Innate Immunity in Heart, Lung and Blood Disease
Programs for Genomic Applications
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European-American Asthma 11:50 Wednesday, February 4, 2004 85
SNP = IL17F_12470
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |G | Total
---------+--------+--------+
Control | 32 | 880 | 912
| 1.73 | 47.62 | 49.35
---------+--------+--------+
Case | 39 | 897 | 936
| 2.11 | 48.54 | 50.65
---------+--------+--------+
Total 71 1777 1848
3.84 96.16 100.00
Frequency Missing = 208
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.5412 0.4619
Likelihood Ratio Chi-Square 1 0.5422 0.4615
Continuity Adj. Chi-Square 1 0.3777 0.5388
Mantel-Haenszel Chi-Square 1 0.5409 0.4621
Phi Coefficient -0.0171
Contingency Coefficient 0.0171
Cramer's V -0.0171
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 32
Left-sided Pr <= F 0.2696
Right-sided Pr >= F 0.8041
Table Probability (P) 0.0737
Two-sided Pr <= P 0.4708
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.8364 0.5193 1.3471
Cohort (Col1 Risk) 0.8421 0.5324 1.3320
Cohort (Col2 Risk) 1.0069 0.9887 1.0254
Effective Sample Size = 1848
Frequency Missing = 208
WARNING: 10% of the data are missing.
European-American Asthma 11:50 Wednesday, February 4, 2004 86
SNP = IL17F_12470
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |3 | Total
---------+--------+
Control | 456 | 456
| 49.35 | 49.35
---------+--------+
Case | 468 | 468
| 50.65 | 50.65
---------+--------+
Total 924 924
100.00 100.00
Frequency Missing = 104
European-American Asthma 11:50 Wednesday, February 4, 2004 87
SNP = IL17F_12489
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |G | Total
---------+--------+--------+
Control | 928 | 44 | 972
| 47.88 | 2.27 | 50.15
---------+--------+--------+
Case | 921 | 45 | 966
| 47.52 | 2.32 | 49.85
---------+--------+--------+
Total 1849 89 1938
95.41 4.59 100.00
Frequency Missing = 118
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.0192 0.8899
Likelihood Ratio Chi-Square 1 0.0192 0.8899
Continuity Adj. Chi-Square 1 0.0009 0.9761
Mantel-Haenszel Chi-Square 1 0.0192 0.8899
Phi Coefficient 0.0031
Contingency Coefficient 0.0031
Cramer's V 0.0031
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 928
Left-sided Pr <= F 0.5975
Right-sided Pr >= F 0.4880
Table Probability (P) 0.0855
Two-sided Pr <= P 0.9139
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0305 0.6734 1.5769
Cohort (Col1 Risk) 1.0014 0.9820 1.0211
Cohort (Col2 Risk) 0.9717 0.6476 1.4582
Effective Sample Size = 1938
Frequency Missing = 118
European-American Asthma 11:50 Wednesday, February 4, 2004 88
SNP = IL17F_12489
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |1 |3 | Total
---------+--------+--------+
Control | 486 | 0 | 486
| 50.15 | 0.00 | 50.15
---------+--------+--------+
Case | 480 | 3 | 483
| 49.54 | 0.31 | 49.85
---------+--------+--------+
Total 966 3 969
99.69 0.31 100.00
Frequency Missing = 59
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 3.0280 0.0818
Likelihood Ratio Chi-Square 1 4.1869 0.0407
Continuity Adj. Chi-Square 1 1.3499 0.2453
Mantel-Haenszel Chi-Square 1 3.0249 0.0820
Phi Coefficient 0.0559
Contingency Coefficient 0.0558
Cramer's V 0.0559
WARNING: 50% of the cells have expected counts less than 5.
(Asymptotic) Chi-Square may not be a valid test.
Pearson Chi-Square Test
----------------------------------
Chi-Square 3.0280
DF 1
Asymptotic Pr > ChiSq 0.0818
Exact Pr >= ChiSq 0.1235
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 486
Left-sided Pr <= F 1.0000
Right-sided Pr >= F 0.1235
Table Probability (P) 0.1235
Two-sided Pr <= P 0.1235
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Cohort (Col1 Risk) 1.0063 0.9992 1.0134
One or more risk estimates not computed --- zero cell.
