Supplementary material
Genotyping and control quality for replication analysis:
Mexico City Childhood Asthma Study: A total of 498 complete case-parent trios with
previously confirmed parentage and DNA were genotyped for 561,466 SNPs using the
Illumina HumanHap 550K beadChip, version 3. DNA was extracted using Gentra
Puregene kits (Gentra Systems, Minneapolis, Minnesota). The subjects studied were
genotyped with an average call rate of 99.7%, missingness, 0.1%, MAF, 0.001%, HWE
p-value (in parents only),10-10, Mendelian errors in more than two families and
heterozygous genotype calls for chromosome X SNPs in more than one male[1, 2].
Genes-environments & Admixture in Latino Americans (GALA II) study: GALA II
subjects were genotyped using the Axiom LAT1 array (World Array 4, Affymetrix, Santa
Clara, Calif) which includes 817,810 single nucleotide polymorphisms (SNPs) and was
specifically designed to capture genetic variation in Latino populations. SNPs that did not
pass quality control procedures were removed from the analyses using the following
criteria: failing Axiom quality controls, <95% call rate or deviation from Hardy-Weinberg
equilibrium (p<10-6) within each defined population (Puerto Rican, Mexican, and other
Latino). Therefore, genotypes for 723,888 high-quality autosomal SNPs were available
for the analyses. SNPs not directly genotyped were imputed using all populations
available from 1000 Genomes Project Phase I v3 (ref: The 1000 Genomes Project
Consortium. Nature 2010; 467:1061-73) as reference by first phasing the genotypes using
the software SHAPE- IT[3] and then imputing with IMPUTE2. Association testing was
performed using PLINK (ref. Purcell S. PLINK: a toolset for whole-genome association
and population-based linkage analysis. American Journal of Human Genetics, 81) only
for those variants that had a high quality imputation score (info score ≥0.4)[4, 5].
Table S1: Quality Control steps for SNPs.
Control quality steps
MAF
HW
Low genotyping for SNPs
Chromosomes X and Y
cutoff
< 1%
p-value < 10-4
> 10%
excluded all
nº of SNPs
354,422
3597
365
47.336
Table S2: The 100 SNPs that are most associated with childhood asthma symptoms.
Rank Chromosome SNP
Position (bp)
1
14 rs1999071
23129207
2
15 rs10519031
60183005
3
15 rs8029377
60191985
4
3 rs77165709
159452876
5
10 rs10159952
77562470
6
9 rs1329568
37037976
7
7 rs1425883
49754984
8
7 rs1543902
49754752
9
18 rs76227669
10787366
10
9 rs4878674
37036329
11
10 rs1244495
7881339
12
1 rs269330
68548590
13
7 rs10268364
28708465
14
7 rs41335
28704468
15
4 rs72998173
173715118
16
3 rs4373023
34077223
17
9 rs1329567
37038326
18
9 rs2381598
37041246
19
15 rs12901887
56941976
20
1 rs79530846
171950308
21
4 rs6535350
83439160
22
15 rs1968687
58822697
23
2 rs113750103
202398743
24
1 rs78521816
171414740
25
7 rs114576775
54243876
Risk allele
C
C
C
T
A
T
T
G
T
T
G
T
C
C
G
T
A
C
G
T
G
G
T
A
A
Gene
INTERGENIC
INTERGENIC
INTERGENIC
IQCJ-SCHIP1
C10orf11
LOC100130458
INTERGENIC
INTERGENIC
PIEZO2
INTERGENICX5
