family. Results Based on linkage analysis, CS in family CS08 mapped to a novel region of 34.17 centimorgan (cM) on chromosome 2q22.3-2q32.1 between markers D2S151 and D2S364, with a maximum log odds (LOD) score of 3.54 (theta = 0) at D2S142. Parallel WES identified a heterozygous variant, LRP2 c.335 A > G (p.Q112R), located in such a linkage interval that completely co-segregated with the disease in the family. Furthermore, another novel heterozygous variant (c.7274A > G, p.D2425G) in LRP2 that co-segregated was detected in 2 additional affected individuals from another unrelated family by WES. Both variants are predicted to be damaging by PolyPhen-2, SIFT and MutationTaster, and were absent in 100 ethnically matched normal controls. Conclusion LRP2 is a novel candidate genetic cause of non-syndromic familial CS. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03155-z.
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Affiliation(s)
- Yue Wang
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Xuejuan Chen
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Tao Jiang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Yayun Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China
| | - Xiaohan Zhang
- Department of Ophthalmology, Wuxi Children's Hospital, Wuxi, China
| | - Wenwen Yuan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Andi Zhao
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Rui Li
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Zijin Wang
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 101 Longmian Rd, NanjingNanjing, 211166, China.
| | - Hu Liu
- Department of Ophthalmology, The First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Rd, Nanjing, 210029, China.
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Candy TR, Cormack LK. Recent understanding of binocular vision in the natural environment with clinical implications. Prog Retin Eye Res 2021; 88:101014. [PMID: 34624515 PMCID: PMC8983798 DOI: 10.1016/j.preteyeres.2021.101014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Technological advances in recent decades have allowed us to measure both the information available to the visual system in the natural environment and the rich array of behaviors that the visual system supports. This review highlights the tasks undertaken by the binocular visual system in particular and how, for much of human activity, these tasks differ from those considered when an observer fixates a static target on the midline. The everyday motor and perceptual challenges involved in generating a stable, useful binocular percept of the environment are discussed, together with how these challenges are but minimally addressed by much of current clinical interpretation of binocular function. The implications for new technology, such as virtual reality, are also highlighted in terms of clinical and basic research application.
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Affiliation(s)
- T Rowan Candy
- School of Optometry, Programs in Vision Science, Neuroscience and Cognitive Science, Indiana University, 800 East Atwater Avenue, Bloomington, IN, 47405, USA.
| | - Lawrence K Cormack
- Department of Psychology, Institute for Neuroscience, and Center for Perceptual Systems, The University of Texas at Austin, Austin, TX, 78712, USA.
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15
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Shen T, Qiu X, Lin X, Lin J, Li X, Chen Q, Pan L, Wang Z, Shen H, Zhang Q, Yan J. Missense mutation in the PAX6 gene can cause a complex mild variable phenotype predominated by concomitant strabismus. Ophthalmic Genet 2021; 43:88-96. [PMID: 34344282 DOI: 10.1080/13816810.2021.1961283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE We aimed to reveal the underlying genetic defect in a multigenerational Chinese family with autosomal dominant concomitant strabismus complicated by multiple ocular developmental abnormalities. METHODS Comprehensive ophthalmic examinations were performed in 14 patients and 24 healthy family members. Whole exome sequencing was performed, and Sanger sequencing was used to confirm the probable mutation in all the family members. RESULTS Concomitant strabismus was the predominant phenotype in the affected family members, although the patients also exhibited variable phenotypes, including nystagmus, mild iris abnormalities, myopia, cataract, and coloboma. An R208W mutation in PAX6 was identified as the pathogenic mutation in the affected family members. CONCLUSIONS We recommend considering PAX6 as a candidate gene in the diagnostic screen for familial concomitant strabismus in order to avoid missed diagnosis of the mild ocular abnormalities. Careful examinations of mild ocular phenotypes are necessary for an accurate diagnosis of varied ocular abnormalities in the families with the PAX6 mutation, and proper diagnosis can facilitate genetic and clinical counseling for affected patients.
