Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of Gene Association Studies Testing
2.2. Data Extraction
2.3. Quanlity Assessment and Control of Risk of Bias
2.4. Genetic Meta-Analysis
2.5. Functional Annotation of Gene Variants
2.6. Power Analysis
3. Results
3.1. Studies Testing XFS/XFG-Associated Genes in PDS/PG
3.2. Genetic Association of LOXL1 with PDS/PG
3.3. Risk of Bias Assessments and Sensitivity Analysis
3.4. Functional Relevance of the LOXL1 Coding Variants
3.5. Power Analysis
4. Discussion
5. Conclusions and Future Directions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
Appendix A. Newcastle–Ottawa Quality Assessment Scale for Case Control Studies
- NEWCASTLE—OTTAWA QUALITY ASSESSMENT SCALE
- CASE CONTROL STUDIES
- (accessed via http://www.ohri.ca/programs/clinical_epidemiology/oxford.asp)
- Note: A study can be awarded a maximum of one star for each numbered item within the Selection and Exposure categories. A maximum of two stars can be given for Comparability.
- Selection
- (1)
- Is the case definition adequate?
- (a)
- Yes, with independent validation.
- (b)
- Yes, e.g., record linkage or based on self-reports.
- (c)
- No description.
- (2)
- Representativeness of the cases
- (a)
- Consecutive or obviously representative series of cases.
- (b)
- Potential for selection biases or not stated.
- (3)
- Selection of Controls
- (a)
- Community controls.
- (b)
- Hospital controls.
- (c)
- No description.
- (4)
- Definition of controls
- (a)
- No history of disease (endpoint).
- (b)
- No description of source.
- Comparability
- (1)
- Comparability of cases and controls on the basis of the design or analysis
- (a)
- Study controls for _______________ (select the most important factor: ethnicity).
- (b)
- Study controls for any additional factor (these criteria could be modified to indicate specific control for a second important factor).
- Exposure
- (1)
- Ascertainment of exposure
- (a)
- Secure record (e.g., surgical records).
- (b)
- Structured interview where blind to case/control status.
- (c)
- Interview not blinded to case/control status.
- (d)
- Written self-report or medical record only.
- (e)
- No description.
- (2)
- Same method of ascertainment for cases and controls
- (a)
- Yes.
- (b)
- No.
- (3)
- Non-response rate
- (a)
- Same rate for both groups.
- (b)
- Non respondents described.
- (c)
- Rate different and no designation.
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Author | Country | Ethnicity | Phenotypes | Sample Size | Age of Cases/Control | Studied SNPs | Ref. | |
---|---|---|---|---|---|---|---|---|
Case | Control | |||||||
Giardina, E., et al. (2014) | Italy | Caucasians | PDS/PG | 84 | 200 | 48.0 ± 4.9 / 46.7 ± 5.2 | rs1048661, rs3825942, rs2165241, rs2304722, rs8818, rs3522 | [39] |
Wolf, C., et al. (2010) | German | Caucasians | PG | 88 | 280 | 53.8 ± 13.5 / 66 ± 13 | rs2165241, rs1048661, rs3825942, rs893818, rs1530169, rs750460, rs1284049 | [38] |
Rao, K.N., et al. (2008) | USA | Caucasians | PDS+PG | 78 | 108 | Not reported | rs1048661, rs3825942, rs2165241 | [37] |
SNP | Position (GRCh38) | Functional Relevance | Author (Year) | Phenotypes Studied | Sample Size | Effect Allele | Ref. Allele | A1 Frequency | ||
---|---|---|---|---|---|---|---|---|---|---|
Case | Control | Cases | Controls | |||||||
rs1048661 | Chr15:73927205 | Exon 1 Arg141Leu | [39] | PDS/PG | 84 | 200 | T | G | 0.340 | 0.290 |
[38] | PG | 88 | 280 | T | G | 0.369 | 0.340 | |||
[37] | PDS + PG | 78 | 108 | T | G | 0.326 | 0.276 | |||
rs3825942 | Chr15:73927241 | Exon 1 Gly153Asp | [39] | PDS/PG | 84 | 200 | A | G | 0.160 | 0.200 |
[38] | PG | 88 | 280 | A | G | 0.119 | 0.154 | |||
[37] | PDS + PG | 78 | 108 | A | G | 0.148 | 0.178 | |||
rs2165241 | Chr15:73929861 | Intron 1 | [39] | PDS/PG | 84 | 200 | T | C | 0.490 | 0.500 |
[38] | PG | 88 | 280 | T | C | 0.488 | 0.491 | |||
[37] | PDS + PG | 78 | 108 | T | C | 0.514 | 0.471 |
Author (Year of Publication) | Newcastle–Ottawa Quality Assessment Scale for Case-Control Studies | Reference | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Selection | Comparability | Exposure | Total Stars | |||||||
1 | 2 | 3 | 4 | 1 | 1 | 2 | 3 | |||
Giardina, E., et al. (2014) | a | a | b | a | age, sex, ethnicity | a | a | a | 8 | [39] |
Wolf, C., et al. (2010) | a | a | b | a | age, sex, ethnicity | a | a | a | 8 | [38] |
Rao, K.N., et al. (2008) | a | a | b | a | not reported | a | a | a | 7 | [37] |
SNP | Position | Gene | Location | SIFT | PolyPhen | CADD | RegulomeDB * | eQTL Tissue (p)—Allele for Higher Expression |
---|---|---|---|---|---|---|---|---|
rs1048661 | Chr15:73927205 | LOXL1 | Exon 1 Arg141Leu | Deleterious | Benign | 24.4 | 1f | Cells—Cultured fibroblasts (1.40 × 10−12)—G |
rs3825942 | Chr15:73927241 | LOXL1 | Exon 1 Gly153Asp | Deleterious | Benign | 22.9 | 1b | Cells—Cultured fibroblasts (8.50 × 10−37)—A |
rs2165241 | Chr15:73929861 | LOXL1 | Intron 1 | na | na | 9.749 | 1f | Pituitary (1.30 × 10−10)—C |
PDS/PG | XFS/XFG | |
---|---|---|
Comparable manifestations | ||
Prevalence | More common in Caucasians | More common in Caucasians |
Cornea | Krukenberg’s spindle | Occasional endothelial pigment |
Iris | Mid-peripheral iris transillumination defects | Transillumination at pupillary border |
Iridocorneal angle | Open, posterior iris bowing, TM pigmentation | Open, TM pigmentation |
Different manifestations | ||
Age of onset | Young | Elderly |
Gender preference | Male | Female |
Inheritance | Autosomal dominant, autosomal recessive, or sporadic | Undefined |
Anterior chamber | Floating pigment | Quiet |
Exfoliation material | None | Visible on pupillary border and anterior lens |
Lens | Normal | Exfoliation material, weak zonules |
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Rong, S.; Yu, X. Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis. Genes 2024, 15, 161. https://doi.org/10.3390/genes15020161
Rong S, Yu X. Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis. Genes. 2024; 15(2):161. https://doi.org/10.3390/genes15020161
Chicago/Turabian StyleRong, Shisong, and Xinting Yu. 2024. "Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis" Genes 15, no. 2: 161. https://doi.org/10.3390/genes15020161
APA StyleRong, S., & Yu, X. (2024). Lack of Association between LOXL1 Variants and Pigment Dispersion Syndrome/Pigmentary Glaucoma: A Meta-Analysis. Genes, 15(2), 161. https://doi.org/10.3390/genes15020161