Effective Sample Size = 969
Frequency Missing = 59
European-American Asthma 11:50 Wednesday, February 4, 2004 89
SNP = IL17F_13063
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |C |G | Total
---------+--------+--------+
Control | 92 | 848 | 940
| 4.89 | 45.11 | 50.00
---------+--------+--------+
Case | 85 | 855 | 940
| 4.52 | 45.48 | 50.00
---------+--------+--------+
Total 177 1703 1880
9.41 90.59 100.00
Frequency Missing = 176
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.3056 0.5804
Likelihood Ratio Chi-Square 1 0.3057 0.5803
Continuity Adj. Chi-Square 1 0.2245 0.6356
Mantel-Haenszel Chi-Square 1 0.3054 0.5805
Phi Coefficient 0.0127
Contingency Coefficient 0.0127
Cramer's V 0.0127
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 92
Left-sided Pr <= F 0.7362
Right-sided Pr >= F 0.3179
Table Probability (P) 0.0540
Two-sided Pr <= P 0.6357
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0913 0.8006 1.4876
Cohort (Col1 Risk) 1.0824 0.8175 1.4331
Cohort (Col2 Risk) 0.9918 0.9633 1.0211
Effective Sample Size = 1880
Frequency Missing = 176
European-American Asthma 11:50 Wednesday, February 4, 2004 90
SNP = IL17F_13063
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |2 |3 | Total
---------+--------+--------+
Control | 86 | 384 | 470
| 9.15 | 40.85 | 50.00
---------+--------+--------+
Case | 84 | 386 | 470
| 8.94 | 41.06 | 50.00
---------+--------+--------+
Total 170 770 940
18.09 81.91 100.00
Frequency Missing = 88
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.0287 0.8654
Likelihood Ratio Chi-Square 1 0.0287 0.8654
Continuity Adj. Chi-Square 1 0.0072 0.9325
Mantel-Haenszel Chi-Square 1 0.0287 0.8655
Phi Coefficient 0.0055
Contingency Coefficient 0.0055
Cramer's V 0.0055
Pearson Chi-Square Test
----------------------------------
Chi-Square 0.0287
DF 1
Asymptotic Pr > ChiSq 0.8654
Exact Pr >= ChiSq 0.9325
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 86
Left-sided Pr <= F 0.6003
Right-sided Pr >= F 0.4662
Table Probability (P) 0.0666
Two-sided Pr <= P 0.9325
European-American Asthma 11:50 Wednesday, February 4, 2004 91
SNP = IL17F_13063
The FREQ Procedure
Statistics for Table of Allele Frequency
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0291 0.7383 1.4347
Cohort (Col1 Risk) 1.0238 0.7799 1.3440
Cohort (Col2 Risk) 0.9948 0.9368 1.0564
Odds Ratio (Case-Control Study)
-----------------------------------
Odds Ratio 1.0291
Asymptotic Conf Limits
95% Lower Conf Limit 0.7383
95% Upper Conf Limit 1.4347
Exact Conf Limits
95% Lower Conf Limit 0.7280
95% Upper Conf Limit 1.4552
Effective Sample Size = 940
Frequency Missing = 88
European-American Asthma 11:50 Wednesday, February 4, 2004 92
SNP = IL17F_6166
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |C |T | Total
---------+--------+--------+
Control | 205 | 607 | 812
| 12.67 | 37.52 | 50.19
---------+--------+--------+
Case | 222 | 584 | 806
| 13.72 | 36.09 | 49.81
---------+--------+--------+
Total 427 1191 1618
26.39 73.61 100.00
Frequency Missing = 438
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 1.0987 0.2945
Likelihood Ratio Chi-Square 1 1.0989 0.2945
Continuity Adj. Chi-Square 1 0.9837 0.3213
Mantel-Haenszel Chi-Square 1 1.0981 0.2947
Phi Coefficient -0.0261
Contingency Coefficient 0.0261
Cramer's V -0.0261
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 205
Left-sided Pr <= F 0.1606
Right-sided Pr >= F 0.8653
Table Probability (P) 0.0260
Two-sided Pr <= P 0.3101
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.8884 0.7121 1.1084
Cohort (Col1 Risk) 0.9166 0.7788 1.0788
Cohort (Col2 Risk) 1.0317 0.9732 1.0937
Effective Sample Size = 1618
Frequency Missing = 438
WARNING: 21% of the data are missing.