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Affiliation(s)
- Tao Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xuan Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoming Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiuling Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qiwen Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Liuqing Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhonghao Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Yan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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16
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Identification of Possible Risk Variants of Familial Strabismus Using Exome Sequencing Analysis. Genes (Basel) 2021; 12:genes12010075. [PMID: 33435129 PMCID: PMC7827096 DOI: 10.3390/genes12010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022] Open
Abstract
PURPOSE To investigate candidate genes associated with familial strabismus and propose a theory of their interaction in familial strabismus associated with early neurodevelopment. METHODS Eighteen families, including 53 patients diagnosed with strabismus and 34 unaffected family members, were analyzed. All patients with strabismus and available unaffected family members were evaluated using whole exome sequencing. The primary outcome was to identify rare occurring variants among affected individuals and investigate the evidence of their genetic heterogeneity. These results were compared with exome sequencing analysis to build a comprehensive genetic profile of the study families. RESULTS We observed 60 variants from 58 genes in 53 patients diagnosed with strabismus. We prioritized the most credible risk variants, which showed clear segregation in family members affected by strabismus. As a result, we found risk variants in four genes (FAT3, KCNH2, CELSR1, and TTYH1) in five families, suggesting their role in development of familial strabismus. In other families, there were several rare genetic variants in affected cases, but we did not find clear segregation pattern across family members. CONCLUSION Genomic sequencing holds great promise in elucidating the genetic causes of strabismus; further research with larger cohorts or other related approaches are warranted.
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17
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Whitman MC, Di Gioia SA, Chan WM, Gelber A, Pratt BM, Bell JL, Collins TE, Knowles JA, Armoskus C, Pato M, Pato C, Shaaban S, Staffieri S, MacKinnon S, Maconachie GDE, Elder JE, Traboulsi EI, Gottlob I, Mackey DA, Hunter DG, Engle EC. Recurrent Rare Copy Number Variants Increase Risk for Esotropia. Invest Ophthalmol Vis Sci 2021; 61:22. [PMID: 32780866 PMCID: PMC7443120 DOI: 10.1167/iovs.61.10.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To determine whether rare copy number variants (CNVs) increase risk for comitant esotropia. Methods CNVs were identified in 1614 Caucasian individuals with comitant esotropia and 3922 Caucasian controls from Illumina SNP genotyping using two Hidden Markov model (HMM) algorithms, PennCNV and QuantiSNP, which call CNVs based on logR ratio and B allele frequency. Deletions and duplications greater than 10 kb were included. Common CNVs were excluded. Association testing was performed with 1 million permutations in PLINK. Significant CNVs were confirmed with digital droplet polymerase chain reaction (ddPCR). Whole genome sequencing was performed to determine insertion location and breakpoints. Results Esotropia patients have similar rates and proportions of CNVs compared with controls but greater total length and average size of both deletions and duplications. Three recurrent rare duplications significantly (P = 1 × 10−6) increase the risk of esotropia: chromosome 2p11.2 (hg19, 2:87428677-87965359), spanning one long noncoding RNA (lncRNA) and two microRNAs (OR 14.16; 95% confidence interval [CI] 5.4–38.1); chromosome 4p15.2 (hg19, 4:25554332-25577184), spanning one lncRNA (OR 11.1; 95% CI 4.6–25.2); chromosome 10q11.22 (hg19, 10:47049547-47703870) spanning seven protein-coding genes, one lncRNA, and four pseudogenes (OR 8.96; 95% CI 5.4–14.9). Overall, 114 cases (7%) and only 28 controls (0.7%) had one of the three rare duplications. No case nor control had more than one of these three duplications. Conclusions Rare CNVs are a source of genetic variation that contribute to the genetic risk for comitant esotropia, which is likely polygenic. Future research into the functional consequences of these recurrent duplications may shed light on the pathophysiology of esotropia.
