Introduction
Materials and methods
Study sample
Phenotype definition and residual creation
Trait | Abbreviation | Gender (N) | Cohort, exam cycle | Adjustment* |
---|---|---|---|---|
Bone mineral density (BMD) | ||||
Femoral BMD** | FNBMD | Combined (1141) | Original, ex. 22–24, Offspring, ex. 6–7 | 1) multivariable-adjusted residuals (age, age2, height, BMI, smoking, physical activity, estrogen therapy) |
FNBMDf | Females (646) | |||
FNBMDm | Males (495) | |||
Trochanter BMD** | TRBMD | Same as above | Same as above | Same as above |
TRBMDf | ||||
TRBMDm | ||||
Lumbar spine BMD** | LSBMD | Combined (1117) | Same as above | Same as above |
LSBMDf | Females (641) | |||
LSBMDm | Males (486) | |||
Quantitative ultrasound (QUS)
| ||||
Broadband ultrasound attenuation** | BUA | Combined (1105) | Original, ex. 24, Offspring, ex. 6–7 | 1) multivariable-adjusted residuals (age, age2, height, BMI, smoking, physical activity, estrogen therapy) |
Speed of Sound | SOS | Combined (1104) | Same as above | Same as above |
Hip geometry
| ||||
Neck-shaft angle** | NSA1 | Combined (1096) | Original, ex. 22–24, Offspring, ex. 6–7 | 1) age, age2 2) multivariable-adjusted ranked residuals (age, age2, height, BMI) |
NSAf | Females (622) | |||
NSAm | Males (474) | |||
Femoral neck length** | NeckLeng1 | Combined (1090) | Same as above | Same as above |
NeckLengf | Females (619) | |||
NeckLengm | Males (471) | |||
Neck width** | NeckW1r | Combined (1095) | Same as above | Same as above |
NeckW1rf | Females (618) | |||
NeckW1rm | Males (477) | |||
Neck section modulus** | NeckZ1r | Combined (1096) | Same as above | Same as above |
NeckZ1rf | Females (618) | |||
NeckZ1rm | Males (478) | |||
Neck Cross-Sectional Moment of Inertia | NeckCSMI1r | Combined (1094) | Same as above | Same as above |
NeckCSMI1rf | Females (618) | |||
NeckCSMI1rm | Males (476) | |||
Neck Average Buckling Ratio | NeckAvgBR1r | Combined (1096) | Same as above | Same as above |
NeckAvgBR1rf | Females (618) | |||
NeckAvgBR1rm | Males (478) | |||
Shaft width** | ShaftW1 | Combined (1028) | Same as above | Same as above |
ShaftW1f | Females (599) | |||
ShaftW1m | Males (429) | |||
Shaft Section modulus** | ShaftZ1r | Combined (1028) | Same as above | Same as above |
ShaftZ1rf | Females (599) | |||
ShaftZ1rm | Males (429) | |||
Shaft Cross-Sectional Moment of Inertia | ShaftCSMIr | Combined (1026) | Same as above | Same as above |
ShaftCSMIrf | Females (599) | |||
ShaftCSMIrm | Males (427) | |||
Shaft Average Buckling Ratio | ShaftAvgBR1r | Combined (1028) | Same as above | Same as above |
ShaftAvgBR1rf | Females (599) | |||
ShaftAvgBR1rm | Males (429) | |||
Inter-Trochanteric Average Buckling Ratio | ITAvgBR1r | Combined (1024) | Same as above | Same as above |
ITAvgBR1rf | Females (596) | |||
ITAvgBR1rm | Males (428) |
Genotyping methods
Statistical analysis methods
Results
2a: Top 25 associations with bone density and geometry based on the lowest p-value of the GEE test | ||||||
---|---|---|---|---|---|---|
Phenotype | SNP | Chrom. | Physical Position | GEE p-value | FBAT p-value | Gene region* |
NeckZ1rf | rs6600671 | 1 | 120,812,532 |
5.85 × 10
-7
| 3.18 × 10-3 | |
NeckZ1 | rs2053506 | 3 | 19,350,795 |
3.74 × 10
-6
| 2.68 × 10-2 | KCNH8 |
TRBMDm | rs10510628 | 3 | 29,828,407 |
2.83 × 10
-6
| 2.91 × 10-2 | RBMS3 |
NeckW1rf | rs2054989 | 3 | 56,505,749 |
6.06 × 10
-7
| 2.36 × 10-3 | ERC2 |
ShaftW1f | rs922948 | 3 | 69,525,327 |
1.75 × 10
-6
| 3.47 × 10-3 | |
ShaftW1 | rs991258 | 3 | 103,256,733 |
5.32 × 10
-7
| 3.12 × 10-2 | |
BUA | rs9291683 | 4 | 10,000,429 |
2.07 × 10
-6
| 7.44 × 10-4 | |
NeckZ1rf | rs2548003 | 5 | 28,783,080 |
2.40 × 10
-7
| 1.30 × 10-1 | |
NeckZ1rf | rs10515148 | 5 | 71,752,684 |
6.10 × 10
-7
| 5.97 × 10-3 | ZNF366 |
LSBMDf | rs10514345 | 5 | 90,460,035 |
2.15 × 10
-6
| 9.85 × 10-2 | GPR98 |
NeckZ1 | Same as above |
1.81 × 10
-7
| 3.03 × 10-2 | |||
NeckW1rf | rs4715166 | 6 | 13,324,037 |
2.69 × 10
-6
| 9.97 × 10-3 | PHACTR1 |
BUA | rs2214681 | 7 | 147,140,340 |
2.72 × 10
-6
| 2.26 × 10-2 | CNTNAP2 |
ShaftZ1R | rs10503887 | 8 | 31,752,989 |
2.23 × 10
-7
| 1.77 × 10-3 | NRG1 |
FNBMDm | rs2165468 | 10 | 3,506,105 |
1.07 × 10
-6
| 6.71 × 10-2 | |
ShaftW1f | rs1452928 | 11 | 84,499,969 |
7.10 × 10
-7
| 7.43 × 10-3 | |
NeckZ1rf | rs638882 | 11 | 115,269,255 |
3.50 × 10
-6
| 6.33 × 10-3 | |
ShaftZ1rf | rs10492096 | 12 | 6,450,843 |
3.35 × 10
-6
| 2.17 × 10-3 | VAMP1 |
TRBMD | rs10506701 | 12 | 72,872,477 |
1.40 × 10
-6
| 1.25 × 10-1 | |
ShaftW1f | rs10506821 | 12 | 78,999,391 |
2.03 × 10
-7
| 1.80 × 10-1 | |
NeckZ1rm | rs1590305 | 13 | 36,933,189 |
3.15 × 10
-6
| 2.21 × 10-2 | |
FNBMDm | rs9317284 | 13 | 62,532,351 |
2.44 × 10
-7
| 2.86 × 10-1 | |
TRBMDf | rs4087296 | 16 | 80,935,282 |
3.11 × 10
-7
| 6.18 × 10-3 | |
NSAm | rs4131805 | 18 | 24,313,110 |
2.07 × 10
-6
| 1.87 × 10-3 | |
TRBMDf | rs4811196 | 20 | 35,903,108 |
1.13 × 10
-6
| 7.03 × 10-4 | CTNNBL1 |
2b: Top 25 associations with bone density and geometry based on the lowest p value of the FBAT test
| ||||||
Phenotype
|
SNP
|
Chrom.
|
Physical Position
|
GEE p-value
|
FBAT p-value
|
Gene region
|
NeckW1rf | rs1395548 | 1 | 162,045,085 | 2.34 × 10-3 |
1.22 × 10
-6
| LMX1A |
FNBMD | rs1538173 | 1 | 165,373,720 | 6.77 × 10-2 |
2.80 × 10
-6
| DPT |
TRBMD | rs3762397 | 1 | 196,821,876 | 5.96 × 10-3 |
2.78 × 10
-7
| NR5A2 |
ShaftZ1rf | rs9287234 | 1 | 236,892,414 | 9.71\ × 10-3 |
7.90 × 10
-6
| FMN2 |
TRBMD | rs914951 | 1 | 239,278,119 | 1.82 × 10-2 |
8.79 × 10
-6
| |
NeckW1 | rs4143244 | 3 | 5,385,364 | 1.07 × 10-2 |
7.05 × 10
-7
| |
NeckW1rf | rs1349205 | 3 | 54,093,157 | 2.22 × 10-2 |
1.42 × 10
-5
| CACNA2D3 |
ShaftW1 | rs1870007 | 3 | 109,458,022 | 1.71 × 10-1 |
1.32 × 10
-5
| IFT57/HHLA2 |
FNBMDf | rs950649 | 3 | 121,567,065 | 7.63 × 10-4 |
2.00 × 10
-5
| FSTL1 |
NSA1 | rs432446 | 4 | 127,906,277 | 2.84 × 10-2 |
5.19 × 10
-6
| |
FNBMD | rs922028 | 4 | 181,162,903 | 9.55 × 10-3 |
1.53 × 10
-5
| |
FNBMD | rs1823926 | 5 | 119,882,620 | 2.62 × 10-1 |
1.27 × 10
-5
| PRR16 |
NSA1 | rs10503733 | 8 | 23,589,963 | 4.29 × 10-4 |
1.79 × 10
-5
| NKX3-1 |
NSAm | rs10503953 | 8 | 33,917,325 | 1.86 × 10-3 |
1.32 × 10
-5
| |
NSAf | rs4876377 | 8 | 118,556,170 | 4.56 × 10-2 |
1.93 × 10
-5
| THRAP6 |
NSAf | rs10505600 | 8 | 133,882,045 | 2.48 × 10-1 |
1.36 × 10
-5
| PHF20L1 |
NSA1 | rs1552896 | 9 | 14,831,387 | 4.02 × 10-1 |
8.87 × 10
-6
| FREM1 |
NeckZ1rm | rs7857590 | 9 | 18,979,893 | 1.36 × 10-1 |
8.08 × 10
-6
| C9orf138 |
BUA | rs700760 | 9 | 86,164,178 | 3.82 × 10-2 |
1.42 × 10
-5
| ZCCHC6 |
FNBMDf | rs2378731 | 9 | 87,175,111 | 5.53 × 10-4 |
1.21 × 10
-5
| |
LSBMDm | rs10512315 | 9 | 103,334,877 | 1.70 × 10-1 |
2.28 × 10
-5
| |
NeckW1rf | rs2048741 | 9 | 117,716,816 | 5.49 × 10-3 |
2.40 × 10
-5
| |
ShaftZ1rm | rs6744 | 9 | 124,988,623 | 9.58 × 10-2 |
1.05 × 10
-5
| C9orf126 |
NeckLengf | rs773985 | 10 | 34,822,758 | 3.18 × 10-2 |
1.05 × 10
-5
| PARD3 |
NeckLengf | rs10490924 | 10 | 124,204,438 | 1.11 × 10-1 |
1.80 × 10
-5
| PLEKHA1/HTRA1 |
FNBMDm | rs10508076 | 13 | 101,270,253 | 5.41 × 10-3 |
4.35 × 10
-6
| FGF14 |
TRBMD | rs1865968 | 16 | 57,535,751 | 1.15 × 10-1 |
1.72 × 10
-5
| |
TRBMD | rs1209921 | 21 | 39,078,145 | 2.51 × 10-4 |
2.41 × 10
-5
| C21orf24/ETS2 |
FNBMDf | Same as above | 5.32 × 10-5 |
6.65 × 10
-3
| |||
2c. Magnitude and Location of Peak LOD scores >2.5 for regions in the bone density and geometry phenotype group
| ||||||
Phenotype
|
marker
|
Chrom.
|
physical location
|
maxLOD
|
1.5 LOD confidence interval
| |
NeckLeng1 | rs1759687 |
1
| 112,663,861 | 2.80 | 102,547,964–119,889,867 | |
ShaftW1 | rs2320625 |
2
| 95,284,610 | 2.85 | 85,198,107–105,339,005 | |
NSA1 | rs1304771 |
2
| 123,061,290 | 2.80 | 108,949,962–129,987,436 | |
BUA | rs842288 |
3
| 16,291,319 | 2.08 | 8,499,321–40,075,261 | |
NeckZ1 | rs1386389 |
4
| 112,310,874 | 2.33 | 102,722,423–131,391,829 | |
NeckW1 | rs2094541 |
10
| 130,314,425 | 2.56 | 128,465,158–135,165,518 | |
LSBMD | rs10492028 |
12
| 111,799,883 | 2.10 | 103,438,302–117,318,152 | |
ShaftZ1 | rs10518923 |
15
| 55,573,538 | 3.02 | 51,336,679–58,934,236 | |
NeckW1 | AFM049xd2 |
16
| 22,945,152 | 2.34 | 16,856,153–24,665,428 | |
BUA | rs10492922 |
16
| 27,519,162 | 2.20 | 26,434,120–50,596,704 | |
NeckZ1 | rs6502901 |
17
| 5,864,832 | 2.37 | 451,209–8,829,083 | |
BUA | rs8081154 |
17
| 46,196,038 | 2.12 | 37,926,265–62,642,504 | |
NeckW1 | rs750160 |
20
| 649,631 | 2.10 | 161,523–4,335,440 | |
ShaftZ1 | rs7290139 |
22
| 44,039,280 | 3.01 | 35,890,398–48,603,847 |
3a: Combination of FBAT and GEE, for grouped BMD phenotypes in men and women combined | |||||||
---|---|---|---|---|---|---|---|
Chrom | Physical Position | SNP | Min p-value by GEE | Min p-value by FBAT | % Significant P-values by GEE & FBAT** | Function | Gene symbol |
1 | 177,489,285 | rs7544774 | 3.34 × 10-4 | 7.55 × 10-3 | 67 | intron | XPR1 |
1 | 231,181,475 | rs7554650 | 1.67 × 10-4 | 5.93 × 10-3 | 67 | unknown | |
2 | 6,719,916 | rs7584788 | 7.55 × 10-3 | 5.19 × 10-4 | 67 | unknown | |
2 | 15,963,228 | rs2380707 | 1.14 × 10-3 | 5.22 × 10-4 | 67 | unknown | |
2 | 79,078,098 | rs1261226 | 1.19 × 10-5 | 4.47 × 10-3 | 67 | unknown | |
4 | 177,742,191 | rs9312601 | 2.22 × 10-3 | 7.03 × 10-4 | 67 | unknown | |
4 | 181,139,118 | rs10520437 | 5.23 × 10-4 | 7.72 × 10-5 | 100 | unknown | |
4 | 181,162,903 | rs922028 | 8.45 × 10-4 | 1.53 × 10-5 | 100 | unknown | |
5 | 26,917,842 | rs1479679 | 1.13 × 10-4 | 2.38 × 10-4 | 67 | intron | CDH9 |
5 | 53,527,854 | rs16882423 | 1.65 × 10-3 | 2.38 × 10-3 | 67 | intron | ARL15 |
7 | 9,739,152 | rs1557978 | 1.73 × 10-4 | 3.97 × 10-4 | 33 | intron | |
7 | 11,301,740 | rs10486135 | 1.67 × 10-4 | 5.95 × 10-4 | 67 | intron | |
7 | 18,183,021 | rs10486301 | 1.94 × 10-4 | 9.43 × 10-4 | 67 | unknown | |
8 | 114,092,330 | rs1156075 | 5.55 × 10-3 | 8.51 × 10-3 | 67 | intron | CSMD3 |
11 | 95,219,586 | rs546809 | 1.41 × 10-3 | 7.10 × 10-5 | 67 | intron | MTMR2 |
12 | 103,526,872 | rs10507180 | 7.18 × 10-4 | 4.16 × 10-3 | 100 | intron | CHST11 |
16 | 76,268,225 | rs8051539 | 2.08 × 10-3 | 5.80 × 10-3 | 67 | unknown | |
18 | 48,132,968 | rs768207 | 1.94 × 10-3 | 2.99 × 10-3 | 67 | intron | DCC |
19 | 42,607,072 | rs1465434 | 1.51 × 10-3 | 7.17 × 10-4 | 67 | intron | ZNF569 |
21 | 39,078,994 | rs1209926 | 2.51 × 10-4 | 3.21 × 10-5 | 33 | unknown | C21orf24/ETS2 |
3b: Sex-specific results for grouped BMD phenotypes
†
| |||||||
Chrom
|
Physical Position
|
SNP
|
Sex
|
Min p-value by GEE
‡
|
Min p-value by FBAT
‡
|
Function
|
Gene symbol
|
1 | 48,261,693 | rs560004 | Males | 8.91 × 10-4 | 3.48 × 10-3 | unknown | |
1 | 200,641,877 | rs1935588 | Females | 6.14 × 10-4 | 7.62 × 10-4 | unknown | |
2 | 125,809,045 | rs1215318 | Males | 1.23 × 10-4 | 2.96 × 10-4 | unknown | |
4 | 181,162,903 | rs922028 | Females | 1.61 × 10-4 | 6.16 × 10-3 | unknown | |
5 | 26,917,842 | rs1479679 | Females | 4.36 × 10-5 | 6.96 × 10-3 | intron | CDH9 |
6 | 47,657,085 | rs9296566 | Females | 2.27 × 10-4 | 5.08 × 10-4 | intron | CD2AP |
6 | 83,666,784 | rs9294266 | Males | 5.32 × 10-4 | 2.01 × 10-3 | intron | C6orf157 |
7 | 33,440,554 | rs10486541 | Males | 1.54 × 10-5 | 1.95 × 10-3 | unknown | |
7 | 35,084,096 | rs10486661 | Females | 9.34 × 10-6 | 9.98 × 10-5 | unknown | TBX20 |
9 | 20,592,188 | rs7867710 | Females | 6.96 × 10-4 | 2.97 × 10-3 | intron | MLLT3 |
9 | 88,679,511 | rs1779308 | Males | 3.09 × 10-3 | 4.94 × 10-3 | unknown | |
11 | 96,720,041 | rs10501872 | Females | 4.03 × 10-4 | 1.02 × 10-3 | unknown | |
12 | 20,059,354 | rs10505843 | Females | 2.02 × 10-4 | 7.38 × 10-3 | unknown | |
13 | 52,997,850 | rs9316628 | Females | 2.51 × 10-3 | 5.22 × 10-4 | unknown | |
13 | 107,573,163 | rs1223978 | Males | 3.42 × 10-4 | 5.07 × 10-4 | unknown | |
15 | 55,974,260 | rs10518945 | Females | 6.19 × 10-5 | 6.15 × 10-4 | unknown | ALDH1A2 |
17 | 11,054,857 | rs2024134 | Males | 4.75 × 10-3 | 6.31 × 10-5 | unknown | |
17 | 53,546,007 | rs181224 | Males | 2.15 × 10-5 | 2.90 × 10-3 | unknown | Dlc2/OR4D1/OR4D2 |
18 | 48,132,968 | rs768207 | Females | 1.35 × 10-4 | 2.57 × 10-4 | intron | DCC |
20 | 18,310,297 | rs2328293 | Females | 7.74 × 10-4 | 4.35 × 10-3 | locus | C20orf12 |
Chrom | Candidate Gene | Published SNP | Ref. | 100K SNP | r2* | Physical Position | Lowest P-value by GEE | GEE Phenotype | Lowest P-value by FBAT | FBAT Phenotype |
---|---|---|---|---|---|---|---|---|---|---|
1 |
MTHFR
| rs1801133 | [38] | rs1801133 | self | 11,790,644 | 0.033 | ShaftZ1rm | 0.042 | NSA1 |
[39] | ||||||||||
[28] | ||||||||||
6 |
ESR1
| rs2234693 | [45] | rs3866461 | 0.223 | 152,238,835 | 0.014 | NSAm |
0.003
| NeckLengf |
rs1884052 | 0.004 | 152,383,480 |
0.002
| ShaftZ1R | 0.023 | NeckW1rf | ||||
rs3778099 | 0.002 | 152,510,689 |
0.003
| BUA | 0.019 | FNBMD | ||||
rs9340799 | [45] | |||||||||
11 |
LRP5
| rs4988321 | [40, 46] | rs4988300 | no data | 67,845,407 | 0.038 | ShaftZ1rm | 0.025 | FNBMDf |
rs627174 | rs4988300 | no data | ||||||||
rs3736228 | [40, 41] | rs4988300 | 0.030 | |||||||
12 |
VDR
| rs11568820 | [29] | rs2189480 | 0.049 | 46,550,095 | 0.011 | NeckZ1rm | 0.021 | LSBMD |
rs10735810 | [29] | rs2189480 | no data | |||||||
rs1544410 | [29] | rs2189480 | 0.045 | |||||||
rs7975232 | [29] | rs2189480 | no data | |||||||
rs731236 | [29] | rs2189480 | no data | |||||||
15 |
CYP19
| rs700518 | [47] | rs10519297 | 0.902 | 49,328,952 |
0.002
| NSA1 | 0.859 | NSA1 |
[48] | rs2008691 | 0.239 | 49,335,602 |
0.003
| NSA1 | 0.012 | NSA1 | |||
rs4775936 | [49] | rs10519297 | 0.58 | |||||||
rs10046 | rs10519297 | 0.82 | ||||||||
rs11575899 | rs10519297 | no data | ||||||||
17 |
COL1A1
| rs1107946 | [50] | rs2075555 | no data | 45,629,290 | 0.034 | NeckW1rf | 0.010 | ShaftWm |
rs11327935 | [51] | rs2075555 | no data | |||||||
rs1800012 | [52] | rs2075555 | no data |