This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 51 focal events and 17 clinical features across 110 patients, 86 significant findings detected with Q value < 0.25.
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amp_1q21.2 cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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amp_4q12 cnv correlated to 'ORIGIN_ASIA'.
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amp_5p15.33 cnv correlated to 'PATHOLOGY_N_STAGE'.
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amp_5q35.1 cnv correlated to 'GENDER', 'SMOKER', and 'COUNTRY_OF_ORIGIN'.
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amp_6q27 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.
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amp_7p11.2 cnv correlated to 'HISTOLOGICAL_TYPE', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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amp_8q13.1 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.
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amp_8q24.21 cnv correlated to 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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amp_8q24.3 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.
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amp_11q13.3 cnv correlated to 'BMI'.
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amp_12p13.33 cnv correlated to 'YEARS_TO_BIRTH' and 'ORIGIN_ASIA'.
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amp_12p11.21 cnv correlated to 'ORIGIN_ASIA'.
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amp_12q15 cnv correlated to 'PATHOLOGY_N_STAGE'.
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amp_14q13.3 cnv correlated to 'YEARS_TO_BIRTH', 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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amp_14q32.33 cnv correlated to 'HISTOLOGICAL_TYPE', 'YEARS_TO_BIRTH', 'SMOKER', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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amp_17q23.1 cnv correlated to 'PATHOLOGY_N_STAGE'.
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amp_20q13.2 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'HISTOLOGIC_GRADE', and 'ORIGIN_ASIA'.
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amp_20q13.33 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'HISTOLOGIC_GRADE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'YEARS_TO_BIRTH'.
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amp_xp22.33 cnv correlated to 'PATHOLOGIC_STAGE', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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amp_xq27.3 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.
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del_3p24.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'YEARS_TO_BIRTH'.
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del_5q15 cnv correlated to 'COUNTRY_OF_ORIGIN' and 'ORIGIN_ASIA'.
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del_6p11.2 cnv correlated to 'YEARS_TO_BIRTH'.
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del_6q16.3 cnv correlated to 'YEARS_TO_BIRTH', 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_8p23.1 cnv correlated to 'HISTOLOGIC_GRADE', 'BMI', and 'ORIGIN_ASIA'.
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del_9p23 cnv correlated to 'GENDER'.
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del_9p21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.
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del_10q25.1 cnv correlated to 'ORIGIN_ASIA'.
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del_13q11 cnv correlated to 'YEARS_TO_BIRTH', 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_15q13.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE', 'SMOKER', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_17p13.1 cnv correlated to 'BMI'.
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del_18q21.31 cnv correlated to 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_19q13.33 cnv correlated to 'GENDER'.
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del_21p11.2 cnv correlated to 'GENDER'.
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del_22p11.2 cnv correlated to 'HISTOLOGICAL_TYPE', 'GENDER', 'RADIATION_THERAPY', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_22q13.32 cnv correlated to 'BMI', 'COUNTRY_OF_ORIGIN', and 'ORIGIN_ASIA'.
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del_xp22.33 cnv correlated to 'GENDER'.
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del_xq28 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'COUNTRY_OF_ORIGIN'.
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del_yq11.223 cnv correlated to 'PATHOLOGIC_STAGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 focal events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 86 significant findings detected.
Clinical Features |
DAYS TO DEATH OR LAST FUP |
HISTOLOGICAL TYPE |
HISTOLOGIC GRADE |
KARNOFSKY PERFORMANCE SCORE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGIC STAGE |
YEARS TO BIRTH |
ETHNICITY | GENDER | RACE |
RADIATION THERAPY |
BMI |
NUMBER PACK YEARS SMOKED |
SMOKER |
COUNTRY OF ORIGIN |
ORIGIN ASIA |
||
nCNV (%) | nWild-Type | logrank test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 14q32 33 | 46 (42%) | 64 |
0.319 (0.769) |
0.0147 (0.19) |
0.556 (0.911) |
0.857 (1.00) |
0.626 (0.928) |
0.479 (0.89) |
0.74 (0.976) |
0.000392 (0.034) |
1 (1.00) |
0.841 (1.00) |
0.485 (0.893) |
0.0295 (0.266) |
0.334 (0.775) |
0.72 (0.96) |
0.00311 (0.0929) |
0.00132 (0.0636) |
0.000704 (0.0423) |
del 22p11 2 | 44 (40%) | 66 |
0.37 (0.812) |
0.00584 (0.12) |
0.319 (0.769) |
0.325 (0.773) |
0.165 (0.612) |
0.957 (1.00) |
0.632 (0.928) |
0.171 (0.618) |
0.477 (0.89) |
0.0231 (0.236) |
1 (1.00) |
0.0112 (0.164) |
0.133 (0.567) |
0.213 (0.663) |
0.557 (0.911) |
0.00956 (0.149) |
0.00916 (0.149) |
amp 14q13 3 | 62 (56%) | 48 |
0.513 (0.908) |
0.0474 (0.359) |
0.0469 (0.359) |
0.863 (1.00) |
0.206 (0.663) |
0.625 (0.928) |
0.341 (0.781) |
0.0074 (0.134) |
0.538 (0.908) |
1 (1.00) |
0.751 (0.981) |
0.142 (0.58) |
0.00038 (0.034) |
0.869 (1.00) |
0.0501 (0.359) |
0.0007 (0.0423) |
0.000346 (0.034) |
amp 20q13 33 | 51 (46%) | 59 |
0.00636 (0.123) |
0.549 (0.908) |
0.0171 (0.2) |
0.0179 (0.204) |
0.92 (1.00) |
0.813 (0.995) |
0.476 (0.89) |
0.0219 (0.229) |
0.538 (0.908) |
1 (1.00) |
0.783 (0.993) |
0.33 (0.773) |
0.688 (0.956) |
0.511 (0.908) |
0.0833 (0.458) |
0.0805 (0.454) |
0.0495 (0.359) |
del 6q16 3 | 58 (53%) | 52 |
0.859 (1.00) |
0.536 (0.908) |
0.156 (0.607) |
0.0986 (0.488) |
0.365 (0.808) |
0.329 (0.773) |
0.22 (0.678) |
0.00481 (0.107) |
0.278 (0.73) |
1 (1.00) |
1 (1.00) |
0.149 (0.595) |
0.00056 (0.0423) |
0.163 (0.611) |
0.118 (0.544) |
0.00404 (0.1) |
0.000853 (0.0438) |
del 13q11 | 64 (58%) | 46 |
0.0755 (0.437) |
0.139 (0.576) |
0.58 (0.921) |
0.0702 (0.417) |
0.6 (0.927) |
0.0626 (0.393) |
0.212 (0.663) |
0.00856 (0.144) |
0.54 (0.908) |
1 (1.00) |
1 (1.00) |
0.467 (0.884) |
0.00434 (0.102) |
0.775 (0.99) |
0.0477 (0.359) |
0.0001 (0.0173) |
6.72e-05 (0.0152) |
del 15q13 1 | 64 (58%) | 46 |
0.37 (0.812) |
0.603 (0.927) |
0.184 (0.64) |
0.0124 (0.174) |
1 (1.00) |
0.0583 (0.386) |
0.265 (0.724) |
0.21 (0.663) |
1 (1.00) |
0.414 (0.852) |
1 (1.00) |
0.805 (0.995) |
0.131 (0.563) |
0.134 (0.568) |
0.0173 (0.2) |
0.00593 (0.12) |
0.0101 (0.152) |
amp 5q35 1 | 35 (32%) | 75 |
0.0911 (0.473) |
0.575 (0.921) |
0.449 (0.883) |
0.061 (0.392) |
0.514 (0.908) |
0.109 (0.515) |
0.515 (0.908) |
0.164 (0.611) |
0.53 (0.908) |
0.00946 (0.149) |
1 (1.00) |
1 (1.00) |
0.202 (0.663) |
0.308 (0.764) |
0.00576 (0.12) |
0.00775 (0.137) |
0.0364 (0.307) |
amp 7p11 2 | 63 (57%) | 47 |
0.766 (0.989) |
0.0209 (0.224) |
0.0623 (0.393) |
0.636 (0.929) |
0.713 (0.96) |
0.207 (0.663) |
0.39 (0.828) |
0.228 (0.691) |
0.275 (0.73) |
1 (1.00) |
1 (1.00) |
0.138 (0.576) |
0.198 (0.657) |
0.443 (0.878) |
0.556 (0.911) |
0.0019 (0.0762) |
0.000732 (0.0423) |
amp 8q24 21 | 65 (59%) | 45 |
0.865 (1.00) |
0.173 (0.618) |
0.32 (0.769) |
0.77 (0.989) |
0.708 (0.96) |
1 (1.00) |
0.628 (0.928) |
0.269 (0.726) |
1 (1.00) |
0.539 (0.908) |
0.75 (0.98) |
0.467 (0.884) |
0.00189 (0.0762) |
0.105 (0.5) |
0.43 (0.866) |
7e-05 (0.0152) |
1.1e-05 (0.0077) |
amp 20q13 2 | 51 (46%) | 59 |
0.00676 (0.127) |
0.21 (0.663) |
0.00238 (0.0825) |
0.263 (0.721) |
0.918 (1.00) |
0.627 (0.928) |
0.456 (0.884) |
0.0273 (0.26) |
0.538 (0.908) |
1 (1.00) |
0.783 (0.993) |
0.33 (0.773) |
0.419 (0.86) |
0.771 (0.989) |
0.0341 (0.295) |
0.0949 (0.483) |
0.0182 (0.205) |
amp xp22 33 | 46 (42%) | 64 |
0.553 (0.911) |
0.0969 (0.483) |
0.812 (0.995) |
0.843 (1.00) |
0.775 (0.99) |
0.158 (0.607) |
0.0173 (0.2) |
0.487 (0.893) |
1 (1.00) |
0.683 (0.956) |
1 (1.00) |
0.806 (0.995) |
0.242 (0.703) |
0.185 (0.64) |
0.0497 (0.359) |
0.00581 (0.12) |
0.00157 (0.0715) |
del 8p23 1 | 58 (53%) | 52 |
0.372 (0.813) |
0.579 (0.921) |
0.012 (0.173) |
0.638 (0.929) |
1 (1.00) |
0.28 (0.731) |
0.952 (1.00) |
0.252 (0.709) |
0.243 (0.705) |
0.686 (0.956) |
0.839 (1.00) |
1 (1.00) |
0.00249 (0.083) |
0.235 (0.701) |
0.24 (0.703) |
0.084 (0.458) |
0.0189 (0.207) |
del 18q21 31 | 61 (55%) | 49 |
0.583 (0.923) |
0.725 (0.963) |
0.333 (0.775) |
0.0282 (0.26) |
0.576 (0.921) |
0.545 (0.908) |
0.535 (0.908) |
0.0533 (0.37) |
1 (1.00) |
0.223 (0.686) |
0.841 (1.00) |
0.809 (0.995) |
0.00023 (0.0285) |
0.161 (0.607) |
0.44 (0.877) |
0.0144 (0.19) |
0.00351 (0.0965) |
del 22q13 32 | 55 (50%) | 55 |
0.631 (0.928) |
0.66 (0.949) |
0.226 (0.691) |
0.354 (0.794) |
0.611 (0.928) |
0.329 (0.773) |
0.684 (0.956) |
0.381 (0.823) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0298 (0.266) |
0.00743 (0.134) |
0.482 (0.891) |
0.244 (0.705) |
0.016 (0.2) |
0.0187 (0.207) |
amp 6q27 | 41 (37%) | 69 |
0.142 (0.58) |
0.0281 (0.26) |
0.21 (0.663) |
0.926 (1.00) |
0.125 (0.548) |
0.667 (0.954) |
0.436 (0.871) |
0.211 (0.663) |
1 (1.00) |
0.534 (0.908) |
1 (1.00) |
0.321 (0.769) |
0.65 (0.937) |
0.705 (0.959) |
0.684 (0.956) |
0.00064 (0.0423) |
0.00238 (0.0825) |
amp 8q13 1 | 47 (43%) | 63 |
0.385 (0.824) |
0.32 (0.769) |
0.909 (1.00) |
0.906 (1.00) |
0.389 (0.828) |
0.844 (1.00) |
0.986 (1.00) |
0.267 (0.726) |
1 (1.00) |
0.542 (0.908) |
0.636 (0.929) |
0.146 (0.587) |
0.0258 (0.254) |
0.41 (0.849) |
1 (1.00) |
0.0167 (0.2) |
0.00288 (0.0925) |
amp 8q24 3 | 69 (63%) | 41 |
0.208 (0.663) |
0.342 (0.781) |
0.173 (0.618) |
0.188 (0.642) |
0.644 (0.933) |
0.559 (0.911) |
0.712 (0.96) |
0.086 (0.461) |
1 (1.00) |
0.678 (0.956) |
0.84 (1.00) |
0.316 (0.769) |
0.0671 (0.402) |
0.14 (0.576) |
0.843 (1.00) |
0.00022 (0.0285) |
1.78e-05 (0.0077) |
amp 12p13 33 | 54 (49%) | 56 |
0.0847 (0.459) |
0.49 (0.896) |
0.102 (0.498) |
0.763 (0.988) |
0.471 (0.887) |
0.879 (1.00) |
0.856 (1.00) |
