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SNP located in an AluJb repeat downstream of TMCO1, rs4657473, is protective for POAG in African Americans
  1. Lana Verkuil1,
  2. Ian Danford1,
  3. Maxwell Pistilli1,
  4. David W Collins1,2,
  5. Harini V Gudiseva1,
  6. Ben T Trachtman1,
  7. Jie He1,
  8. Sonika Rathi1,
  9. Naqi Haider1,
  10. Gui-shuang Ying3,
  11. Venkata R M Chavali1,
  12. Joan Marie O'Brien1
  1. 1 Ophthalmology, Scheie Eye Institute, Philadelphia, Pennsylvania, USA
  2. 2 Emeryville, California, USA
  3. 3 Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
  1. Correspondence to Dr Venkata R M Chavali, Ophthalmology, Scheie Eye Institute, Philadelphia, PA 19104, USA; vchavali{at}


Aims To determine the association of single nucleotide polymorphisms (SNPs) downstream from the TMCO1 gene with primary open-angle glaucoma (POAG) in African Americans (AA).

Methods AA subjects were recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study from the Scheie Eye Institute and its satellite sites in Philadelphia. A region containing an AluJb repeat and seven SNPs, including rs4656461 near the TMCO1 gene, were PCR-Sanger sequenced from POAAGG cases (n=1537) and controls (n=1570). Association between POAG and SNPs near TMCO1 was investigated by logistic regression analysis. Phenotypic trait associations with these SNPs were assessed by analysis of variance. Electrophoretic mobility shift assay (EMSA) was performed to assess the affinity of human T-box 5 (TBX5) protein for a predicted binding motif in the TMCO1 region. Dual Luciferase assays were performed by transfecting recombinant plasmids containing the region surrounding the above SNPs in HEK293T and trabecular meshwork cells.

Results The SNP rs4657473 (C>T) was associated with POAG; the TT genotype was protective (OR 0.20, 95% CI 0.09 to 0.42; p<0.001). No significant associations were found between the TMCO1 variants and phenotypic traits. EMSA confirmed the affinity of TBX5 for a predicted binding motif containing TMCO1 SNP rs4657475. Luciferase assays demonstrated a regulatory function for the genomic region around SNP rs4656561, located within AluJb repeat.

Conclusion Our results demonstrate that a SNP downstream of TMCO1, rs4657473, is associated with POAG in an AA population. Our studies suggest a regulatory role for the previously POAG-associated locus near the TMCO1 gene that may affect gene expression.

  • genetics
  • pathology
  • primary open-angle glaucoma
  • TMCO1
  • AluJb repeat

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  • Contributors LV, VRMC, MP, JMO and G-sY designed the study. LV, SR, NH, ID, JH, HVG, BTT and DWC performed experiments and interpreted data. LV, VRMC, G-sY, MP and JMO wrote the manuscript.

  • Funding This work was supported by the National Eye Institute, Bethesda, Maryland (grant #1RO1EY023557-01) and the Department of Ophthalmology at the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. Funds also come from the F.M. Kirby Foundation, Research to Prevent Blindness, The Paul and Evanina Bell Mackall Foundation Trust and the National Eye Institute, National Institutes of Health, Department of Health and Human Services, under eyeGENETM and contract Nos. HHSN260220700001C and HHSN263201200001C.

  • Disclaimer The sponsor or funding organisation had no role in the design or conduct of this research.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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