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. Author manuscript; available in PMC: 2015 Aug 20.
Published in final edited form as: Ophthalmic Genet. 2014 Feb 20;37(1):109–110. doi: 10.3109/13816810.2014.889172

Linkage analysis of high-density SNPs confirms keratoconus locus at 5q chromosomal region

Yelena Bykhovskaya 1,2, Xiaohui Li 1,3, Kent D Taylor 3, Talin Haritunians 4, Jerome I Rotter 3, Yaron S Rabinowitz 1,2
PMCID: PMC4139481  NIHMSID: NIHMS568580  PMID: 24555746

Letter to the Editor:

Dear Dr. Traboulsi,

Previously we reported on a two-stage genome-wide linkage scan using microsatellite markers in a four-generation Caucasian family with autosomal-dominant keratoconus[1]which identified a peak of 8.2 MB with LOD of 3.53 located at the 5q14.1-q21.1 chromosomal region [2]. To confirm this linkage region we performed a second scan using high density single nucleotide polymorphisms (SNPs) and tested them for genetic linkage and association with keratoconus in twenty seven family members including those diagnosed with keratoconus (Figure 1A). The study was approved by the Institutional Review Board (IRB) and conducted in accordance with the provisions of the Declaration of Helsinki.525K SNPs (HumanOmniExpress BeadChip, Illumina, Inc.)were tested for linkage under an autosomal dominant model with the same parameters (phenocopy rate of 0.01 and penetrance of 0.5) and pedigree-splitting method as was described in our original paper[2] using Merlin 1.1.2[3]. Maximum Lod score of 2.49 was calculated at approximately 99 MB region of chromosome 5 overlapping the original linkage peak (Figure 1B). In addition, based on Lod scores greater than 2 we narrowed down linkage region to 5MB between 95MB to 100MB located at 5q15-5q21.1.

Figure 1.

Figure 1

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A. Family structure of the four generation Caucasian family with keratoconus. * denotes genotyped individuals. B. Results of parametric linkage analysis.

We also tested for genetic association 445 SNPs located in this region using generalized estimation equation models accounting for familial correlations (GWAF) [4]. Association tests under the dominant model identified 32 SNPs with p values ranging from 0.05 to 0.004; three associated SNPs were located within 50 KB of known genes. These SNPs were rs3853203 (p=0.01), rs39597 (p=0.03), and rs11738579 (p=0.05) located in or adjacent to genes CAST,RIOK2, and RHOBTB3, respectively. All three genes were present in the human keratoconus cornea cDNA library constructed by our group [5]; however, variants in CAST gene were implicated in genetic susceptibility to keratoconus in family and case-control panels by our group [6] making it a top candidate gene in the region.

In short, confirmation of this linkage locus makes 5q chromosomal region the strongest candidate for potential identification of a genetic defect associated with familiar nonsyndromic keratoconus in this family as well as possibly in other families with familiar keratoconus [7 8].

Best wishes,

Acknowledgments

This work was supported by National Eye Institute grant NEI 09052 and the Eye Defects Research Foundation Inc. (to Y.S.R.); NCRR grant M01-RR00425 and Southern California Diabetes Endocrinology Research Center grant DK063491 (to K.D.T).

References

  • 1.Rabinowitz YS, Maumenee IH, Lundergan MK, et al. Molecular genetic analysis in autosomal dominant keratoconus. Cornea. 1992;11(4):302–308. doi: 10.1097/00003226-199207000-00005. [DOI] [PubMed] [Google Scholar]
  • 2.Tang YG, Rabinowitz YS, Taylor KD, et al. Genomewide linkage scan in a multigeneration Caucasian pedigree identifies a novel locus for keratoconus on chromosome 5q14.3-q21.1. Genet Med. 2005;7(6):397–405. doi: 10.1097/01.gim.0000170772.41860.54. [DOI] [PubMed] [Google Scholar]
  • 3.Abecasis GR, Cherny SS, Cookson WO, et al. Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30(1):97–101. doi: 10.1038/ng786. doi: 10.1038/ng786[published Online First: Epub Date]|. [DOI] [PubMed] [Google Scholar]
  • 4.Chen MH, Yang Q. GWAF: an R package for genome-wide association analyses with family data. Bioinformatics. 2010;26(4):580–581. doi: 10.1093/bioinformatics/btp710. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Rabinowitz YS, Dong L, Wistow G. Gene expression profile studies of human keratoconus cornea for NEIBank: a novel cornea-expressed gene and the absence of transcripts for aquaporin 5. Invest Ophthalmol Vis Sci. 2005;46(4):1239–1246. doi: 10.1167/iovs.04-1148. [DOI] [PubMed] [Google Scholar]
  • 6.Li X, Bykhovskaya Y, Tang YG, et al. An association between the calpastatin (CAST) gene and keratoconus. Cornea. 2013;32(5):696–701. doi: 10.1097/ICO.0b013e3182821c1c. doi: 10.1097/ICO.0b013e3182821c1c[published Online First: Epub Date]|. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Li X, Rabinowitz YS, Tang YG, et al. Two-stage genome-wide linkage scan in keratoconus sib pair families. Invest Ophthalmol Vis Sci. 2006;47(9):3791–3795. doi: 10.1167/iovs.06-0214. [DOI] [PubMed] [Google Scholar]
  • 8.Bisceglia L, De Bonis P, Pizzicoli C, et al. Linkage analysis in keratoconus: replication of locus 5q21.2 and identification of other suggestive Loci. Invest Ophthalmol Vis Sci. 2009;50(3):1081–1086. doi: 10.1167/iovs.08-2382. [DOI] [PubMed] [Google Scholar]

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