0.00419 (0.101) |
0.537 (0.908) |
0.23 (0.692) |
0.754 (0.982) |
0.229 (0.691) |
0.789 (0.993) |
0.167 (0.615) |
0.0517 (0.368) |
0.028 (0.26) |
0.00344 (0.0965) |
amp xq27 3 | 60 (55%) | 50 |
0.323 (0.769) |
0.197 (0.656) |
0.0642 (0.395) |
0.979 (1.00) |
0.781 (0.993) |
0.569 (0.917) |
0.688 (0.956) |
0.16 (0.607) |
0.241 (0.703) |
0.227 (0.691) |
1 (1.00) |
0.467 (0.884) |
0.121 (0.544) |
0.246 (0.707) |
0.122 (0.544) |
0.00356 (0.0965) |
0.00301 (0.0929) |
del 3p24 1 | 53 (48%) | 57 |
0.955 (1.00) |
0.395 (0.83) |
0.0399 (0.321) |
0.302 (0.754) |
0.0141 (0.188) |
0.847 (1.00) |
0.871 (1.00) |
0.0161 (0.2) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.519 (0.908) |
0.716 (0.96) |
1 (1.00) |
0.481 (0.89) |
0.562 (0.911) |
del 5q15 | 43 (39%) | 67 |
0.252 (0.709) |
0.296 (0.744) |
0.373 (0.813) |
0.064 (0.395) |
0.915 (1.00) |
0.588 (0.923) |
0.18 (0.632) |
0.518 (0.908) |
1 (1.00) |
0.0378 (0.309) |
0.589 (0.923) |
0.613 (0.928) |
0.228 (0.691) |
0.302 (0.754) |
1 (1.00) |
0.00452 (0.103) |
0.0101 (0.152) |
del xq28 | 24 (22%) | 86 |
0.996 (1.00) |
0.344 (0.782) |
0.921 (1.00) |
0.00195 (0.0762) |
0.547 (0.908) |
0.395 (0.83) |
0.719 (0.96) |
0.0873 (0.465) |
0.362 (0.804) |
0.151 (0.596) |
1 (1.00) |
1 (1.00) |
0.0808 (0.454) |
0.107 (0.505) |
0.352 (0.794) |
0.00397 (0.1) |
0.24 (0.703) |
amp 1q21 2 | 89 (81%) | 21 |
0.58 (0.921) |
0.631 (0.928) |
0.421 (0.861) |
0.333 (0.775) |
0.453 (0.884) |
0.873 (1.00) |
0.51 (0.908) |
0.755 (0.983) |
0.172 (0.618) |
1 (1.00) |
1 (1.00) |
0.384 (0.824) |
0.864 (1.00) |
0.00959 (0.149) |
0.633 (0.928) |
0.361 (0.804) |
0.624 (0.928) |
amp 4q12 | 20 (18%) | 90 |
0.469 (0.887) |
0.883 (1.00) |
0.749 (0.98) |
0.26 (0.715) |
0.705 (0.959) |
0.933 (1.00) |
0.692 (0.956) |
0.175 (0.618) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.715 (0.96) |
0.71 (0.96) |
0.604 (0.927) |
0.213 (0.663) |
0.0192 (0.209) |
amp 5p15 33 | 76 (69%) | 34 |
0.769 (0.989) |
0.593 (0.924) |
0.567 (0.916) |
0.62 (0.928) |
0.189 (0.642) |
0.0163 (0.2) |
0.292 (0.737) |
0.547 (0.908) |
0.554 (0.911) |
0.663 (0.95) |
0.783 (0.993) |
1 (1.00) |
0.286 (0.734) |
0.791 (0.993) |
0.536 (0.908) |
0.0658 (0.401) |
0.0584 (0.386) |
amp 11q13 3 | 46 (42%) | 64 |
0.868 (1.00) |
0.58 (0.921) |
0.105 (0.5) |
0.715 (0.96) |
0.628 (0.928) |
0.284 (0.734) |
0.187 (0.642) |
0.0765 (0.437) |
1 (1.00) |
0.683 (0.956) |
1 (1.00) |
0.328 (0.773) |
0.00861 (0.144) |
0.801 (0.995) |
1 (1.00) |
0.0631 (0.394) |
0.0296 (0.266) |
amp 12p11 21 | 37 (34%) | 73 |
0.0599 (0.389) |
0.792 (0.993) |
0.795 (0.993) |
0.104 (0.5) |
0.471 (0.887) |
0.0327 (0.286) |
0.204 (0.663) |
0.0997 (0.488) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0373 (0.309) |
0.52 (0.908) |
0.769 (0.989) |
0.155 (0.607) |
0.131 (0.563) |
0.013 (0.179) |
amp 12q15 | 33 (30%) | 77 |
0.812 (0.995) |
0.823 (1.00) |
0.161 (0.607) |
0.968 (1.00) |
0.316 (0.769) |
0.0216 (0.228) |
0.12 (0.544) |
0.441 (0.877) |
0.548 (0.908) |
0.509 (0.908) |
1 (1.00) |
0.287 (0.734) |
0.194 (0.653) |
0.721 (0.96) |
0.292 (0.737) |
0.979 (1.00) |
0.201 (0.662) |
amp 17q23 1 | 54 (49%) | 56 |
0.124 (0.545) |
0.561 (0.911) |
0.212 (0.663) |
0.0614 (0.392) |
0.0352 (0.302) |
0.0167 (0.2) |
0.235 (0.701) |
0.601 (0.927) |
0.257 (0.714) |
1 (1.00) |
1 (1.00) |
0.627 (0.928) |
0.851 (1.00) |
0.61 (0.927) |
0.847 (1.00) |
0.0922 (0.475) |
0.248 (0.707) |
del 6p11 2 | 12 (11%) | 98 |
0.134 (0.568) |
0.272 (0.728) |
0.313 (0.769) |
0.852 (1.00) |
0.315 (0.769) |
0.0953 (0.483) |
0.0269 (0.259) |
0.0138 (0.187) |
0.0811 (0.454) |
1 (1.00) |
0.696 (0.956) |
0.84 (1.00) |
0.741 (0.976) |
0.759 (0.983) |
0.307 (0.764) |
0.0714 (0.421) |
|
del 9p23 | 63 (57%) | 47 |
0.949 (1.00) |
0.805 (0.995) |
0.588 (0.923) |
0.25 (0.709) |
0.881 (1.00) |
0.036 (0.306) |
0.722 (0.96) |
0.0533 (0.37) |
0.568 (0.916) |
0.00202 (0.0762) |
1 (1.00) |
0.463 (0.884) |
0.694 (0.956) |
0.959 (1.00) |
0.169 (0.618) |
0.734 (0.973) |
0.694 (0.956) |
del 9p21 3 | 67 (61%) | 43 |
0.353 (0.794) |
0.0229 (0.236) |
0.387 (0.827) |
0.278 (0.73) |
0.398 (0.831) |
0.218 (0.677) |
0.699 (0.957) |
0.27 (0.726) |
0.544 (0.908) |
0.0378 (0.309) |
1 (1.00) |
0.457 (0.884) |
0.647 (0.935) |
0.461 (0.884) |
0.164 (0.611) |
0.429 (0.866) |
0.694 (0.956) |
del 10q25 1 | 39 (35%) | 71 |
0.597 (0.925) |
0.158 (0.607) |
0.123 (0.545) |
0.52 (0.908) |
0.53 (0.908) |
0.285 (0.734) |
0.239 (0.703) |
0.289 (0.735) |
0.53 (0.908) |
0.139 (0.576) |
0.544 (0.908) |
0.794 (0.993) |
0.253 (0.709) |
0.955 (1.00) |
0.312 (0.769) |
0.122 (0.544) |
0.0242 (0.244) |
del 17p13 1 | 75 (68%) | 35 |
0.336 (0.775) |
0.707 (0.96) |
0.63 (0.928) |
0.0862 (0.461) |
1 (1.00) |
0.0672 (0.402) |
0.745 (0.98) |
0.393 (0.83) |
0.604 (0.927) |
1 (1.00) |
0.458 (0.884) |
0.804 (0.995) |
0.00635 (0.123) |
0.0561 (0.383) |
0.536 (0.908) |
0.0308 (0.272) |
0.091 (0.473) |
del 19q13 33 | 43 (39%) | 67 |
0.173 (0.618) |
0.709 (0.96) |
0.747 (0.98) |
0.423 (0.863) |
0.207 (0.663) |
0.704 (0.959) |
0.527 (0.908) |
0.0542 (0.373) |
1 (1.00) |
0.0125 (0.174) |
0.256 (0.714) |
0.448 (0.882) |
0.0879 (0.465) |
0.811 (0.995) |
0.842 (1.00) |
0.922 (1.00) |
0.55 (0.909) |
del 21p11 2 | 66 (60%) | 44 |
0.0388 (0.315) |
0.634 (0.928) |
0.0662 (0.401) |
0.0589 (0.387) |
0.248 (0.707) |
0.838 (1.00) |
0.41 (0.849) |
0.687 (0.956) |
0.105 (0.5) |
0.00399 (0.1) |
0.457 (0.884) |
0.0523 (0.369) |
0.17 (0.618) |
0.475 (0.89) |
0.691 (0.956) |
0.0482 (0.359) |
0.0487 (0.359) |
del xp22 33 | 23 (21%) | 87 |
0.433 (0.868) |
0.273 (0.728) |
1 (1.00) |
0.46 (0.884) |
0.12 (0.544) |
0.144 (0.583) |
0.0574 (0.386) |
0.525 (0.908) |
1 (1.00) |
0.000859 (0.0438) |
0.54 (0.908) |
0.758 (0.983) |
0.633 (0.928) |
0.285 (0.734) |
0.0601 (0.389) |
0.774 (0.99) |
0.465 (0.884) |
del yq11 223 | 69 (63%) | 41 |
0.62 (0.928) |
0.632 (0.928) |
0.197 (0.656) |
0.121 (0.544) |
0.112 (0.521) |
0.177 (0.624) |
0.00823 (0.143) |
0.692 (0.956) |
1 (1.00) |
0.0966 (0.483) |
0.815 (0.996) |
0.619 (0.928) |
0.5 (0.908) |
0.873 (1.00) |
1 (1.00) |
0.0755 (0.437) |
0.547 (0.908) |
amp 1p34 2 | 26 (24%) | 84 |
0.885 (1.00) |
0.991 (1.00) |
0.337 (0.775) |
0.365 (0.808) |
0.499 (0.908) |
0.309 (0.766) |
0.323 (0.769) |
0.819 (1.00) |
0.562 (0.911) |
0.0577 (0.386) |
1 (1.00) |
1 (1.00) |
0.993 (1.00) |
0.341 (0.781) |
0.821 (1.00) |
0.69 (0.956) |
1 (1.00) |
amp 6p21 1 | 44 (40%) | 66 |
0.278 (0.73) |
0.799 (0.995) |
0.905 (1.00) |
0.573 (0.921) |
0.522 (0.908) |
0.589 (0.923) |
0.807 (0.995) |
0.135 (0.57) |
0.548 (0.908) |
0.683 (0.956) |
1 (1.00) |
0.0839 (0.458) |
0.796 (0.993) |
0.879 (1.00) |
0.171 (0.618) |
0.112 (0.521) |
0.112 (0.521) |
amp 13q31 1 | 30 (27%) | 80 |
0.182 (0.636) |
0.281 (0.733) |
0.211 (0.663) |
0.351 (0.794) |
0.536 (0.908) |
0.947 (1.00) |
0.463 (0.884) |
0.584 (0.923) |
0.477 (0.89) |
0.257 (0.714) |
0.43 (0.866) |
0.415 (0.853) |
0.911 (1.00) |
0.0762 (0.437) |
0.0445 (0.347) |
0.315 (0.769) |
0.194 (0.653) |
amp 19q12 | 33 (30%) | 77 |
0.347 (0.787) |
0.674 (0.956) |
0.128 (0.554) |
0.989 (1.00) |
0.39 (0.828) |
0.522 (0.908) |
0.79 (0.993) |
0.906 (1.00) |
0.562 (0.911) |
0.0816 (0.454) |
1 (1.00) |
0.794 (0.993) |
0.463 (0.884) |
0.813 (0.995) |
0.527 (0.908) |
0.0926 (0.475) |
0.673 (0.956) |
amp 20p11 21 | 27 (25%) | 83 |
0.0423 (0.336) |
0.382 (0.823) |
0.321 (0.769) |
0.24 (0.703) |
0.894 (1.00) |
0.672 (0.956) |
0.87 (1.00) |
0.48 (0.89) |
1 (1.00) |
0.36 (0.804) |
1 (1.00) |
0.786 (0.993) |
0.738 (0.976) |
0.286 (0.734) |
0.654 (0.941) |
0.607 (0.927) |
0.371 (0.813) |
amp 21p12 | 24 (22%) | 86 |
0.893 (1.00) |
0.609 (0.927) |
0.278 (0.73) |
0.527 (0.908) |
0.578 (0.921) |
0.374 (0.813) |
0.159 (0.607) |
0.142 (0.58) |
1 (1.00) |
0.464 (0.884) |
1 (1.00) |
1 (1.00) |
0.269 (0.726) |
0.697 (0.956) |
0.159 (0.607) |
0.785 (0.993) |
0.485 (0.893) |
amp yq11 223 | 25 (23%) | 85 |
0.429 (0.866) |
0.428 (0.866) |
0.26 (0.715) |
0.26 (0.715) |
0.368 (0.811) |
0.0489 (0.359) |
0.047 (0.359) |
0.756 (0.983) |
1 (1.00) |
0.0963 (0.483) |
0.545 (0.908) |
0.375 (0.813) |
0.203 (0.663) |
0.585 (0.923) |
0.159 (0.607) |
0.456 (0.884) |
0.645 (0.933) |
del 1p13 3 | 38 (35%) | 72 |
0.15 (0.595) |
0.892 (1.00) |
0.642 (0.932) |
0.722 (0.96) |
0.607 (0.927) |
0.627 (0.928) |
0.89 (1.00) |
0.68 (0.956) |
1 (1.00) |
0.399 (0.831) |
0.591 (0.923) |
0.122 (0.544) |
0.63 (0.928) |
0.678 (0.956) |
0.0256 (0.254) |
0.526 (0.908) |
0.0995 (0.488) |
del 4q35 2 | 37 (34%) | 73 |
0.608 (0.927) |
0.889 (1.00) |
0.59 (0.923) |
0.0895 (0.47) |
1 (1.00) |
0.955 (1.00) |
0.295 (0.743) |
0.595 (0.924) |
0.537 (0.908) |
0.394 (0.83) |
0.251 (0.709) |
0.795 (0.993) |
0.247 (0.707) |
0.944 (1.00) |
0.151 (0.596) |
0.593 (0.924) |
1 (1.00) |
del 12p13 1 | 44 (40%) | 66 |
0.186 (0.641) |
0.83 (1.00) |
0.663 (0.95) |
0.239 (0.703) |
0.336 (0.775) |
0.127 (0.554) |
0.279 (0.73) |
0.272 (0.728) |
0.0721 (0.422) |
0.413 (0.852) |
1 (1.00) |
0.46 (0.884) |
0.436 (0.871) |
0.409 (0.849) |
0.549 (0.908) |
0.199 (0.657) |
0.694 (0.956) |
del 16q24 3 | 42 (38%) | 68 |
0.544 (0.908) |
0.844 (1.00) |
0.265 (0.724) |
0.187 (0.642) |
0.639 (0.93) |
0.194 (0.653) |
0.231 (0.692) |
0.7 (0.958) |
0.537 (0.908) |
1 (1.00) |
0.717 (0.96) |
1 (1.00) |
0.0428 (0.338) |
0.174 (0.618) |
0.688 (0.956) |
0.442 (0.878) |
0.0268 (0.259) |
del 21q11 2 | 25 (23%) | 85 |
0.771 (0.989) |
0.289 (0.735) |
0.604 (0.927) |
0.396 (0.83) |
0.748 (0.98) |
0.431 (0.866) |
0.446 (0.88) |
0.895 (1.00) |
1 (1.00) |
0.337 (0.775) |
1 (1.00) |
0.382 (0.823) |
0.145 (0.583) |
0.739 (0.976) |
0.487 (0.893) |
0.782 (0.993) |
0.356 (0.797) |
P value = 0.00959 (Wilcoxon-test), Q value = 0.15
Table S1. Gene #2: 'amp_1q21.2' versus Clinical Feature #14: 'NUMBER_PACK_YEARS_SMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 27.3 (23.6) |
AMP PEAK 2(1Q21.2) MUTATED | 45 | 23.8 (21.8) |
AMP PEAK 2(1Q21.2) WILD-TYPE | 9 | 44.9 (25.6) |
Figure S1. Get High-res Image Gene #2: 'amp_1q21.2' versus Clinical Feature #14: 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0192 (Fisher's exact test), Q value = 0.21
Table S2. Gene #3: 'amp_4q12' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 3(4Q12) MUTATED | 16 | 3 |
AMP PEAK 3(4Q12) WILD-TYPE | 47 | 42 |
Figure S2. Get High-res Image Gene #3: 'amp_4q12' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0163 (Wilcoxon-test), Q value = 0.2
Table S3. Gene #4: 'amp_5p15.33' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
N0 | N1 | N2 | |
---|---|---|---|
ALL | 73 | 17 | 19 |
AMP PEAK 4(5P15.33) MUTATED | 49 | 16 | 10 |
AMP PEAK 4(5P15.33) WILD-TYPE | 24 | 1 | 9 |
Figure S3. Get High-res Image Gene #4: 'amp_5p15.33' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.00946 (Fisher's exact test), Q value = 0.15
Table S4. Gene #5: 'amp_5q35.1' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
AMP PEAK 5(5Q35.1) MUTATED | 18 | 17 |
AMP PEAK 5(5Q35.1) WILD-TYPE | 19 | 56 |
Figure S4. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #10: 'GENDER'