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Affiliation(s)
- Mary C Whitman
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Alon Gelber
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Brandon M Pratt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Jessica L Bell
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Thomas E Collins
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - James A Knowles
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Christopher Armoskus
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Michele Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Present address: Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Sandra Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Gail D E Maconachie
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Elias I Traboulsi
- Department of Pediatric Ophthalmology and Strabismus, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia.,Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - David G Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Elizabeth C Engle
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
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18
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Ye XC, Roslin NM, Paterson AD, Lyons CJ, Pegado V, Richmond P, Shyr C, Fornes O, Han X, Higginson M, Ross CJ, Giaschi D, Gregory-Evans C, Patel MS, Wasserman WW. Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region. J Med Genet 2020; 59:46-55. [PMID: 33257509 PMCID: PMC8685624 DOI: 10.1136/jmedgenet-2020-107226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/05/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022]
Abstract
Strabismus is a common condition, affecting 1%–4% of individuals. Isolated strabismus has been studied in families with Mendelian inheritance patterns. Despite the identification of multiple loci via linkage analyses, no specific genes have been identified from these studies. The current study is based on a seven-generation family with isolated strabismus inherited in an autosomal dominant manner. A total of 13 individuals from a common ancestor have been included for linkage analysis. Among these, nine are affected and four are unaffected. A single linkage signal has been identified at an 8.5 Mb region of chromosome 14q12 with a multipoint LOD (logarithm of the odds) score of 4.69. Disruption of this locus is known to cause FOXG1 syndrome (or congenital Rett syndrome; OMIM #613454 and *164874), in which 84% of affected individuals present with strabismus. With the incorporation of next-generation sequencing and in-depth bioinformatic analyses, a 4 bp non-coding deletion was prioritised as the top candidate for the observed strabismus phenotype. The deletion is predicted to disrupt regulation of FOXG1, which encodes a transcription factor of the Forkhead family. Suggestive of an autoregulation effect, the disrupted sequence matches the consensus FOXG1 and Forkhead family transcription factor binding site and has been observed in previous ChIP-seq studies to be bound by Foxg1 in early mouse brain development. Future study of this specific deletion may shed light on the regulation of FOXG1 expression and may enhance our understanding of the mechanisms contributing to strabismus and FOXG1 syndrome.
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Affiliation(s)
- Xin Cynthia Ye
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, Hospital for Sick Children Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Andrew D Paterson
- The Centre for Applied Genomics, Hospital for Sick Children Research Institute, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher J Lyons
- BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Victor Pegado
- Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip Richmond
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Casper Shyr
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - XiaoHua Han
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Higginson
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin J Ross
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Deborah Giaschi
- BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl Gregory-Evans
- Department of Ophthalmology and Visual Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Millan S Patel
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada .,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada .,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, British Columbia, Canada
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19
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Senaldi L, Smith-Raska M. Evidence for germline non-genetic inheritance of human phenotypes and diseases. Clin Epigenetics 2020; 12:136. [PMID: 32917273 PMCID: PMC7488552 DOI: 10.1186/s13148-020-00929-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
It is becoming increasingly apparent that certain phenotypes are inherited across generations independent of the information contained in the DNA sequence, by factors in germ cells that remain largely uncharacterized. As evidence for germline non-genetic inheritance of phenotypes and diseases continues to grow in model organisms, there are fewer reports of this phenomenon in humans, due to a variety of complications in evaluating this mechanism of inheritance in humans. This review summarizes the evidence for germline-based non-genetic inheritance in humans, as well as the significant challenges and important caveats that must be considered when evaluating this process in human populations. Most reports of this process evaluate the association of a lifetime exposure in ancestors with changes in DNA methylation or small RNA expression in germ cells, as well as the association between ancestral experiences and the inheritance of a phenotype in descendants, down to great-grandchildren in some cases. Collectively, these studies provide evidence that phenotypes can be inherited in a DNA-independent manner; the extent to which this process contributes to disease development, as well as the cellular and molecular regulation of this process, remain largely undefined.
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Affiliation(s)
- Liana Senaldi
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA. .,Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA.