TAF3
GNG12-AS1
CREB5
CREB6
GALNTL6
INTERGENIC
LOC100130458
INTERGENIC
ZNF280D
vDNM3
TMEM150C
LIPC
ALS2CR11
INTERGENIC
INTERGENIC
Odds ratio
1.782
3.008
2.495
2.275
2.041
1.933
0.6043
0.6044
4.063
1.9
0.6137
1.749
1.593
0.6373
1.758
1.57
1.969
1.968
0.5567
3.078
1.593
1.542
2.391
2.299
4.023
CI(95%)
(1.453 – 2.185)
(2.017 – 4.487)
(1.763 – 3.53)
(1.661 – 3.117)
(1.533 – 2.717)
(1.473 – 2.537)
(0.4908 – 0.7439)
(0.4907 – 0.7444)
(2.241 – 7.366)
(1.446 – 2.497)
(0.4985 – 0.7555)
(1.377 – 2.221)
(1.305 – 1.945)
(0.5254 – 0.773)
(1.38 – 2.239)
(1.294 – 1.906)
(1.47 – 2.636)
(1.47 – 2.636)
(0.4318 – 0.7177)
(1.882 – 5.035)
(1.299 – 1.954)
(1.275 – 1.864)
(1.629 – 3.509)
(1.594 – 3.317)
(2.179 – 7.428)
p
2.834E-08
6.676E-08
2.454E-07
3.045E-07
1.016E-06
2.02E-06
2.037E-06
2.164E-06
3.881E-06
4.027E-06
4.169E-06
4.669E-06
4.671E-06
4.793E-06
4.848E-06
4.977E-06
5.46E-06
5.474E-06
6.224E-06
7.542E-06
7.816E-06
7.826E-06
8.431E-06
8.483E-06
8.642E-06
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
3
20
7
5
9
3
15
11
15
3
20
7
3
1
3
7
9
1
14
1
6
12
9
4
11
3
15
rs80316500
rs1555852
rs78980017
rs10069226
rs4880052
rs7622659
rs35743173
rs7928089
rs4775232
rs9827639
rs942992
rs58285948
rs9815657
rs78063878
rs6767038
rs77188806
rs1948308
rs17097444
rs1681581
rs116375634
rs113623387
rs78201583
rs2774241
rs75957247
rs58478357
rs16831149
rs8042498
159982507
19536127
54227948
31271333
37036285
45357777
101324457
68574429
60310375
45342749
19564963
7305712
45345904
172018390
159453369
64926662
87616257
69918002
23118663
154273469
43162490
20700554
93665453
114692320
119628335
159976271
29605931
C
T
G
A
A
A
A
A
C
T
T
C
T
G
T
T
T
C
G
T
G
C
A
T
C
T
A
IFT80
SLC24A3
INTERGENIC
CDH6
INTERGENIC
INTERGENIC
LOC440313
CPT1A
INTERGENIC
INTERGENIC
SLC24A3
INTERGENIC
INTERGENIC
DNM3
SCHIP1
INTERGENIC
NTRK2
INTERGENIC
INTERGENIC
INTERGENIC
CUL9
PDE3A
INTERGENIC
INTERGENIC
LOC101929156
IFT80
FAM189A1
1.594
1.72
4.008
2.344
1.893
2.324
2.498
1.55
1.525
2.372
1.787
2.222
2.37
3.126
1.561
4.664
0.6569
3.487
1.694
3.085
1.535
2.644
1.758
1.664
1.664
1.564
2654
(1.298 – 1.958)
(1.354 - 2.186)
(2.171 - 7.4)
(1.606 – 3.421)
(1.425 – 2.515)
(1.596 – 3.383)
(1.661 – 3.756)
(1.275 – 1.886)
(1.263 – 1.842)
(1.612 – 3.49)
(1.378 – 2.316)
(1.555 – 3.176)
(1.611 – 3.486)
(1.875 – 5.211)
(1.278 – 1.906)
(2.337 – 9.307)
(0.544 – 0.7932)
(1.988 – 6.116)
(1.335 – 2.149)
(1.853 – 5.136)
(1.264 – 1.864)
(1.701 – 4.109)
(1.361 – 2.271)
(1.32 – 2.097)
(1.32 – 2.099)
(1.275 – 1.919)
(1.698 – 4.148)
8.742E-06
8.959E-06
9.092E-06
1.013E-05
1.078E-05
1.083E-05
1.09E-05
1.118E-05
1.143E-05
1.159E-05
1.161E-05
1.172E-05
1.187E-05
1.233E-05
1.245E-05
1.252E-05
1.259E-05
1.316E-05
1.435E-05
1.482E-05
1.51E-05
1.546E-05
1.56E-05
1.62E-05
1.67E-05
1.801E-05
1.824E-05
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
4
8
9
7
1
2
4
6
17
2
7
5
5
5
4
1
20
4
10
9
3
2
8
15
11
7
13
rs13124037
rs59811079
rs7860117
rs77053500
rs115763417
rs77540829
rs78129004
rs2273709
rs115798120
rs75681688
rs982947
rs17341817
rs11950703