P value = 0.00576 (Fisher's exact test), Q value = 0.12
Table S5. Gene #5: 'amp_5q35.1' versus Clinical Feature #15: 'SMOKER'
nPatients | NON-SMOKER | SMOKER |
---|---|---|
ALL | 46 | 61 |
AMP PEAK 5(5Q35.1) MUTATED | 21 | 12 |
AMP PEAK 5(5Q35.1) WILD-TYPE | 25 | 49 |
Figure S5. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #15: 'SMOKER'

P value = 0.00775 (Fisher's exact test), Q value = 0.14
Table S6. Gene #5: 'amp_5q35.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 5(5Q35.1) MUTATED | 1 | 0 | 13 | 0 | 0 | 0 | 0 | 1 | 7 | 12 |
AMP PEAK 5(5Q35.1) WILD-TYPE | 1 | 1 | 5 | 1 | 2 | 2 | 1 | 2 | 26 | 33 |
Figure S6. Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00064 (Fisher's exact test), Q value = 0.042
Table S7. Gene #7: 'amp_6q27' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 7(6Q27) MUTATED | 0 | 1 | 14 | 0 | 0 | 1 | 0 | 1 | 6 | 17 |
AMP PEAK 7(6Q27) WILD-TYPE | 2 | 0 | 4 | 1 | 2 | 1 | 1 | 2 | 27 | 28 |
Figure S7. Get High-res Image Gene #7: 'amp_6q27' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00238 (Fisher's exact test), Q value = 0.083
Table S8. Gene #7: 'amp_6q27' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 7(6Q27) MUTATED | 31 | 9 |
AMP PEAK 7(6Q27) WILD-TYPE | 32 | 36 |
Figure S8. Get High-res Image Gene #7: 'amp_6q27' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0209 (Fisher's exact test), Q value = 0.22
Table S9. Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'
nPatients | ACINAR ADENOCARCINOMA | ADENOCARCINOMA | BASALOID SQUAMOUS CELL CARCINOMA | INVASIVE MUCINOUS ADENOCARCINOMA | LEPIDIC ADENOCARCINOMA | MICROPAPILLARY ADENOCARCINOMA | OTHER | PAPILLARY ADENOCARCINOMA | SOLID ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 13 | 68 | 1 | 3 | 1 | 2 | 7 | 5 | 8 | 2 |
AMP PEAK 8(7P11.2) MUTATED | 6 | 46 | 0 | 0 | 0 | 0 | 4 | 1 | 4 | 2 |
AMP PEAK 8(7P11.2) WILD-TYPE | 7 | 22 | 1 | 3 | 1 | 2 | 3 | 4 | 4 | 0 |
Figure S9. Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