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20
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Plotnikov D, Shah RL, Rodrigues JN, Cumberland PM, Rahi JS, Hysi PG, Atan D, Williams C, Guggenheim JA. A commonly occurring genetic variant within the NPLOC4-TSPAN10-PDE6G gene cluster is associated with the risk of strabismus. Hum Genet 2019; 138:723-737. [PMID: 31073882 PMCID: PMC6611893 DOI: 10.1007/s00439-019-02022-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/20/2019] [Indexed: 12/31/2022]
Abstract
Strabismus refers to an abnormal alignment of the eyes leading to the loss of central binocular vision. Concomitant strabismus occurs when the angle of deviation is constant in all positions of gaze and often manifests in early childhood when it is considered to be a neurodevelopmental disorder of the visual system. As such, it is inherited as a complex genetic trait, affecting 2-4% of the population. A genome-wide association study (GWAS) for self-reported strabismus (1345 cases and 65,349 controls from UK Biobank) revealed a single genome-wide significant locus on chromosome 17q25. Approximately 20 variants across the NPLOC4-TSPAN10-PDE6G gene cluster and in almost perfect linkage disequilibrium (LD) were most strongly associated (lead variant: rs75078292, OR = 1.26, p = 2.24E-08). A recessive model provided a better fit to the data than an additive model. Association with strabismus was independent of refractive error, and the degree of association with strabismus was minimally attenuated after adjustment for amblyopia. The association with strabismus was replicated in an independent cohort of clinician-diagnosed children aged 7 years old (116 cases and 5084 controls; OR = 1.85, p = 0.009). The associated variants included 2 strong candidate causal variants predicted to have functional effects: rs6420484, which substitutes tyrosine for a conserved cysteine (C177Y) in the TSPAN10 gene, and a 4-bp deletion variant, rs397693108, predicted to cause a frameshift in TSPAN10. The population-attributable risk for the locus was approximately 8.4%, indicating an important role in conferring susceptibility to strabismus.
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Affiliation(s)
- Denis Plotnikov
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Rupal L Shah
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Jamille N Rodrigues
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road, Bristol, BS8 1NU, UK
| | - Phillippa M Cumberland
- Life Course Epidemiology and Biostatistics Section, Institute of Child Health, University College London, London, WC1N 1EH, UK
- Ulverscroft Vision Research Group, University College London Institute of Child Health, London, WC1N 1EH, UK
| | - Jugnoo S Rahi
- Life Course Epidemiology and Biostatistics Section, Institute of Child Health, University College London, London, WC1N 1EH, UK
- Ulverscroft Vision Research Group, University College London Institute of Child Health, London, WC1N 1EH, UK
- University College London Great Ormond Street Institute of Child Health, London, WC1N 3JH, UK
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and University College London Institute of Ophthalmology, London, WC1E 6BT, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London, SE1 7EH, UK
| | - Denize Atan
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road, Bristol, BS8 1NU, UK
| | - Cathy Williams
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road, Bristol, BS8 1NU, UK.
| | - Jeremy A Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK.
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Zhang W, Chen Z, Yin Q, Zhang D, Racowsky C, Zhang Y. Maternal-biased H3K27me3 correlates with paternal-specific gene expression in the human morula. Genes Dev 2019; 33:382-387. [PMID: 30808660 PMCID: PMC6446541 DOI: 10.1101/gad.323105.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022]
Abstract
In this study from Zhang et al., the authors found that H3K27me3 is strongly biased toward the maternal allele with some associated with DNA methylation–independent paternally expressed genes (PEGs) in human morulae. Their findings uncover the H3K27me3 landscape and establish a correlation between maternal-biased H3K27me3 and PEGs in human morulae. Genomic imprinting is an epigenetic mechanism by which genes are expressed in a parental origin–dependent manner. We recently discovered that, like DNA methylation, oocyte-inherited H3K27me3 can also serve as an imprinting mark in mouse preimplantation embryos. In this study, we found H3K27me3 is strongly biased toward the maternal allele with some associated with DNA methylation–independent paternally expressed genes (PEGs) in human morulae. The H3K27me3 domains largely overlap with DNA partially methylated domains (PMDs) and occupy developmental gene promoters. Thus, our study not only reveals the H3K27me3 landscape but also establishes a correlation between maternal-biased H3K27me3 and PEGs in human morulae.
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Affiliation(s)
- Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Qiangzong Yin
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Dan Zhang
- Center for Infertility and Reproductive Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, P.R. China
| | - Catherine Racowsky
- Center for Infertility and Reproductive Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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