Table 1 Primers used in the study
Gene
|
SNP
|
1st-PCRP
|
2nd-PCRP
|
UEP_DIR
|
UEP_SEQ
|
COL9A1
|
rs3806093
|
ACGTTGGATGAAGGACTCCAGTTTGAACAC
|
ACGTTGGATGTGAACATCTAGGTTTCTGAC
|
R
|
cGGTGTTTTCAAACACAACACTTA
|
|
rs603410
|
ACGTTGGATGCCTTACTATAGTCTTACTC
|
ACGTTGGATGGCAGTTAGCAGGAAGTTAGG
|
R
|
ggacTAATCACAACAGGCAGATCTT
|
|
rs621347
|
ACGTTGGATGCCAGGACAACATGTTAGGAC
|
ACGTTGGATGGTCAGATGTTACAGTAACAC
|
F
|
agTATGAAATAACTATGCAGAAAACC
|
COL19A1
|
rs9346371
|
ACGTTGGATGCTTGTATATGGAAATCACAG
|
ACGTTGGATGAACTCTTGTTTGCACTCCAG
|
F
|
gACAAAATAATTATGGGCCATGA
|
|
rs555313
|
ACGTTGGATGTGGGTAATTGGCTTCTGCAC
|
ACGTTGGATGGGTTCAGTCAGCTTGAAATG
|
F
|
TCCAAATAATCAAATCGATCA
|
SNP, single nucleotide polymorphism; PCRP, polymerase chain reaction primer; UEP, unextended mini sequencing primer; DIR, direction; SEQ, sequence
Table 2 Characteristics of study subjects
Characteristics
|
Cases (N = 316)
|
Controls (N = 320)
|
P value
|
Age
|
54.70 ± 17.14
|
19.00 ± 1.60
|
< 0.001
|
Sex
|
|
|
< 0.001
|
Man
|
183 (57.91%)
|
239 (74.69%)
|
|
Woman
|
133 (42.09%)
|
81 (25.31%)
|
|
Table 3 The loci information of five SNPs in COL9A1 and COL19A1
Gene
|
SNP
|
Chromosome position
|
Alleles
|
SNP location
|
MAF (cases)
|
MAF (controls)
|
HWE test (P)
|
COL9A1
|
rs3806093
|
6: 70273226
|
A/G
|
intron
|
0.163
|
0.166
|
0.550
|
|
rs603410
|
6: 70274945
|
T/G
|
intron
|
0.214
|
0.214
|
1.000
|
|
rs621347
|
6: 70276646
|
A/G
|
intron
|
0.375
|
0.381
|
1.000
|
COL19A1
|
rs9346371
|
6: 70210157
|
T/C
|
3’UTR
|
0.349
|
0.361
|
0.278
|
|
rs555313
|
6: 70214317
|
T/C
|
3’UTR
|
0.465
|
0.441
|
1.000
|
SNP, single nucleotide polymorphism; MAF, minor allele frequency; HWE, Hardy-Weinberg equilibrium
Table 4 Association of COL9A1 and COL19A1 polymorphisms with
Kaschin-Beck
disease risk
SNP
|
Genotype
|
Count (case)
|
Count (control)
|
Model
|
OR (95%CI)
|
P
|
Study power
|
FDR- P
|
rs3806093
|
A/G
|
103/529
|
106/534
|
Allele
|
0.98(0.73-1.32)
|
0.899
|
|
0.944
|
|
AA
|
8
|
7
|
Co-dominant
|
14.80(1.42-154.80)
|
0.024
|
100%
|
0.072
|
|
AG
|
87
|
92
|
|
0.68(0.19-2.38)
|
0.542
|
|
0.813
|
|
GG
|
221
|
221
|
|
1
|
|
|
|
|
AA-AG
|
95
|
99
|
Dominant
|
1.04(0.34-3.15)
|
0.944
|
|
0.944
|
|
GG
|
221
|
221
|
|
1
|
|
|
|
|
AA
|
8
|
7
|
Recessive
|
16.39(1.60-168.20)
|
0.019
|
100%
|
0.072
|
|
AG-GG
|
308
|
313
|
|
1
|
|
|
|
|
|
|
|
Additive
|
1.51(0.59-3.87)
|
0.386
|
|
0.772
|
rs603410
|
T/G
|
135/497
|
135/497
|
Allele
|
1.00(0.76-1.31)
|
1.000
|
|
1.000
|
|
TT
|
15
|
14
|
Co-dominant
|
0.41(0.01-11.54)
|
0.599
|
|
0.784
|
|
TG
|
105
|
107
|
|
0.70(0.24-2.05)
|
0.517
|
|
0.784
|
|
GG
|
196
|
195
|
|
1
|
|
|
|
|
TT-TG
|
120
|
121
|
Dominant
|
0.68(0.24-1.94)
|
0.469
