Innate Immunity in Heart, Lung and Blood Disease
Programs for Genomic Applications
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European-American Asthma 14:10 Wednesday, October 22, 2003 57
SNP = IIPGA_IRAK3_27210
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |G | Total
---------+--------+--------+
Control | 77 | 935 | 1012
| 3.83 | 46.47 | 50.30
---------+--------+--------+
Case | 57 | 943 | 1000
| 2.83 | 46.87 | 49.70
---------+--------+--------+
Total 134 1878 2012
6.66 93.34 100.00
Frequency Missing = 60
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 2.9477 0.0860
Likelihood Ratio Chi-Square 1 2.9588 0.0854
Continuity Adj. Chi-Square 1 2.6486 0.1036
Mantel-Haenszel Chi-Square 1 2.9462 0.0861
Phi Coefficient 0.0383
Contingency Coefficient 0.0382
Cramer's V 0.0383
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 77
Left-sided Pr <= F 0.9648
Right-sided Pr >= F 0.0516
Table Probability (P) 0.0164
Two-sided Pr <= P 0.0898
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.3624 0.9561 1.9415
Cohort (Col1 Risk) 1.3349 0.9586 1.8588
Cohort (Col2 Risk) 0.9798 0.9572 1.0029
Effective Sample Size = 2012
Frequency Missing = 60
European-American Asthma 14:10 Wednesday, October 22, 2003 58
SNP = IIPGA_IRAK3_27210
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |AA |GA |GG | Total
---------+--------+--------+--------+
Control | 2 | 73 | 431 | 506
| 0.20 | 7.26 | 42.84 | 50.30
---------+--------+--------+--------+
Case | 1 | 55 | 444 | 500
| 0.10 | 5.47 | 44.14 | 49.70
---------+--------+--------+--------+
Total 3 128 875 1006
0.30 12.72 86.98 100.00
Frequency Missing = 30
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 2 3.0220 0.2207
Likelihood Ratio Chi-Square 2 3.0368 0.2191
Mantel-Haenszel Chi-Square 1 3.0153 0.0825
Phi Coefficient 0.0548
Contingency Coefficient 0.0547
Cramer's V 0.0548
WARNING: 33% of the cells have expected counts less than 5.
(Asymptotic) Chi-Square may not be a valid test.
Pearson Chi-Square Test
----------------------------------
Chi-Square 3.0220
DF 2
Asymptotic Pr > ChiSq 0.2207
Exact Pr >= ChiSq 0.3040
Effective Sample Size = 1006
Frequency Missing = 30
European-American Asthma 14:10 Wednesday, October 22, 2003 59
SNP = IIPGA_IRAK3_3570
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |C |T | Total
---------+--------+--------+
Control | 299 | 697 | 996
| 15.16 | 35.34 | 50.51
---------+--------+--------+
Case | 284 | 692 | 976
| 14.40 | 35.09 | 49.49
---------+--------+--------+
Total 583 1389 1972
29.56 70.44 100.00
Frequency Missing = 100
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 0.2011 0.6538
Likelihood Ratio Chi-Square 1 0.2011 0.6538
Continuity Adj. Chi-Square 1 0.1593 0.6898
Mantel-Haenszel Chi-Square 1 0.2010 0.6539
Phi Coefficient 0.0101
Contingency Coefficient 0.0101
Cramer's V 0.0101
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 299
Left-sided Pr <= F 0.6907
Right-sided Pr >= F 0.3449
Table Probability (P) 0.0356
Two-sided Pr <= P 0.6573
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.0453 0.8614 1.2684
Cohort (Col1 Risk) 1.0317 0.9002 1.1823
Cohort (Col2 Risk) 0.9870 0.9321 1.0451
Effective Sample Size = 1972
Frequency Missing = 100
European-American Asthma 14:10 Wednesday, October 22, 2003 60
SNP = IIPGA_IRAK3_3570
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |CC |CT |TT | Total
---------+--------+--------+--------+
Control | 40 | 219 | 239 | 498
| 4.06 | 22.21 | 24.24 | 50.51
---------+--------+--------+--------+
Case | 46 | 192 | 250 | 488
| 4.67 | 19.47 | 25.35 | 49.49
---------+--------+--------+--------+
Total 86 411 489 986
8.72 41.68 49.59 100.00
Frequency Missing = 50
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 2 2.3386 0.3106
Likelihood Ratio Chi-Square 2 2.3400 0.3104
Mantel-Haenszel Chi-Square 1 0.2011 0.6538
Phi Coefficient 0.0487
Contingency Coefficient 0.0486
Cramer's V 0.0487
Pearson Chi-Square Test
----------------------------------
Chi-Square 2.3386
DF 2
Asymptotic Pr > ChiSq 0.3106
Exact Pr >= ChiSq 0.3103
Effective Sample Size = 986
Frequency Missing = 50
European-American Asthma 14:10 Wednesday, October 22, 2003 61
SNP = IIPGA_IRAK3_56398
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |A |T | Total
---------+--------+--------+
Control | 470 | 504 | 974
| 24.23 | 25.98 | 50.21
---------+--------+--------+
Case | 439 | 527 | 966
| 22.63 | 27.16 | 49.79
---------+--------+--------+
Total 909 1031 1940
46.86 53.14 100.00
Frequency Missing = 132
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 1 1.5373 0.2150
Likelihood Ratio Chi-Square 1 1.5376 0.2150
Continuity Adj. Chi-Square 1 1.4266 0.2323
Mantel-Haenszel Chi-Square 1 1.5365 0.2151
Phi Coefficient 0.0282
Contingency Coefficient 0.0281
Cramer's V 0.0282
Fisher's Exact Test
----------------------------------
Cell (1,1) Frequency (F) 470
Left-sided Pr <= F 0.9007
Right-sided Pr >= F 0.1162
Table Probability (P) 0.0168
Two-sided Pr <= P 0.2195
Estimates of the Relative Risk (Row1/Row2)
Type of Study Value 95% Confidence Limits
-----------------------------------------------------------------
Case-Control (Odds Ratio) 1.1195 0.9365 1.3381
Cohort (Col1 Risk) 1.0618 0.9657 1.1675
Cohort (Col2 Risk) 0.9485 0.8724 1.0312
Effective Sample Size = 1940
Frequency Missing = 132
European-American Asthma 14:10 Wednesday, October 22, 2003 62
SNP = IIPGA_IRAK3_56398
The FREQ Procedure
Table of Allele Frequency
Allele Frequency
Frequency|
Percent |AA |TA |TT | Total
---------+--------+--------+--------+
Control | 114 | 242 | 131 | 487
| 11.75 | 24.95 | 13.51 | 50.21
---------+--------+--------+--------+
Case | 103 | 233 | 147 | 483
| 10.62 | 24.02 | 15.15 | 49.79
---------+--------+--------+--------+
Total 217 475 278 970
22.37 48.97 28.66 100.00
Frequency Missing = 66
Statistics for Table of Allele Frequency
Statistic DF Value Prob
------------------------------------------------------
Chi-Square 2 1.6325 0.4421
Likelihood Ratio Chi-Square 2 1.6333 0.4419
Mantel-Haenszel Chi-Square 1 1.5105 0.2191
Phi Coefficient 0.0410
Contingency Coefficient 0.0410
Cramer's V 0.0410
Pearson Chi-Square Test
----------------------------------
Chi-Square 1.6325
DF 2
Asymptotic Pr > ChiSq 0.4421
Exact Pr >= ChiSq 0.4384
Effective Sample Size = 970
Frequency Missing = 66