European-American Asthma 11:50 Wednesday, February 4, 2004 93
SNP = IL17F_6166
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |2 |4 | Total
---------+--------+--------+
Control | 179 | 227 | 406
| 22.13 | 28.06 | 50.19
---------+--------+--------+
Case | 196 | 207 | 403
| 24.23 | 25.59 | 49.81
---------+--------+--------+
Total 375 434 809
46.35 53.65 100.00
Frequency Missing = 219
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 1.6812 0.1948
Likelihood Ratio Chi-Square 1 1.6818 0.1947
Continuity Adj. Chi-Square 1 1.5034 0.2202
Mantel-Haenszel Chi-Square 1 1.6791 0.1950
Phi Coefficient -0.0456
Contingency Coefficient 0.0455
Cramer's V -0.0456
Pearson Chi-Square Test
----------------------------------
Chi-Square 1.6812
DF 1
Asymptotic Pr > ChiSq 0.1948
Exact Pr >= ChiSq 0.2048
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 179
Left-sided Pr <= F 0.1101
Right-sided Pr >= F 0.9142
Table Probability (P) 0.0243
Two-sided Pr <= P 0.2048
European-American Asthma 11:50 Wednesday, February 4, 2004 94
SNP = IL17F_6166
The FREQ Procedure
Statistics for Table of Allele Frequency
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.8328 0.6315 1.0982
Cohort (Col1 Risk) 0.9065 0.7814 1.0517
Cohort (Col2 Risk) 1.0885 0.9574 1.2377
Odds Ratio (Case-Control Study)
-----------------------------------
Odds Ratio 0.8328
Asymptotic Conf Limits
95% Lower Conf Limit 0.6315
95% Upper Conf Limit 1.0982
Exact Conf Limits
95% Lower Conf Limit 0.6254
95% Upper Conf Limit 1.1088
Effective Sample Size = 809
Frequency Missing = 219
WARNING: 21% of the data are missing.
European-American Asthma 11:50 Wednesday, February 4, 2004 95
SNP = IL17F_7368
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |C |T | Total
---------+--------+--------+
Control | 435 | 367 | 802
| 25.68 | 21.66 | 47.34
---------+--------+--------+
Case | 517 | 375 | 892
| 30.52 | 22.14 | 52.66
---------+--------+--------+
Total 952 742 1694
56.20 43.80 100.00
Frequency Missing = 362
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 2.3744 0.1233
Likelihood Ratio Chi-Square 1 2.3742 0.1234
Continuity Adj. Chi-Square 1 2.2257 0.1357
Mantel-Haenszel Chi-Square 1 2.3730 0.1234
Phi Coefficient -0.0374
Contingency Coefficient 0.0374
Cramer's V -0.0374
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 435
Left-sided Pr <= F 0.0679
Right-sided Pr >= F 0.9441
Table Probability (P) 0.0119
Two-sided Pr <= P 0.1286
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.8597 0.7093 1.0420
Cohort (Col1 Risk) 0.9358 0.8599 1.0185
Cohort (Col2 Risk) 1.0885 0.9773 1.2124
Effective Sample Size = 1694
Frequency Missing = 362
WARNING: 18% of the data are missing.
European-American Asthma 11:50 Wednesday, February 4, 2004 96
SNP = IL17F_7368
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |2 |4 | Total
---------+--------+--------+
Control | 315 | 86 | 401
| 37.19 | 10.15 | 47.34
---------+--------+--------+
Case | 363 | 83 | 446
| 42.86 | 9.80 | 52.66
---------+--------+--------+
Total 678 169 847
80.05 19.95 100.00
Frequency Missing = 181
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 1.0637 0.3024
Likelihood Ratio Chi-Square 1 1.0624 0.3027
Continuity Adj. Chi-Square 1 0.8935 0.3445
Mantel-Haenszel Chi-Square 1 1.0624 0.3027
Phi Coefficient -0.0354
Contingency Coefficient 0.0354
Cramer's V -0.0354
Pearson Chi-Square Test
----------------------------------
Chi-Square 1.0637
DF 1
Asymptotic Pr > ChiSq 0.3024
Exact Pr >= ChiSq 0.3436
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 315
Left-sided Pr <= F 0.1722
Right-sided Pr >= F 0.8681
Table Probability (P) 0.0403
Two-sided Pr <= P 0.3436
European-American Asthma 11:50 Wednesday, February 4, 2004 97
SNP = IL17F_7368
The FREQ Procedure
Statistics for Table of Allele Frequency
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 0.8375 0.5978 1.1734
Cohort (Col1 Risk) 0.9651 0.9020 1.0328
Cohort (Col2 Risk) 1.1524 0.8800 1.5092
Odds Ratio (Case-Control Study)
-----------------------------------
Odds Ratio 0.8375
Asymptotic Conf Limits
95% Lower Conf Limit 0.5978
95% Upper Conf Limit 1.1734
Exact Conf Limits
95% Lower Conf Limit 0.5891
95% Upper Conf Limit 1.1905
Effective Sample Size = 847
Frequency Missing = 181
WARNING: 18% of the data are missing.