P value = 0.0019 (Fisher's exact test), Q value = 0.076
Table S10. Gene #8: 'amp_7p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 8(7P11.2) MUTATED | 1 | 1 | 16 | 0 | 0 | 1 | 0 | 1 | 13 | 29 |
AMP PEAK 8(7P11.2) WILD-TYPE | 1 | 0 | 2 | 1 | 2 | 1 | 1 | 2 | 20 | 16 |
Figure S10. Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.000732 (Fisher's exact test), Q value = 0.042
Table S11. Gene #8: 'amp_7p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 8(7P11.2) MUTATED | 45 | 17 |
AMP PEAK 8(7P11.2) WILD-TYPE | 18 | 28 |
Figure S11. Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0167 (Fisher's exact test), Q value = 0.2
Table S12. Gene #9: 'amp_8q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 9(8Q13.1) MUTATED | 2 | 0 | 9 | 0 | 1 | 0 | 0 | 0 | 8 | 25 |
AMP PEAK 9(8Q13.1) WILD-TYPE | 0 | 1 | 9 | 1 | 1 | 2 | 1 | 3 | 25 | 20 |
Figure S12. Get High-res Image Gene #9: 'amp_8q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00288 (Fisher's exact test), Q value = 0.092
Table S13. Gene #9: 'amp_8q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 9(8Q13.1) MUTATED | 34 | 11 |
AMP PEAK 9(8Q13.1) WILD-TYPE | 29 | 34 |
Figure S13. Get High-res Image Gene #9: 'amp_8q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00189 (Fisher's exact test), Q value = 0.076
Table S14. Gene #10: 'amp_8q24.21' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
AMP PEAK 10(8Q24.21) MUTATED | 40 | 3 | 10 | 2 | 10 |
AMP PEAK 10(8Q24.21) WILD-TYPE | 13 | 7 | 18 | 1 | 6 |
Figure S14. Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #13: 'BMI'