rs2162716
rs12506762
rs3004245
rs6046176
rs7655284
rs1244480
rs11140831
rs74887681
rs114446331
rs115506651
rs115302036
rs7127256
rs7780465
rs56087514
173085238
1625732
87770429
7903345
30939086
202400872
81117017
43184132
43405024
202383927
28708856
103579857
103576747
94762306
173712840
9111626
19532518
105869702
7870324
87647454
52890196
43225774
56047932
60183951
90525490
7076459
27778960
T
G
G
A
A
A
A
C
T
A
C
T
T
C
T
A
C
G
T
G
T
C
G
T
A
T
C
GALNTL6
DLGAP2
INTERGENIC
LOC729852
INTERGENIC
ALS2CR11
PRDM8
CUL9
INTERGENIC
ALS2CR11
CREB5
INTERGENIC
INTERGENIC
FAM81B
GALNTL6
SLC2A5
SLC24A3
INTERGENIC
TAF3
INTERGENIC
TMEM110-MUSTN1
INTERGENIC
XKR4
INTERGENIC
INTERGENIC
INTERGENIC
INTERGENIC
0.6454
0.6484
1.801
4.725
2.705
2.582
4.149
1.525
1.574
2.623
0.6451
2.543
2.543
1.559
1.513
0.6425
1.665
1.517
1.515
0.6083
5.34
3.541
3.407
3.186
1.507
1.538
0.6346
(0.5283 – 0.7886)
(0.5317 – 0.7907)
(1.376 – 2.359)
(2.319 – 9.629)
(1.714 – 4.271)
(1.67 – 3.991)
(2.159 – 7.975)
(1.256 – 1.851)
(1.278 – 1.94)
(1.682 – 4.091)
(0.5271 – 0.7896)
(1.654 – 3.911)
(1.654 – 3.911)
(1.27 – 1.913)
(1.25 – 1.833)
(0.5237 – 0.7882)
(1.315 – 2.11)
(1.25 – 1.841)
(1.249 – 1.837)
(0.4828 – 0.7663)
(2.448 – 11.65)
(1.965 – 6.379)
(1.924 – 6.032)
(1.856 – 5.468)
(1.245 – 1.825)
(1.258 – 1.881)
(0.5133 – 0.7846)
1.831E-05
1.863E-05
1.87E-05
1.907E-05
1.928E-05
1.971E-05
1.975E-05
2E-05
2.049E-05
2.111E-05
2.122E-05
2.126E-05
2.126E-05
2.196E-05
2.207E-05
2.215E-05
2.378E-05
2.438E-05
2.439E-05
2.463E-05
2.557E-05
2.567E-05
2.616E-05
2.626E-05
2.652E-05
2.652E-05
2.654E-05
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
1
9
3
2
9
7
14
15
7
5
6
10
4
9
4
8
3
20
1
3
6
rs80295800
rs424539
rs116448590
rs16986498
rs7873362
rs6956273
rs1465118
rs10518870
rs115972708
rs73767458
rs9472022
rs79846008
rs74426337
rs4419891
rs77924825
rs2952238
rs76336861
rs529058
rs74081353
rs9867680
rs6914964
235771726
14442595
142841697
19665812
74918896
63435537
68032874
57017888
65372483
82346803
43152573
128542978
170929983
87609384
170923535
10095328
45368350
926945
68544206
45361222
43146387
G
C
G
G
T
T
A
G
A
A
G
A
T
T
C
A
G
A
G
T
G
GNG4
INTERGENIC
CHST2
LOC101928196
LINC01504
INTERGENIC
PLEKHH1
ZNF280D
VKORC1L1
INTERGENIC
CUL9
LOC728065
MFAP3L
NTRK2
MFAP3L
MSRA
INTERGENIC
INTERGENIC
LOC100289178
INTERGENIC
SRF
1.925
0.6509
5.27
0.4067
1.765
1.6
1.508
0.5888
4.399
2.574
1.506
2.679
3.031
1.531
3.027
1.735
2.055
2.098
2.02
2.046
1.615
(1.418 – 2.614)
(0.5323 – 0.7958)
(2.417 – 11.49)
(0.2665 – 0.6204)
(1.352 – 2.306)
(1.283 – 1.995)
(1.243 – 1.829)
(0.459 – 0.7554)
(2.187 – 8.85)
(1.648 – 4.022)
(1.241 – 1.828)
(1.681 – 4.268)
(1.793 – 5.123)
(1.251 – 1.872)
(1.791 – 5.118)
(1.336 – 2.253)
(1.46 – 2.892)
(1.475 – 2.982)
(1.446 – 2.821)
(1.455 – 2.878)
(1.285 – 2.029)
2.718E-05
2.833E-05
2.929E-05
2.983E-05
3.031E-05
3.046E-05
3.074E-05
3.085E-05
3.261E-05
3.287E-05
3.357E-05
3.368E-05
3.477E-05
3.477E-05
3.538E-05
3.587E-05
3.61E-05
3.678E-05
3.696E-05
3.917E-05
3.927E-05
Table S3: Combined analysis.
SCAALA
Chromosome
1
1
1
2
3
3
4
4
7
7
7
7
7
9
9
9
9
10
10
14
14
SNP
rs269330
rs78521816
rs79530846
rs113750103
rs4373023
rs77165709
rs6535350
rs72998173
rs10268364
rs114576775
rs1425883
rs1543902
rs41335
rs1329567
rs1329568
rs2381598
rs4878674
rs10159952
rs1244495
rs10131634
rs10131924
Risk
allele
T
T
A
T
T
T
G
G
C
A
T
G
C
A
T
C
T
A
G
T
A
OR
1.75
2.30
3.08
2.39
1.57
2.28
1.59
1.76
1.59
4.02
0.60
0.60
0.64
1.97
1.93
1.97
1.90
2.04
0.61
1.66
1.66
p-value
4.67E-06
8.48E-06
7.54E-06
8.43E-06
4.98E-06
3.05E-07
7.82E-06
4.85E-06
4.67E-06
8.64E-06
2.04E-06
2.16E-06
4.79E-06
5.46E-06
2.02E-06
5.47E-06
4.03E-06
1.02E-06
4.17E-06
1.39E-06
1.51E-06
GALA II
Risk
allele
T
A
T
T
C
T
G
G
C
A
C
T
G
G
G
T
G
A
T
A
OR
1.130
1.000
1.084
0.756
1.040
0.907
0.900
1.119
1.059
1.161
1.041
1.039
1.032
0.999
0.976
1.002
0.972
1.370
1.036
1.036
p-value
0.289
0.999
0.783
0.158
0.520
0.507
0.168
0.130
0.345
0.705
0.448
0.468
0.560
0.995
0.838
0.986
0.803
0.014
0.524
0.525
OR
combined
1.40
1.53
1.85
1.35
1.22
1.43
1.19
1.39
1.29
2.21
0.77
0.77
0.79
1.40
1.40
1.40
1.39
1.66
1.32
1.31
Combined¹
p-value
combined
0.12
0.31
0.24
0.61
0.42
0.43
0.54
0.15
0.21
0.20
0.26
0.26
0.27
0.32
0.29
0.33
0.28
0.01
0.25
0.25
MCCA
Effect
++
+++
++++++
++
++
---++
++
+++
++
++
++
p-value
0.24
0.40
0.47
0.36
0.43
0.43
0.49
0.25
-
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
14
15
15
15
15
15
rs10143684
rs10144348
rs10151422
rs1242937
rs1242938
rs1242940
rs1242941
rs1242942
rs1681581
rs1681582
rs1958322
rs1999070
rs1999071
rs28523687
rs34222671
rs34226211
rs34437928
rs35622014
rs35622551
rs56861039
rs8008677
rs10519031
rs112012489
rs115302036
rs116765599
rs12901887
T
T
C
T
T
T
C
T
G
C
G
G
C
C
C
T
A
T
G
C
G
C
C
T
T
G
1.64
1.66
1.67
1.70
1.61
1.61
1.65
1.62
1.67
1.61
1.71
1.70
1.78
1.69
1.62
1.62
1.65
1.64
1.76
1.66
1.65
3.01
2.72
3.15
2.17
0.56
2.50E-06
1.39E-06
1.05E-06
1.53E-05
6.58E-05
6.58E-05
3.89E-06
5.70E-06
2.48E-05
7.89E-05
6.02E-07
1.53E-07
2.83E-08
7.24E-07
3.87E-06
4.18E-06
1.75E-06
2.82E-06
2.45E-07
1.47E-06
1.42E-06
6.68E-08
2.85E-06
3.09E-05
2.93E-05
6.22E-06
T
T
C
T
T
T
C
T
G
C
G
G
C
C
C
T
A
T
G
C
G
C
C
T
T
G
1.042
1.032
1.036
1.069
1.067
1.065
1.049
1.038
1.066
1.065
1.104
1.066
1.059
1.072
1.036
1.036
1.036
1.035
1.098
1.035
1.036
0.834
0.838
1.069
1.267
0.980
0.453
0.560
0.516
0.332
0.334
0.353
0.413
0.522
0.357
0.353
0.101
0.266
0.318
0.228
0.516
0.518
0.520
0.534
0.123
0.533
0.517
0.527
0.539
0.849
0.287
0.739
1.31
1.31
1.32
1.35
1.32
1.32
1.32
1.30
1.34
1.32
1.38
1.35
1.36
1.35
1.30
1.30
1.31
1.31
1.40
1.31
1.31
1.61
1.57
1.94
1.74
0.75
0.23
0.25
0.24
0.19
0.18
0.18
0.22
0.24
0.19
0.18
0.14
0.20
0.23
0.19
0.24
0.24
0.24
0.24
