Association Genotype Test
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You can perform Genotypic Association Tests here.


graphic


SNPs are taken one by one. For every SNP 4 contingency tables are built taking into account whether the genotypes come from case or from control Samples.

Imagine that we have an SNP with two alleles: A and B. The possible genotypes are:

      AA AB BB.

The 4 contingency tables are:

AA          /    AB+BB       2x2
AB          /    AA+BB       2x2
BB          /    AA+AB       2x2
AA     /    AB     /    BB          3x2

Calculations are performed with these contingency tables and presented in a final Report that will be sent to the User Results section. .

The workflow is as follows:

graphic

Then you need to select the values defining cases and controls:

graphic

Samples with values other than the ones declared here will be discarded and not used in the process.

When more than two possible values exist in a field. You may want to enter only one of these values in either the "Case" or the "Control" boxes, leaving the other box untouched (that is, leaving the "[Select Item]" option there). By doing so, those samples that match your explicit selection are being defined as, say, Cases (or Controls, if you selected so). All the remaining samples having other values will be used as the other option (Controls, in this example).

If a blank is selected " ", that means that there are Samples with no value in the field and that those are being selected as a case or control.



- Fisher's exact test.

Performs Fisher's Exact Test upon the contingency table in addition to the Chi-square test that is always done. A combo box allows the user to select weather to do it for every SNP or only in those cases in which the Chi-square test has Validity=N (See below).

- Odds Ratio - Haldane Correction.

If some value of the original contingency table is 0, this option tells SNPator to perform the Haldane Correction when computing Odds Ratios and their Confidence Intervals. 

- Logistic Regression.

The association value can be adjusted by some of the fields in the samples table using logistic regression. Results from logistic regression association test will be collected in a different file from the rest of the analysis. The following restrictions are applied in the regression process in order to avoid inconsistent results when dealing with incomplete data:

Those fields with only one value in all the selected samples will be excluded from the regression.

For each grouping (AA vs AB+BB, AB vs AA+BB, etc) a case- control/genotype-value contingency table is created and groupings with blanks in this table are discarded.

For each grouping and for each non numeric adjusting field a case-control/field-value contingency table is created and groupings with blanks in this table are discarded.

Fields with all numeric values are treated always as covariables even if the original SNPator field is of categoric type.

- Batch mode.

This is a fundamental time-saving feature. Selecting one of the fields in the Samples or SNP table, SNPator will run this analysis as many times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you have defined your samples in the "sex" field as "M" or "W", selecting "sex" as the attribute of the Sample batch mode will result in having two runs of the analysis, taking separately men and women.

If you select at the same time sample and SNP batch fields, you are going to obtain as many runs of the analysis as all possible combinations of the values of samples and SNPs in the fields you selected.


Job               : G_Association
Description       : Genotipic
User              : advanced
Study             : Pruebas_2
Request time      : 2005-10-06 16:28:51
Start time        : 2005-10-06 16:28:52
End time          : 2005-10-06 16:28:52
Ready to use time : 2005-10-06 16:28:56

Filter Information:
     Filter: 0
     Filter description: central
     Filter version: 2


                   |-----------------------------------------------------------------|
                   |                           AA+AB / BB                            |
|------------------|-----------------------------------------------------------------|--------|
|       SNP        | pValue *  Major V   Odds Ratio            IC95         Fisher * |   N    |
|------------------|-----------------------------------------------------------------|--------|
| rs1342476        | 0.0038 ** TT    Y      45.0000 +   1.49 - 1,358.36 +  0.0101 *  |     12 |
| rs2104604        | 0.0034 ** CC+CG Y      47.6667 +   1.60 - 1,422.78 +  0.0152 *  |     12 |
| rs1886340        | 0.3774    CC+CT N       2.5385 +      0.09 - 75.77 +  1.0000    |     12 |
| rs1998626        | 0.1515    CC+CG N       6.4286 +     0.23 - 181.83 +  0.4444    |      9 |
| rs912537         | 0.1982    CC+CT Y       5.3333        0.38 - 75.78    0.2929    |     12 |
| rs618675         | 0.2165    CC+CT N       5.0000 +     0.17 - 150.93 +  0.4167    |     12 |
|------------------|-----------------------------------------------------------------|--------|
     + Haldane correction applied

                   |-----------------------------------------------------------------|
                   |                           AA+BB / AB                            |
|------------------|-----------------------------------------------------------------|--------|
|       SNP        | pValue *  Major V   Odds Ratio            IC95         Fisher * |   N    |
|------------------|-----------------------------------------------------------------|--------|
| rs1342476        | 0.4076    CC+TT Y       3.0000        0.21 - 42.63    0.5758    |     12 |
| rs2104604        | 0.3105    CG    Y       4.0000        0.25 - 63.95    0.5227    |     12 |
| rs1886340        | 0.1982    CC+TT Y       5.3333        0.38 - 75.78    0.2929    |     12 |
| rs1998626        | 0.1515    CG    N       6.4286 +     0.23 - 181.83 +  0.4444    |      9 |
| rs912537         | 0.5582    CT    Y       2.0000        0.19 - 20.61    1.0000    |     12 |
| rs618675         | 0.2165    CT    N       5.0000 +     0.17 - 150.93 +  0.4167    |     12 |
|------------------|-----------------------------------------------------------------|--------|