P value = 7e-05 (Fisher's exact test), Q value = 0.015
Table S15. Gene #10: 'amp_8q24.21' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 10(8Q24.21) MUTATED | 2 | 0 | 14 | 0 | 1 | 1 | 0 | 0 | 11 | 34 |
AMP PEAK 10(8Q24.21) WILD-TYPE | 0 | 1 | 4 | 1 | 1 | 1 | 1 | 3 | 22 | 11 |
Figure S15. Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.0077
Table S16. Gene #10: 'amp_8q24.21' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 10(8Q24.21) MUTATED | 48 | 15 |
AMP PEAK 10(8Q24.21) WILD-TYPE | 15 | 30 |
Figure S16. Get High-res Image Gene #10: 'amp_8q24.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00022 (Fisher's exact test), Q value = 0.028
Table S17. Gene #11: 'amp_8q24.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 11(8Q24.3) MUTATED | 1 | 1 | 14 | 0 | 1 | 1 | 0 | 0 | 13 | 36 |
AMP PEAK 11(8Q24.3) WILD-TYPE | 1 | 0 | 4 | 1 | 1 | 1 | 1 | 3 | 20 | 9 |
Figure S17. Get High-res Image Gene #11: 'amp_8q24.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.0077
Table S18. Gene #11: 'amp_8q24.3' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 11(8Q24.3) MUTATED | 50 | 17 |
AMP PEAK 11(8Q24.3) WILD-TYPE | 13 | 28 |
Figure S18. Get High-res Image Gene #11: 'amp_8q24.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00861 (Fisher's exact test), Q value = 0.14
Table S19. Gene #12: 'amp_11q13.3' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
AMP PEAK 12(11Q13.3) MUTATED | 28 | 4 | 5 | 0 | 9 |
AMP PEAK 12(11Q13.3) WILD-TYPE | 25 | 6 | 23 | 3 | 7 |
Figure S19. Get High-res Image Gene #12: 'amp_11q13.3' versus Clinical Feature #13: 'BMI'

P value = 0.00419 (Wilcoxon-test), Q value = 0.1
Table S20. Gene #13: 'amp_12p13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
AMP PEAK 13(12P13.33) MUTATED | 54 | 60.3 (8.6) |
AMP PEAK 13(12P13.33) WILD-TYPE | 56 | 64.9 (10.1) |
Figure S20. Get High-res Image Gene #13: 'amp_12p13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00344 (Fisher's exact test), Q value = 0.096
Table S21. Gene #13: 'amp_12p13.33' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 13(12P13.33) MUTATED | 38 | 14 |
AMP PEAK 13(12P13.33) WILD-TYPE | 25 | 31 |
Figure S21. Get High-res Image Gene #13: 'amp_12p13.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.013 (Fisher's exact test), Q value = 0.18
Table S22. Gene #14: 'amp_12p11.21' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 14(12P11.21) MUTATED | 28 | 9 |
AMP PEAK 14(12P11.21) WILD-TYPE | 35 | 36 |
Figure S22. Get High-res Image Gene #14: 'amp_12p11.21' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0216 (Wilcoxon-test), Q value = 0.23
Table S23. Gene #15: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
N0 | N1 | N2 | |
---|---|---|---|
ALL | 73 | 17 | 19 |
AMP PEAK 15(12Q15) MUTATED | 16 | 9 | 8 |
AMP PEAK 15(12Q15) WILD-TYPE | 57 | 8 | 11 |
Figure S23. Get High-res Image Gene #15: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.0074 (Wilcoxon-test), Q value = 0.13
Table S24. Gene #17: 'amp_14q13.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
AMP PEAK 17(14Q13.3) MUTATED | 62 | 60.5 (8.8) |
AMP PEAK 17(14Q13.3) WILD-TYPE | 48 | 65.3 (10.1) |
Figure S24. Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00038 (Fisher's exact test), Q value = 0.034
Table S25. Gene #17: 'amp_14q13.3' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
AMP PEAK 17(14Q13.3) MUTATED | 40 | 6 | 9 | 0 | 7 |
AMP PEAK 17(14Q13.3) WILD-TYPE | 13 | 4 | 19 | 3 | 9 |
Figure S25. Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #13: 'BMI'

P value = 7e-04 (Fisher's exact test), Q value = 0.042
Table S26. Gene #17: 'amp_14q13.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 17(14Q13.3) MUTATED | 2 | 0 | 14 | 1 | 0 | 0 | 0 | 2 | 11 | 31 |
AMP PEAK 17(14Q13.3) WILD-TYPE | 0 | 1 | 4 | 0 | 2 | 2 | 1 | 1 | 22 | 14 |
Figure S26. Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.000346 (Fisher's exact test), Q value = 0.034
Table S27. Gene #17: 'amp_14q13.3' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 17(14Q13.3) MUTATED | 45 | 16 |
AMP PEAK 17(14Q13.3) WILD-TYPE | 18 | 29 |
Figure S27. Get High-res Image Gene #17: 'amp_14q13.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0147 (Fisher's exact test), Q value = 0.19
Table S28. Gene #18: 'amp_14q32.33' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'
nPatients | ACINAR ADENOCARCINOMA | ADENOCARCINOMA | BASALOID SQUAMOUS CELL CARCINOMA | INVASIVE MUCINOUS ADENOCARCINOMA | LEPIDIC ADENOCARCINOMA | MICROPAPILLARY ADENOCARCINOMA | OTHER | PAPILLARY ADENOCARCINOMA | SOLID ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 13 | 68 | 1 | 3 | 1 | 2 | 7 | 5 | 8 | 2 |
AMP PEAK 18(14Q32.33) MUTATED | 1 | 33 | 0 | 1 | 0 | 2 | 1 | 3 | 5 | 0 |
AMP PEAK 18(14Q32.33) WILD-TYPE | 12 | 35 | 1 | 2 | 1 | 0 | 6 | 2 | 3 | 2 |
Figure S28. Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

P value = 0.000392 (Wilcoxon-test), Q value = 0.034
Table S29. Gene #18: 'amp_14q32.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
AMP PEAK 18(14Q32.33) MUTATED | 46 | 59.1 (8.7) |
AMP PEAK 18(14Q32.33) WILD-TYPE | 64 | 65.2 (9.5) |
Figure S29. Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00311 (Fisher's exact test), Q value = 0.093
Table S30. Gene #18: 'amp_14q32.33' versus Clinical Feature #15: 'SMOKER'
nPatients | NON-SMOKER | SMOKER |
---|---|---|
ALL | 46 | 61 |
AMP PEAK 18(14Q32.33) MUTATED | 27 | 18 |
AMP PEAK 18(14Q32.33) WILD-TYPE | 19 | 43 |
Figure S30. Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #15: 'SMOKER'