0.16
0.25
0.24
0.46
0.45
0.22
0.04
0.30
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++
++++
++
--
0.24
0.28
0.34
-
15
15
15
15
15
15
15
15
15
15
15
15
15
15
15
15
15
18
rs139751352
rs149023356
rs16941890
rs16942157
rs16942159
rs180995748
rs1968687
rs201996260
rs4775232
rs56036906
rs56856389
rs73419027
rs73419030
rs76270731
rs78573950
rs8029377
rs993192
rs76227669
A
C
C
C
C
C
G
T
A
T
G
A
G
A
C
C
T
In bold: SNP replicated in GALA II study.
3.87
6.35
2.78
1.75
1.74
4.40
1.54
5.65
1.52
1.79
2.25
2.62
2.66
2.33
2.62
2.50
2.43
4.06
8.94E-05
3.78E-05
1.65E-06
5.25E-05
7.33E-05
5.59E-05
7.83E-06
6.37E-05
1.23E-05
4.05E-05
1.31E-05
1.44E-05
8.79E-06
6.85E-05
5.69E-06
2.45E-07
3.17E-05
3.88E-06
A
C
C
C
C
C
T
T
A
T
G
A
G
A
C
C
T
1.646
1.392
0.839
0.923
0.923
1.420
1.075
1.039
1.147
0.924
0.993
0.988
1.065
0.840
0.927
1.074
0.815
0.225
0.475
0.541
0.568
0.568
0.453
0.232
0.590
0.363
0.744
0.978
0.964
0.738
0.544
0.756
0.703
0.520
2.79
3.19
1.58
1.29
1.29
2.75
1.19
1.22
1.47
1.49
1.67
1.68
1.61
1.54
1.54
1.65
1.82
0.01
0.12
0.44
0.42
0.43
0.07
0.49
0.39
0.08
0.37
0.29
0.30
0.22
0.45
0.38
0.22
0.45
++
++
+++++
++++
+++++
++++
+-
0.29
0.30
0.30
-
Figure S1: Analysis of the principal components in the SCAALA population with all of
the SNPs in order to deduce population structure.
Figure S2: Phenotypic variance explained for each chromosome.
Variance
0.25
4
0.20
7
15 13
0.15
10
0.10
6
5
3
11
0.05
9
2
1
16
0.00
-1.00
18
21 221920
17
49.00
14
99.00
12
8
149.00
199.00
249.00
REFERENCE:
1. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE et
al. Meta-analysis of genome-wide association studies of asthma in ethnically diverse
North American populations. Nature genetics. 2011;43(9):887-92. doi:10.1038/ng.888
2. Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY et al. Genome-wide
association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in
mexican
children.
PLoS
genetics.
2009;5(8):e1000623.
doi:10.1371/journal.pgen.1000623.
3. Delaneau O, Marchini J, Zagury JF. A linear complexity phasing method for thousands
of genomes. Nature methods. 2012;9(2):179-81. doi:10.1038/nmeth.1785.
4. Nishimura KK, Galanter JM, Roth LA, Oh SS, Thakur N, Nguyen EA et al. Early-life
air pollution and asthma risk in minority children. The GALA II and SAGE II studies.
American journal of respiratory and critical care medicine. 2013;188(3):309-18.
doi:10.1164/rccm.201302-0264OC.
5. Pino-Yanes M, Thakur N, Gignoux CR, Galanter JM, Roth LA, Eng C et al. Genetic
ancestry influences asthma susceptibility and lung function among Latinos. The Journal
of allergy and clinical immunology. 2015;135(1):228-35. doi:10.1016/j.jaci.2014.07.053.