                   |-----------------------------------------------------------------|
                   |                           AB+BB / AA                            |
|------------------|-----------------------------------------------------------------|--------|
|       SNP        | pValue *  Major V   Odds Ratio            IC95         Fisher * |   N    |
|------------------|-----------------------------------------------------------------|--------|
| rs1342476        | 0.0384 *  CT+TT Y      14.1429 +     0.57 - 352.02 +  0.0808    |     12 |
| rs2104604        | 0.0180 *  CC    Y      21.0000 +     0.78 - 564.18 +  0.0455 *  |     12 |
| rs1886340        | 0.0790    CC    Y      10.0000       0.65 - 154.40    0.2424    |     12 |
| rs1998626        |      -    -     -       1.2222 +      0.02 - 74.73 +  1.0000    |      9 |
| rs912537         | 0.2165    CC    N       5.0000 +     0.17 - 150.93 +  0.4167    |     12 |
| rs618675         |      -    -     -       1.3636 +      0.02 - 79.97 +  1.0000    |     12 |
|------------------|-----------------------------------------------------------------|--------|
     + Haldane correction applied

                   |--------------------|
                   |    AA / AB / BB    |
|------------------|--------------------|--------|
|       SNP        | pValue *  Major V  |   N    |
|------------------|--------------------|--------|
| rs1342476        | 0.0116 *  TT    Y  |     12 |
| rs2104604        | 0.0098 ** CC    Y  |     12 |
| rs1886340        | 0.1996    CC    N  |     12 |
| rs1998626        |      -    -     -  |      9 |
| rs912537         | 0.2812    CC    N  |     12 |
| rs618675         |      -    -     -  |     12 |
|------------------|--------------------|--------|


-----------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------


                   |-----------------------------------------------------------------|
                   |                           AA+AB / BB                            |
|------------------|-----------------------------------------------------------------|--------|
|       SNP        | pValue *  Major V   Odds Ratio            IC95         Fisher * |   N    |
|------------------|-----------------------------------------------------------------|--------|
| rs1342476        | 0.0038 ** TT    Y      45.0000 +   1.49 - 1,358.36 +  0.0101 *  |     12 |
| rs2104604        | 0.0034 ** CC+CG Y      47.6667 +   1.60 - 1,422.78 +  0.0152 *  |     12 |
| rs1886340        | 0.3774    CC+CT N       2.5385 +      0.09 - 75.77 +  1.0000    |     12 |
| rs1998626        | 0.1515    CC+CG N       6.4286 +     0.23 - 181.83 +  0.4444    |      9 |
| rs912537         | 0.1982    CC+CT Y       5.3333        0.38 - 75.78    0.2929    |     12 |
| rs618675         | 0.2165    CC+CT N       5.0000 +     0.17 - 150.93 +  0.4167    |     12 |
|------------------|-----------------------------------------------------------------|--------|
     + Haldane correction applied


- RS1342476

          | TT     | CC+CT  |   Chi Squared:        8.4000
          |--------|--------|   pValue:             0.0038 **
  Case    |      4 |      1 |   Odds Ratio:        45.0000 +
  Control |      0 |      7 |   CI 95%:      1.49 - 1,358.36 +
          |--------|--------|


- RS2104604

          | GG     | CC+CG  |   Chi Squared:        8.5714
          |--------|--------|   pValue:             0.0034 **
  Case    |      0 |      5 |   Odds Ratio:        47.6667 +
  Control |      6 |      1 |   CI 95%:      1.60 - 1,422.78 +
          |--------|--------|

(...)

At the top, you can find the usual header informing you about dates and times of performance, user, study, filters applied and other data.

Below that, the association results are printed in several columns, containing:

- SNP
Code of the SNP

- pValue
P-value from the chi square test applied to the 2x2 contingency table for each SNP.

- Significance
* for pValue<0.05, ** for pValue<0.01

- Major
The genotype positively associated with cases.

- Validity
Not valid (N) when there is some expected value in the chi- squared contingency table that is equal or below 1.

- Odds Ratio
The Odds Ratio resulting from the association analysis of each genotype. If the Haldane Correction has been used, the OR it is marked with a "+" sign.

- CI95
It is the 95% Confidence Interval for the Odds Ratio value obtained before. Here, too, if Haldane correction has been applied it will be flagged with a "+" sign.

- Fisher_p
P-value from the Fisher exact test applied to the 2x2 contingency table for each SNP.

- Significance (of the of Fisher's Exact Test)
* for P-values<0.05, ** for P-values<0.01

- N
Number of genotypes used in the calculation.


Finally, for each genotype, the contingency table with some of the statistics is printed.

- SNP
Code of the SNP

- Major
The genotype or grouping of genotypes positively associated with cases.

- Odds Ratio
The Odds Ratio equivalent coming from the Logistic Regression coefficient.

- CI95Inf - CI95Sup
The limits of the 95% interval confidence for the Odds Ratio value.
   
- pValue


- Haploid data treatment:

SNPs presenting haploid genotypes will be excluded from the analysis.