P value = 0.00132 (Fisher's exact test), Q value = 0.064
Table S31. Gene #18: 'amp_14q32.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 18(14Q32.33) MUTATED | 1 | 0 | 10 | 1 | 0 | 1 | 0 | 2 | 5 | 25 |
AMP PEAK 18(14Q32.33) WILD-TYPE | 1 | 1 | 8 | 0 | 2 | 1 | 1 | 1 | 28 | 20 |
Figure S31. Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.000704 (Fisher's exact test), Q value = 0.042
Table S32. Gene #18: 'amp_14q32.33' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 18(14Q32.33) MUTATED | 35 | 10 |
AMP PEAK 18(14Q32.33) WILD-TYPE | 28 | 35 |
Figure S32. Get High-res Image Gene #18: 'amp_14q32.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0167 (Wilcoxon-test), Q value = 0.2
Table S33. Gene #19: 'amp_17q23.1' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'
N0 | N1 | N2 | |
---|---|---|---|
ALL | 73 | 17 | 19 |
AMP PEAK 19(17Q23.1) MUTATED | 39 | 11 | 4 |
AMP PEAK 19(17Q23.1) WILD-TYPE | 34 | 6 | 15 |
Figure S33. Get High-res Image Gene #19: 'amp_17q23.1' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

P value = 0.00676 (logrank test), Q value = 0.13
Table S34. Gene #22: 'amp_20q13.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 110 | 11 | 0.2 - 35.0 (13.1) |
AMP PEAK 22(20Q13.2) MUTATED | 47 | 1 | 0.2 - 35.0 (13.6) |
AMP PEAK 22(20Q13.2) WILD-TYPE | 55 | 10 | 0.2 - 27.4 (12.0) |
Figure S34. Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00238 (Fisher's exact test), Q value = 0.083
Table S35. Gene #22: 'amp_20q13.2' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'
nPatients | G1 | G2 | G3 | G4 | GX |
---|---|---|---|---|---|
ALL | 7 | 65 | 31 | 1 | 6 |
AMP PEAK 22(20Q13.2) MUTATED | 0 | 35 | 15 | 1 | 0 |
AMP PEAK 22(20Q13.2) WILD-TYPE | 7 | 30 | 16 | 0 | 6 |
Figure S35. Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

P value = 0.0182 (Fisher's exact test), Q value = 0.21
Table S36. Gene #22: 'amp_20q13.2' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 22(20Q13.2) MUTATED | 35 | 14 |
AMP PEAK 22(20Q13.2) WILD-TYPE | 28 | 31 |
Figure S36. Get High-res Image Gene #22: 'amp_20q13.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00636 (logrank test), Q value = 0.12
Table S37. Gene #23: 'amp_20q13.33' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 110 | 11 | 0.2 - 35.0 (13.1) |
AMP PEAK 23(20Q13.33) MUTATED | 48 | 1 | 0.2 - 35.0 (13.6) |
AMP PEAK 23(20Q13.33) WILD-TYPE | 54 | 10 | 0.2 - 27.4 (12.0) |
Figure S37. Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.0171 (Fisher's exact test), Q value = 0.2
Table S38. Gene #23: 'amp_20q13.33' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'
nPatients | G1 | G2 | G3 | G4 | GX |
---|---|---|---|---|---|
ALL | 7 | 65 | 31 | 1 | 6 |
AMP PEAK 23(20Q13.33) MUTATED | 1 | 35 | 14 | 1 | 0 |
AMP PEAK 23(20Q13.33) WILD-TYPE | 6 | 30 | 17 | 0 | 6 |
Figure S38. Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

P value = 0.0179 (Wilcoxon-test), Q value = 0.2
Table S39. Gene #23: 'amp_20q13.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 81.7 (9.0) |
AMP PEAK 23(20Q13.33) MUTATED | 35 | 79.1 (8.2) |
AMP PEAK 23(20Q13.33) WILD-TYPE | 35 | 84.3 (9.2) |
Figure S39. Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0219 (Wilcoxon-test), Q value = 0.23
Table S40. Gene #23: 'amp_20q13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
AMP PEAK 23(20Q13.33) MUTATED | 51 | 60.5 (9.3) |
AMP PEAK 23(20Q13.33) WILD-TYPE | 59 | 64.4 (9.7) |
Figure S40. Get High-res Image Gene #23: 'amp_20q13.33' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.0173 (Fisher's exact test), Q value = 0.2
Table S41. Gene #25: 'amp_xp22.33' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IV |
---|---|---|---|---|---|---|---|---|
ALL | 2 | 22 | 34 | 17 | 13 | 1 | 20 | 1 |
AMP PEAK 25(XP22.33) MUTATED | 0 | 10 | 8 | 11 | 4 | 0 | 12 | 1 |
AMP PEAK 25(XP22.33) WILD-TYPE | 2 | 12 | 26 | 6 | 9 | 1 | 8 | 0 |
Figure S41. Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

P value = 0.00581 (Fisher's exact test), Q value = 0.12
Table S42. Gene #25: 'amp_xp22.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 25(XP22.33) MUTATED | 0 | 0 | 14 | 0 | 0 | 1 | 0 | 0 | 10 | 21 |
AMP PEAK 25(XP22.33) WILD-TYPE | 2 | 1 | 4 | 1 | 2 | 1 | 1 | 3 | 23 | 24 |
Figure S42. Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00157 (Fisher's exact test), Q value = 0.072
Table S43. Gene #25: 'amp_xp22.33' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 25(XP22.33) MUTATED | 35 | 11 |
AMP PEAK 25(XP22.33) WILD-TYPE | 28 | 34 |
Figure S43. Get High-res Image Gene #25: 'amp_xp22.33' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00356 (Fisher's exact test), Q value = 0.096
Table S44. Gene #26: 'amp_xq27.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
AMP PEAK 26(XQ27.3) MUTATED | 2 | 1 | 13 | 0 | 1 | 1 | 1 | 0 | 11 | 30 |
AMP PEAK 26(XQ27.3) WILD-TYPE | 0 | 0 | 5 | 1 | 1 | 1 | 0 | 3 | 22 | 15 |
Figure S44. Get High-res Image Gene #26: 'amp_xq27.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00301 (Fisher's exact test), Q value = 0.093
Table S45. Gene #26: 'amp_xq27.3' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
AMP PEAK 26(XQ27.3) MUTATED | 43 | 17 |
AMP PEAK 26(XQ27.3) WILD-TYPE | 20 | 28 |
Figure S45. Get High-res Image Gene #26: 'amp_xq27.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0141 (Wilcoxon-test), Q value = 0.19
Table S46. Gene #29: 'del_3p24.1' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'
T1 | T2 | T3 | |
---|---|---|---|
ALL | 27 | 70 | 13 |
DEL PEAK 2(3P24.1) MUTATED | 13 | 29 | 11 |
DEL PEAK 2(3P24.1) WILD-TYPE | 14 | 41 | 2 |
Figure S46. Get High-res Image Gene #29: 'del_3p24.1' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

P value = 0.0161 (Wilcoxon-test), Q value = 0.2
Table S47. Gene #29: 'del_3p24.1' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
DEL PEAK 2(3P24.1) MUTATED | 53 | 60.1 (9.6) |
DEL PEAK 2(3P24.1) WILD-TYPE | 57 | 64.9 (9.1) |
Figure S47. Get High-res Image Gene #29: 'del_3p24.1' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00452 (Fisher's exact test), Q value = 0.1
Table S48. Gene #31: 'del_5q15' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 4(5Q15) MUTATED | 1 | 1 | 6 | 1 | 0 | 0 | 0 | 2 | 6 | 25 |
DEL PEAK 4(5Q15) WILD-TYPE | 1 | 0 | 12 | 0 | 2 | 2 | 1 | 1 | 27 | 20 |
Figure S48. Get High-res Image Gene #31: 'del_5q15' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.0101 (Fisher's exact test), Q value = 0.15
Table S49. Gene #31: 'del_5q15' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 4(5Q15) MUTATED | 31 | 11 |
DEL PEAK 4(5Q15) WILD-TYPE | 32 | 34 |
Figure S49. Get High-res Image Gene #31: 'del_5q15' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0138 (Wilcoxon-test), Q value = 0.19
Table S50. Gene #32: 'del_6p11.2' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
DEL PEAK 5(6P11.2) MUTATED | 12 | 56.0 (10.4) |
DEL PEAK 5(6P11.2) WILD-TYPE | 98 | 63.4 (9.3) |
Figure S50. Get High-res Image Gene #32: 'del_6p11.2' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00481 (Wilcoxon-test), Q value = 0.11
Table S51. Gene #33: 'del_6q16.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
DEL PEAK 6(6Q16.3) MUTATED | 58 | 60.1 (9.4) |
DEL PEAK 6(6Q16.3) WILD-TYPE | 52 | 65.4 (9.2) |
Figure S51. Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00056 (Fisher's exact test), Q value = 0.042
Table S52. Gene #33: 'del_6q16.3' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 6(6Q16.3) MUTATED | 33 | 3 | 7 | 2 | 13 |
DEL PEAK 6(6Q16.3) WILD-TYPE | 20 | 7 | 21 | 1 | 3 |
Figure S52. Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #13: 'BMI'

