Correlation between mutation rate and clinical features
Rectum Adenocarcinoma (Primary solid tumor)
17 October 2014 | analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C11V5CXJ
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mutation rate and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11V5CXJ
Overview
Introduction

This pipeline uses various statistical tests to identify selected clinical features related to mutation rate.

Summary

Testing the association between 2 variables and 11 clinical features across 69 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one variables.

- 2 variables correlated to 'AGE_mutation.rate'.

- MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT

- 2 variables correlated to 'HISTOLOGICAL.TYPE'.

- MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT

- No variables correlated to 'Time to Death', 'AGE', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'GENDER', 'COMPLETENESS.OF.RESECTION', and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of variables that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature | Statistical test | Significant variables | Associated with |  | Associated with |
--- | --- | --- | --- | --- | --- | ---
Time to Death | Cox regression test | N=0 |  |  |  |
AGE | Spearman correlation test | N=0 |  |  |  |
AGE | Linear Regression Analysis | N=2 |  |  |  |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=0 |  |  |  |
PATHOLOGY T STAGE | Spearman correlation test | N=0 |  |  |  |
PATHOLOGY N STAGE | Spearman correlation test | N=0 |  |  |  |
PATHOLOGY M STAGE | Wilcoxon test | N=0 |  |  |  |
GENDER | Wilcoxon test | N=0 |  |  |  |
HISTOLOGICAL TYPE | Wilcoxon test | N=2 | rectal mucinous adenocarcinoma | N=2 | rectal adenocarcinoma | N=0
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |  |  |  |

Clinical variable #1: 'Time to Death'

No variable related to 'Time to Death'.

Table S1. Basic characteristics of clinical feature: 'Time to Death'

Time to Death | Duration (Months) | 1-117.1 (median=17)
| censored | N = 54
| death | N = 9
| Significant variables | N = 0

Clinical variable #2: 'AGE'

No variable related to 'AGE'.

Table S2. Basic characteristics of clinical feature: 'AGE'

AGE | Mean (SD) | 66.32 (11)
| Significant variables | N = 0

Clinical variable #3: 'AGE'

2 variables related to 'AGE'.

Table S3. Basic characteristics of clinical feature: 'AGE'

AGE | Mean (SD) | 66.32 (11)
| Significant variables | N = 2

List of 2 variables associated with 'AGE'

Table S4. Get Full Table List of 2 variables significantly correlated to 'AGE' by Linear regression analysis [lm (mutation rate ~ age)]. Compared to a correlation analysis testing for interdependence of the variables, a regression model attempts to describe the dependence of a variable on one (or more) explanatory variables assuming that there is a one-way causal effect from the explanatory variable(s) to the response variable. If 'Residuals vs Fitted' plot (a standard residual plot) shows a random pattern indicating a good fit for a linear model, it explains linear regression relationship between Mutation rate and age factor. Adj.R-squared (= Explained variation / Total variation) indicates regression model's explanatory power.

| Adj.R.squared | F | P | Residual.std.err | DF | coef(intercept) | coef.p(intercept)
--- | --- | --- | --- | --- | --- | --- | ---
MUTATIONRATE_NONSYNONYMOUS | 0.119 | 10.2 | 0.00219 | 3.6e-05 | 67 | -1.28e-06 ( 9.32e-05 ) | 0.00219 ( 0.000989 )
MUTATIONRATE_SILENT | 0.115 | 9.83 | 0.00255 | 9.11e-06 | 67 | -3.19e-07 ( 2.34e-05 ) | 0.00255 ( 0.00105 )

Clinical variable #4: 'NEOPLASM.DISEASESTAGE'

No variable related to 'NEOPLASM.DISEASESTAGE'.

Table S5. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE | Labels | N
| STAGE I | 18
| STAGE II | 6
| STAGE IIA | 19
| STAGE III | 4
| STAGE IIIB | 8
| STAGE IIIC | 4
| STAGE IV | 10
| Significant variables | N = 0

Clinical variable #5: 'PATHOLOGY.T.STAGE'

No variable related to 'PATHOLOGY.T.STAGE'.

Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE | Mean (SD) | 2.7 (0.67)
|  | N
| 1 | 5
| 2 | 14
| 3 | 47
| 4 | 3
| Significant variables | N = 0

Clinical variable #6: 'PATHOLOGY.N.STAGE'

No variable related to 'PATHOLOGY.N.STAGE'.

Table S7. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE | Mean (SD) | 0.55 (0.78)
|  | N
| 0 | 43
| 1 | 14
| 2 | 12
| Significant variables | N = 0

Clinical variable #7: 'PATHOLOGY.M.STAGE'

No variable related to 'PATHOLOGY.M.STAGE'.

Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE | Labels | N
| M0 | 59
| M1 | 10
| Significant variables | N = 0

Clinical variable #8: 'GENDER'

No variable related to 'GENDER'.

Table S9. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 30
| MALE | 39
| Significant variables | N = 0

Clinical variable #9: 'HISTOLOGICAL.TYPE'

2 variables related to 'HISTOLOGICAL.TYPE'.

Table S10. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE | Labels | N
| RECTAL ADENOCARCINOMA | 57
| RECTAL MUCINOUS ADENOCARCINOMA | 8
| Significant variables | N = 2
| Higher in RECTAL MUCINOUS ADENOCARCINOMA | 2
| Higher in RECTAL ADENOCARCINOMA | 0

List of 2 variables associated with 'HISTOLOGICAL.TYPE'

Table S11. Get Full Table List of 2 variables differentially expressed by 'HISTOLOGICAL.TYPE'

| W(pos if higher in 'RECTAL MUCINOUS ADENOCARCINOMA') | wilcoxontestP | Q | AUC
--- | --- | --- | --- | ---
MUTATIONRATE_NONSYNONYMOUS | 59 | 0.0007662 | 0.00153 | 0.8706
MUTATIONRATE_SILENT | 90 | 0.006032 | 0.00603 | 0.8026

Clinical variable #10: 'COMPLETENESS.OF.RESECTION'

No variable related to 'COMPLETENESS.OF.RESECTION'.

Table S12. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 59
| R1 | 1
| R2 | 8
| Significant variables | N = 0

Clinical variable #11: 'NUMBER.OF.LYMPH.NODES'

No variable related to 'NUMBER.OF.LYMPH.NODES'.

Table S13. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.29 (5.5)
| Significant variables | N = 0

Methods & Data
Input

- Expresson data file = READ-TP.patients.counts_and_rates.txt

- Clinical data file = READ-TP.merged_data.txt

- Number of patients = 69

- Number of variables = 2

- Number of clinical features = 11

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

Q value calculation

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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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