|
|
0.784
|
|
GG
|
196
|
195
|
|
1
|
|
|
|
|
TT
|
15
|
14
|
Recessive
|
0.47(0.02-12.43)
|
0.653
|
|
0.784
|
|
TG-GG
|
301
|
302
|
|
1
|
|
|
|
|
|
|
|
Additive
|
0.68(0.26-1.77)
|
0.434
|
|
0.784
|
rs621747
|
A/G
|
237/395
|
244/396
|
Allele
|
0.97(0.78-1.22)
|
0.818
|
|
0.941
|
|
AA
|
47
|
46
|
Co-dominant
|
1.37(0.35-5.35)
|
0.649
|
|
0.941
|
|
AG
|
143
|
152
|
|
0.49(0.16-1.49)
|
0.206
|
|
0.822
|
|
GG
|
126
|
122
|
|
1
|
|
|
|
|
AA-AG
|
190
|
198
|
Dominant
|
0.66(0.25-1.78)
|
0.411
|
|
0.822
|
|
GG
|
126
|
122
|
|
1
|
|
|
|
|
AA
|
47
|
46
|
Recessive
|
1.93(0.54-6.88)
|
0.313
|
|
0.822
|
|
AG-GG
|
269
|
274
|
|
1
|
|
|
|
|
|
|
|
Additive
|
0.97(0.48-1.99)
|
0.941
|
|
0.941
|
rs9346371
|
T/C
|
219/409
|
231/409
|
Allele
|
0.95(0.75-1.19)
|
0.650
|
|
0.780
|
|
TT
|
33
|
37
|
Co-dominant
|
3.69(0.85-16.00)
|
0.081
|
|
0.243
|
|
TC
|
153
|
157
|
|
0.95(0.31-2.93)
|
0.929
|
|
0.929
|
|
CC
|
128
|
126
|
|
1
|
|
|
|
|
TT-TC
|
186
|
194
|
Dominant
|
1.27(0.45-3.58)
|
0.649
|
|
0.780
|
|
CC
|
128
|
126
|
|
1
|
|
|
|
|
TT
|
33
|
37
|
Recessive
|
3.80(1.01-14.27)
|
0.048
|
100%
|
0.243
|
|
TC-CC
|
281
|
283
|
|
1
|
|
|
|
|
|
|
|
Additive
|
1.68(0.77-3.66)
|
0.192
|
|
0.384
|
rs555313
|
T/C
|
294/338
|
282/358
|
Allele
|
1.10(0.89-1.38)
|
0.379
|
|
0.379
|
|
TT
|
74
|
62
|
Co-dominant
|
0.30(0.06-1.56)
|
0.152
|
|
0.304
|
|
TC
|
146
|
158
|
|
0.48(0.15-1.50)
|
0.205
|
|
0.307
|
|
CC
|
96
|
100
|
|
1
|
|
|
|
|
TT-TC
|
210
|
220
|
Dominant
|
0.44(0.15-1.31)
|
0.139
|
|
0.304
|
|
CC
|
96
|
100
|
|
1
|
|
|
|
|
TT
|
74
|
62
|
Recessive
|
0.50(0.12-2.09)
|
0.345
|
|
0.379
|
|
TC-CC
|
242
|
258
|
|
1
|
|
|
|
|
|
|
|
Additive
|
0.53(0.24-1.19)
|
0.124
|
|
0.304
|
SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval; FDR, false discovery rate.
Bold data means significant difference (p < 0.05)
Table 5 Haplotype analysis of COL9A1 and COL19A1 polymorphisms with
Kaschin-Beck
disease risk
Gene
|
SNPs
|
Haplotype
|
Frequency in cases
|
Frequency in controls
|
Without adjustment
|
With adjustment
|
|
|
|
|
|
OR (95%CI)
|
P
|
OR (95%CI)
|
P
|
COL9A1
|
rs3806093|rs603410|rs621347
|
GTA
|
0.212
|
0.216
|
0.98(0.75-1.28)
|
0.876
|
0.66(0.26-1.69)
|
0.392
|
|
|
AGA
|
0.163
|
0.166
|
0.98(0.73-1.32)
|
0.897
|
1.51(0.59-3.87)
|
0.386
|
|
|
GGG
|
0.377
|
0.381
|
0.98(0.78-1.23)
|
0.865
|
0.97(0.48-1.99)
|
0.941
|
COL19A1
|
rs9346371|rs555313
|
CT
|
0.463
|
0.441
|
1.09(0.88-1.36)
|
0.424
|
0.53(0.24-1.19)
|
0.124
|
|
|
TC
|
0.347
|
0.361
|
0.94(0.74-1.19)
|
0.595
|
1.68(0.77-3.66)
|
0.192
|
|
|
CC
|
0.188
|
0.198
|
0.94(0.71-1.23)
|
0.640
|
1.15(0.48-2.77)
|
0.750
|
SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval