| Literature DB >> 25648366 |
Valentina Bravatà1, Luigi Minafra2, Giusi I Forte3, Francesco P Cammarata4, Michele Saporito5, Filippo Boniforti6, Domenico Lio7, Maria C Gilardi8,9,10, Cristina Messa11,12,13.
Abstract
BACKGROUND: Osteoarthritis (OA) is a degenerative joints disorder influenced by genetic predisposition. We reported that rs11718863 DVWA SNP was represented in Sicilian with a more severe Kellgren and Lawrence (KL) radiographic grade, displaying its predictive role as OA marker progression. Here, we describe the DVWA SNPs: rs11718863, rs7639618, rs7651842, rs7639807 and rs17040821 probably able to induce protein functional changes.Entities:
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Year: 2015 PMID: 25648366 PMCID: PMC4323016 DOI: 10.1186/s13104-015-0987-1
Source DB: PubMed Journal: BMC Res Notes ISSN: 1756-0500
Haplotype and allele frequencies used for Linkage Disequilibrium analyses
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Figure 1This figure display the r2 LD plot, where the perfect LD between SNPs pair is (r2 = 1) dark marked, whereas the LD absence (r2 = 0) is white marked.
Genetic analysis results
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| rs11718863 | |||||||||
| TT | WT | 41 | 67 | T = 100 | 82 | 72 | 72 | T = 100 | 72 |
| TA | H | 18 | 30 | A = 22 | 18 | 25 | 25 | A = 56 | 28 |
| AA | MUT | 2 | 3 | 3 | 3 | ||||
| rs7639618 | |||||||||
| GG | WT | 41 | 67 | G = 100 | 82 | 72 | 72 | G = 144 | 72 |
| GA | H | 18 | 30 | A = 22 | 18 | 25 | 25 | A = 56 | 28 |
| AA | MUT | 2 | 3 | 3 | 3 | ||||
| rs7651842 | |||||||||
| AA | WT | 44 | 72,1 | A = 103 | 84,4 | 85 | 85 | A = 170 | 85 |
| AG | H | 15 | 24,6 | G = 19 | 15,6 | 14 | 14 | G = 30 | 15 |
| GG | MUT | 2 | 3,3 | 1 | 1 | ||||
| rs7639807 | |||||||||
| GG | WT | 44 | 72,1 | A = 103 | 84,4 | 85 | 85 | G = 170 | 85 |
| GA | H | 15 | 24,6 | G = 19 | 15,6 | 14 | 14 | A = 30 | 15 |
| AA | MUT | 2 | 3,3 | 1 | 1 | ||||
| rs17040821 | |||||||||
| CC | WT | 44 | 72,1 | C = 103 | 84,4 | 85 | 85 | C = 170 | 85 |
| CT | H | 15 | 24,6 | T = 19 | 15,6 | 14 | 14 | T = 30 | 15 |
| TT | MUT | 2 | 3,3 | 1 | 1 |
n = number of patients.
Genetic analysis results according to KL grading groups
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| rs11718863 | ||||||||||
| TT | WT | 15 | 75 | 17 | 81 | 9 | 45 | |||
| TA | H | 4 | 20 | 0,33 | 4 | 19 | 0,63 | 10 | 50 | 0,39 |
| AA | MUT | 1 | 5 | 0 | 0 | 1 | 5 | |||
| rs7639618 | ||||||||||
| GG | WT | 15 | 75 | 17 | 81 | 9 | 45 | |||
| GA | H | 4 | 20 | 0,33 | 4 | 19 | 0,63 | 10 | 50 | 0,39 |
| AA | MUT | 1 | 5 | 0 | 0 | 1 | 5 | |||
| rs7651842 | ||||||||||
| AA | WT | 14 | 70 | 15 | 71,4 | 15 | 75 | |||
| AG | H | 6 | 30 | 0,43 | 5 | 23,8 | 0,51 | 4 | 20 | 0,33 |
| GG | MUT | 0 | 1 | 4,8 | 1 | 5 | ||||
| rs7639807 | ||||||||||
| GG | WT | 14 | 70 | 15 | 71,4 | 15 | 75 | |||
| GA | H | 6 | 30 | 0,43 | 5 | 23,8 | 0,51 | 4 | 20 | 0,33 |
| AA | MUT | 0 | 1 | 4,8 | 1 | 5 | ||||
| rs17040821 | ||||||||||
| CC | WT | 14 | 70 | 15 | 71,4 | 15 | 75 | |||
| CT | H | 6 | 30 | 0,43 | 5 | 23,8 | 0,51 | 4 | 20 | 0,33 |
| TT | MUT | 0 | 1 | 4,8 | 1 | 5 | ||||
Genotype and alleles statistical association with KL grade
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| A | 15 | 75 | 5 | 25 | A | 34 | 85 | 6 | 15 | |||
| rs11718863 | B | 17 | 81 | 4 | 19 | 0,03 | B | 38 | 90,5 | 4 | 9,5 | 0,04 |
| C | 9 | 45 | 11 | 55 | C | 28 | 70 | 12 | 30 | |||
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| A | 15 | 75 | 5 | 25 | A | 34 | 85 | 6 | 15 | |||
| rs7639618 | B | 17 | 81 | 4 | 19 | 0,03 | B | 38 | 90,5 | 4 | 9,5 | 0,04 |
| C | 9 | 45 | 11 | 55 | C | 28 | 70 | 12 | 30 | |||
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| A | 14 | 70 | 6 | 30 | A | 34 | 85 | 6 | 25 | |||
| rs7651842 | B | 15 | 71,4 | 6 | 28,6 | 0,936 | B | 35 | 83,3 | 7 | 16,7 | 0,9713 |
| C | 15 | 75 | 5 | 25 | C | 34 | 85 | 6 | 25 | |||
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| A | 14 | 70 | 6 | 30 | A | 34 | 85 | 6 | 25 | |||
| rs7639807 | B | 15 | 71,4 | 6 | 28,6 | 0,936 | B | 35 | 83,3 | 7 | 16,7 | 0,9713 |
| C | 15 | 75 | 5 | 25 | C | 34 | 85 | 6 | 25 | |||
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| A | 14 | 70 | 6 | 30 | A | 34 | 85 | 6 | 25 | |||
| rs17040821 | B | 15 | 71,4 | 6 | 28,6 | 0,936 | B | 35 | 83,3 | 7 | 16,7 | 0,9713 |
| C | 15 | 75 | 5 | 25 | C | 34 | 85 | 6 | 25 | |||
*Chi-Squared Test.
Figure 2SNPs alleles frequencies and MAF values for individuals of various geographic areas.