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G. Wang, K. L. Spencer, W. K. Scott, B. L. Court, S. G. Schwartz, J. L. Kovach, A. Agarwal, E. A. Postel, J. L. Haines, M. A. Pericak-Vance; Analysis of the Indel at 3’UTR of ARMS2 Gene and Its Effects on mRNA Stability. Invest. Ophthalmol. Vis. Sci. 2009;50(13):3452.
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Controversy remains as to the responsible gene at the chromosome 10q26 locus for age-related macular degeneration (AMD), and statistical genetic analysis is confounded due to the strong linkage disequilibrium across this region. Functional analysis of the related genetic variations and biological studies on the genes ARMS2 and HTRA1 can help to solve this puzzle. Recently Fritsche et al reported that AMD is associated with unstable ARMS2 transcripts caused mainly by a complex insertion/deletion (indel; consisting of a 443bp deletion and an adjacent 54bp insertion) in its 3’UTR. To validate this indel, we analyzed our samples by sequencing.
Reverse transcription-PCR (RT-PCR) and sequencing were used to analyze this 3’UTR indel in ARMS2.
No indel was found in the 4 samples homozygous for allele G at the ARMS2 AMD-associated SNP rs10490924 while indels were found in all 5 samples homozygous for the risk allele T. Interestingly, in the 5 samples heterozygous at rs10490924, 2 were homozygous for the indels, whereas the other 3 were heterozygous for the indels. We also found that this indel is even more complex and composed of two side-by-side indels separated by 17bp: (1) 9bp deletion with 10bp insertion; (2) 417bp deletion with 27bp insertion.
We suggest that this indel in the 3’UTR of ARMS2 could be an additional risk allele that is incompletely correlated with rs10490924 polymorphism. We are currently analyzing this complex indel in a large case-control dataset and evaluating its effects on ARMS2 mRNA level.
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