P value = 0.00404 (Fisher's exact test), Q value = 0.1
Table S53. Gene #33: 'del_6q16.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 6(6Q16.3) MUTATED | 2 | 0 | 11 | 0 | 1 | 1 | 0 | 0 | 11 | 31 |
DEL PEAK 6(6Q16.3) WILD-TYPE | 0 | 1 | 7 | 1 | 1 | 1 | 1 | 3 | 22 | 14 |
Figure S53. Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.000853 (Fisher's exact test), Q value = 0.044
Table S54. Gene #33: 'del_6q16.3' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 6(6Q16.3) MUTATED | 42 | 15 |
DEL PEAK 6(6Q16.3) WILD-TYPE | 21 | 30 |
Figure S54. Get High-res Image Gene #33: 'del_6q16.3' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.012 (Fisher's exact test), Q value = 0.17
Table S55. Gene #34: 'del_8p23.1' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'
nPatients | G1 | G2 | G3 | G4 | GX |
---|---|---|---|---|---|
ALL | 7 | 65 | 31 | 1 | 6 |
DEL PEAK 7(8P23.1) MUTATED | 0 | 39 | 16 | 1 | 2 |
DEL PEAK 7(8P23.1) WILD-TYPE | 7 | 26 | 15 | 0 | 4 |
Figure S55. Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #3: 'HISTOLOGIC_GRADE'

P value = 0.00249 (Fisher's exact test), Q value = 0.083
Table S56. Gene #34: 'del_8p23.1' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 7(8P23.1) MUTATED | 33 | 6 | 6 | 2 | 11 |
DEL PEAK 7(8P23.1) WILD-TYPE | 20 | 4 | 22 | 1 | 5 |
Figure S56. Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #13: 'BMI'

P value = 0.0189 (Fisher's exact test), Q value = 0.21
Table S57. Gene #34: 'del_8p23.1' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 7(8P23.1) MUTATED | 39 | 17 |
DEL PEAK 7(8P23.1) WILD-TYPE | 24 | 28 |
Figure S57. Get High-res Image Gene #34: 'del_8p23.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00202 (Fisher's exact test), Q value = 0.076
Table S58. Gene #35: 'del_9p23' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
DEL PEAK 8(9P23) MUTATED | 29 | 34 |
DEL PEAK 8(9P23) WILD-TYPE | 8 | 39 |
Figure S58. Get High-res Image Gene #35: 'del_9p23' versus Clinical Feature #10: 'GENDER'

P value = 0.0229 (Fisher's exact test), Q value = 0.24
Table S59. Gene #36: 'del_9p21.3' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'
nPatients | ACINAR ADENOCARCINOMA | ADENOCARCINOMA | BASALOID SQUAMOUS CELL CARCINOMA | INVASIVE MUCINOUS ADENOCARCINOMA | LEPIDIC ADENOCARCINOMA | MICROPAPILLARY ADENOCARCINOMA | OTHER | PAPILLARY ADENOCARCINOMA | SOLID ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 13 | 68 | 1 | 3 | 1 | 2 | 7 | 5 | 8 | 2 |
DEL PEAK 9(9P21.3) MUTATED | 8 | 41 | 1 | 0 | 1 | 1 | 7 | 4 | 2 | 2 |
DEL PEAK 9(9P21.3) WILD-TYPE | 5 | 27 | 0 | 3 | 0 | 1 | 0 | 1 | 6 | 0 |
Figure S59. Get High-res Image Gene #36: 'del_9p21.3' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

P value = 0.0242 (Fisher's exact test), Q value = 0.24
Table S60. Gene #37: 'del_10q25.1' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 10(10Q25.1) MUTATED | 28 | 10 |
DEL PEAK 10(10Q25.1) WILD-TYPE | 35 | 35 |
Figure S60. Get High-res Image Gene #37: 'del_10q25.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00856 (Wilcoxon-test), Q value = 0.14
Table S61. Gene #39: 'del_13q11' versus Clinical Feature #8: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 110 | 62.6 (9.6) |
DEL PEAK 12(13Q11) MUTATED | 64 | 60.7 (9.6) |
DEL PEAK 12(13Q11) WILD-TYPE | 46 | 65.3 (9.1) |
Figure S61. Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #8: 'YEARS_TO_BIRTH'

P value = 0.00434 (Fisher's exact test), Q value = 0.1
Table S62. Gene #39: 'del_13q11' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 12(13Q11) MUTATED | 34 | 4 | 10 | 2 | 14 |
DEL PEAK 12(13Q11) WILD-TYPE | 19 | 6 | 18 | 1 | 2 |
Figure S62. Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #13: 'BMI'

P value = 1e-04 (Fisher's exact test), Q value = 0.017
Table S63. Gene #39: 'del_13q11' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 12(13Q11) MUTATED | 2 | 0 | 11 | 0 | 0 | 1 | 1 | 1 | 11 | 36 |
DEL PEAK 12(13Q11) WILD-TYPE | 0 | 1 | 7 | 1 | 2 | 1 | 0 | 2 | 22 | 9 |
Figure S63. Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 6.72e-05 (Fisher's exact test), Q value = 0.015
Table S64. Gene #39: 'del_13q11' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 12(13Q11) MUTATED | 47 | 16 |
DEL PEAK 12(13Q11) WILD-TYPE | 16 | 29 |
Figure S64. Get High-res Image Gene #39: 'del_13q11' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0124 (Wilcoxon-test), Q value = 0.17
Table S65. Gene #40: 'del_15q13.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 81.7 (9.0) |
DEL PEAK 13(15Q13.1) MUTATED | 46 | 79.8 (8.3) |
DEL PEAK 13(15Q13.1) WILD-TYPE | 24 | 85.4 (9.3) |
Figure S65. Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0173 (Fisher's exact test), Q value = 0.2
Table S66. Gene #40: 'del_15q13.1' versus Clinical Feature #15: 'SMOKER'
nPatients | NON-SMOKER | SMOKER |
---|---|---|
ALL | 46 | 61 |
DEL PEAK 13(15Q13.1) MUTATED | 33 | 29 |
DEL PEAK 13(15Q13.1) WILD-TYPE | 13 | 32 |
Figure S66. Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #15: 'SMOKER'

P value = 0.00593 (Fisher's exact test), Q value = 0.12
Table S67. Gene #40: 'del_15q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 13(15Q13.1) MUTATED | 1 | 1 | 9 | 0 | 0 | 0 | 0 | 2 | 16 | 35 |
DEL PEAK 13(15Q13.1) WILD-TYPE | 1 | 0 | 9 | 1 | 2 | 2 | 1 | 1 | 17 | 10 |
Figure S67. Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.0101 (Fisher's exact test), Q value = 0.15
Table S68. Gene #40: 'del_15q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 13(15Q13.1) MUTATED | 44 | 20 |
DEL PEAK 13(15Q13.1) WILD-TYPE | 19 | 25 |
Figure S68. Get High-res Image Gene #40: 'del_15q13.1' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00635 (Fisher's exact test), Q value = 0.12
Table S69. Gene #42: 'del_17p13.1' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 15(17P13.1) MUTATED | 34 | 7 | 15 | 3 | 16 |
DEL PEAK 15(17P13.1) WILD-TYPE | 19 | 3 | 13 | 0 | 0 |
Figure S69. Get High-res Image Gene #42: 'del_17p13.1' versus Clinical Feature #13: 'BMI'

P value = 0.00023 (Fisher's exact test), Q value = 0.028
Table S70. Gene #43: 'del_18q21.31' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 16(18Q21.31) MUTATED | 32 | 5 | 8 | 1 | 15 |
DEL PEAK 16(18Q21.31) WILD-TYPE | 21 | 5 | 20 | 2 | 1 |
Figure S70. Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #13: 'BMI'

P value = 0.0144 (Fisher's exact test), Q value = 0.19
Table S71. Gene #43: 'del_18q21.31' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 16(18Q21.31) MUTATED | 1 | 1 | 10 | 0 | 0 | 1 | 0 | 0 | 14 | 32 |
DEL PEAK 16(18Q21.31) WILD-TYPE | 1 | 0 | 8 | 1 | 2 | 1 | 1 | 3 | 19 | 13 |
Figure S71. Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00351 (Fisher's exact test), Q value = 0.096
Table S72. Gene #43: 'del_18q21.31' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 16(18Q21.31) MUTATED | 42 | 17 |
DEL PEAK 16(18Q21.31) WILD-TYPE | 21 | 28 |
Figure S72. Get High-res Image Gene #43: 'del_18q21.31' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.0125 (Fisher's exact test), Q value = 0.17
Table S73. Gene #44: 'del_19q13.33' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
DEL PEAK 17(19Q13.33) MUTATED | 21 | 22 |
DEL PEAK 17(19Q13.33) WILD-TYPE | 16 | 51 |
Figure S73. Get High-res Image Gene #44: 'del_19q13.33' versus Clinical Feature #10: 'GENDER'

P value = 0.00399 (Fisher's exact test), Q value = 0.1
Table S74. Gene #45: 'del_21p11.2' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
DEL PEAK 18(21P11.2) MUTATED | 15 | 51 |
DEL PEAK 18(21P11.2) WILD-TYPE | 22 | 22 |
Figure S74. Get High-res Image Gene #45: 'del_21p11.2' versus Clinical Feature #10: 'GENDER'

P value = 0.00584 (Fisher's exact test), Q value = 0.12
Table S75. Gene #47: 'del_22p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'
nPatients | ACINAR ADENOCARCINOMA | ADENOCARCINOMA | BASALOID SQUAMOUS CELL CARCINOMA | INVASIVE MUCINOUS ADENOCARCINOMA | LEPIDIC ADENOCARCINOMA | MICROPAPILLARY ADENOCARCINOMA | OTHER | PAPILLARY ADENOCARCINOMA | SOLID ADENOCARCINOMA | SQUAMOUS CELL CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 13 | 68 | 1 | 3 | 1 | 2 | 7 | 5 | 8 | 2 |
DEL PEAK 20(22P11.2) MUTATED | 1 | 29 | 0 | 2 | 1 | 0 | 2 | 1 | 7 | 1 |
DEL PEAK 20(22P11.2) WILD-TYPE | 12 | 39 | 1 | 1 | 0 | 2 | 5 | 4 | 1 | 1 |
Figure S75. Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

P value = 0.0231 (Fisher's exact test), Q value = 0.24
Table S76. Gene #47: 'del_22p11.2' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
DEL PEAK 20(22P11.2) MUTATED | 9 | 35 |
DEL PEAK 20(22P11.2) WILD-TYPE | 28 | 38 |
Figure S76. Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #10: 'GENDER'

P value = 0.0112 (Fisher's exact test), Q value = 0.16
Table S77. Gene #47: 'del_22p11.2' versus Clinical Feature #12: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 71 | 22 |
DEL PEAK 20(22P11.2) MUTATED | 20 | 13 |
DEL PEAK 20(22P11.2) WILD-TYPE | 51 | 9 |
Figure S77. Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #12: 'RADIATION_THERAPY'

P value = 0.00956 (Fisher's exact test), Q value = 0.15
Table S78. Gene #47: 'del_22p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 20(22P11.2) MUTATED | 2 | 0 | 7 | 0 | 0 | 0 | 1 | 1 | 7 | 25 |
DEL PEAK 20(22P11.2) WILD-TYPE | 0 | 1 | 11 | 1 | 2 | 2 | 0 | 2 | 26 | 20 |
Figure S78. Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00916 (Fisher's exact test), Q value = 0.15
Table S79. Gene #47: 'del_22p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 20(22P11.2) MUTATED | 32 | 11 |
DEL PEAK 20(22P11.2) WILD-TYPE | 31 | 34 |
Figure S79. Get High-res Image Gene #47: 'del_22p11.2' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.00743 (Fisher's exact test), Q value = 0.13
Table S80. Gene #48: 'del_22q13.32' versus Clinical Feature #13: 'BMI'
nPatients | NORMAL | OBESE | OVERWEIGHT | SEVERELY OBESE | UNDERWEIGHT |
---|---|---|---|---|---|
ALL | 53 | 10 | 28 | 3 | 16 |
DEL PEAK 21(22Q13.32) MUTATED | 31 | 7 | 6 | 2 | 9 |
DEL PEAK 21(22Q13.32) WILD-TYPE | 22 | 3 | 22 | 1 | 7 |
Figure S80. Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #13: 'BMI'

P value = 0.016 (Fisher's exact test), Q value = 0.2
Table S81. Gene #48: 'del_22q13.32' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 21(22Q13.32) MUTATED | 2 | 1 | 9 | 0 | 0 | 1 | 1 | 1 | 10 | 29 |
DEL PEAK 21(22Q13.32) WILD-TYPE | 0 | 0 | 9 | 1 | 2 | 1 | 0 | 2 | 23 | 16 |
Figure S81. Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.0187 (Fisher's exact test), Q value = 0.21
Table S82. Gene #48: 'del_22q13.32' versus Clinical Feature #17: 'ORIGIN_ASIA'
nPatients | ASIAN | WESTERN |
---|---|---|
ALL | 63 | 45 |
DEL PEAK 21(22Q13.32) MUTATED | 38 | 16 |
DEL PEAK 21(22Q13.32) WILD-TYPE | 25 | 29 |
Figure S82. Get High-res Image Gene #48: 'del_22q13.32' versus Clinical Feature #17: 'ORIGIN_ASIA'

P value = 0.000859 (Fisher's exact test), Q value = 0.044
Table S83. Gene #49: 'del_xp22.33' versus Clinical Feature #10: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 37 | 73 |
DEL PEAK 22(XP22.33) MUTATED | 15 | 8 |
DEL PEAK 22(XP22.33) WILD-TYPE | 22 | 65 |
Figure S83. Get High-res Image Gene #49: 'del_xp22.33' versus Clinical Feature #10: 'GENDER'

P value = 0.00195 (Wilcoxon-test), Q value = 0.076
Table S84. Gene #50: 'del_xq28' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 70 | 81.7 (9.0) |
DEL PEAK 23(XQ28) MUTATED | 18 | 76.1 (6.1) |
DEL PEAK 23(XQ28) WILD-TYPE | 52 | 83.7 (9.1) |
Figure S84. Get High-res Image Gene #50: 'del_xq28' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00397 (Fisher's exact test), Q value = 0.1
Table S85. Gene #50: 'del_xq28' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'
nPatients | BULGARIA | CANADA | CHINA | JAMAICA | MEXICO | POLAND | RUSSIA | UKRAINE | UNITED STATES | VIETNAM |
---|---|---|---|---|---|---|---|---|---|---|
ALL | 2 | 1 | 18 | 1 | 2 | 2 | 1 | 3 | 33 | 45 |
DEL PEAK 23(XQ28) MUTATED | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 4 | 17 |
DEL PEAK 23(XQ28) WILD-TYPE | 2 | 1 | 18 | 1 | 1 | 2 | 1 | 1 | 29 | 28 |
Figure S85. Get High-res Image Gene #50: 'del_xq28' versus Clinical Feature #16: 'COUNTRY_OF_ORIGIN'

P value = 0.00823 (Fisher's exact test), Q value = 0.14
Table S86. Gene #51: 'del_yq11.223' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IV |
---|---|---|---|---|---|---|---|---|
ALL | 2 | 22 | 34 | 17 | 13 | 1 | 20 | 1 |
DEL PEAK 24(YQ11.223) MUTATED | 1 | 14 | 29 | 10 | 7 | 0 | 8 | 0 |
DEL PEAK 24(YQ11.223) WILD-TYPE | 1 | 8 | 5 | 7 | 6 | 1 | 12 | 1 |
Figure S86. Get High-res Image Gene #51: 'del_yq11.223' versus Clinical Feature #7: 'PATHOLOGIC_STAGE'

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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/5f3cf94d-1fd8-4096-b606-bcdd9599f833/correlate_genomic_events_all/3441da4a-c848-4650-95a4-60c86ad83a57/call-preprocess_genomic_event/transformed.cor.cli.txt
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Clinical data file = /cromwell_root/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/39eab10a-1791-41cf-866c-13e6472ce02e/normalize_clinical_cptac/df4eac3a-77b6-4ce7-961f-e1027c1ad609/call-normalize_clinical_cptac_task_1/CPTAC3-LUAD-TP.clin.merged.picked.txt
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Number of patients = 110
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Number of significantly focal cnvs = 51
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Number of selected clinical features = 17
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.