Correlation between mutation rate and clinical features

Brain Lower Grade Glioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

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/C1445K7R

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 9 clinical features across 282 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one variables.

1 variable correlated to 'Time to Death'.

MUTATIONRATE_NONSYNONYMOUS

2 variables correlated to 'AGE'.

MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT

2 variables correlated to 'AGE_mutation.rate'.

MUTATIONRATE_SILENT , MUTATIONRATE_NONSYNONYMOUS

2 variables correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

MUTATIONRATE_NONSYNONYMOUS , MUTATIONRATE_SILENT

No variables correlated to 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'RACE', and 'ETHNICITY'.

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=1	shorter survival	N=1	longer survival	N=0
AGE	Spearman correlation test	N=2	older	N=2	younger	N=0
AGE	Linear Regression Analysis	N=2
GENDER	Wilcoxon test	N=0
KARNOFSKY PERFORMANCE SCORE	Spearman correlation test	N=0
HISTOLOGICAL TYPE	Kruskal-Wallis test	N=0
RADIATIONS RADIATION REGIMENINDICATION	Wilcoxon test	N=2	yes	N=2	no	N=0
RACE	Kruskal-Wallis test	N=0
ETHNICITY	Wilcoxon test	N=0

Clinical variable #1: 'Time to Death'

One variable related to 'Time to Death'.

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


Time to Death	Duration (Months)	0-182.3 (median=15)
	censored	N = 223
	death	N = 57

	Significant variables	N = 1
	associated with shorter survival	1
	associated with longer survival	0

List of one variable associated with 'Time to Death'

Table S2. Get Full Table List of one variable significantly associated with 'Time to Death' by Cox regression test

	HazardRatio	Wald_P	Q	C_index
MUTATIONRATE_NONSYNONYMOUS	Inf	0.006471	0.013	0.72

Clinical variable #2: 'AGE'

2 variables related to 'AGE'.

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


AGE	Mean (SD)	42.72 (13)
	Significant variables	N = 2
	pos. correlated	2
	neg. correlated	0

List of 2 variables associated with 'AGE'

Table S4. Get Full Table List of 2 variables significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
MUTATIONRATE_NONSYNONYMOUS	0.5996	6.382e-29	1.28e-28
MUTATIONRATE_SILENT	0.5393	1.106e-22	1.11e-22

Clinical variable #3: 'AGE'

2 variables related to 'AGE'.

Table S5. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	42.72 (13)
	Significant variables	N = 2

List of 2 variables associated with 'AGE'

Table S6. 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_SILENT	0.0873	27.9	2.59e-07	3.54e-07	280	8.28e-09 ( -4.98e-08 )	2.59e-07 ( 0.479 )
MUTATIONRATE_NONSYNONYMOUS	0.114	37.1	3.72e-09	8.16e-07	280	2.2e-08 ( 5.1e-08 )	3.72e-09 ( 0.753 )

Clinical variable #4: 'GENDER'

No variable related to 'GENDER'.

Table S7. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	124
	MALE	158

	Significant variables	N = 0

Clinical variable #5: 'KARNOFSKY.PERFORMANCE.SCORE'

No variable related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S8. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	86.42 (12)
	Significant variables	N = 0

Clinical variable #6: 'HISTOLOGICAL.TYPE'

No variable related to 'HISTOLOGICAL.TYPE'.

Table S9. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	ASTROCYTOMA	94
	OLIGOASTROCYTOMA	76
	OLIGODENDROGLIOMA	112

	Significant variables	N = 0

Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

2 variables related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S10. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	85
	YES	197

	Significant variables	N = 2
	Higher in YES	2
	Higher in NO	0

List of 2 variables associated with 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S11. Get Full Table List of 2 variables differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

	W(pos if higher in 'YES')	wilcoxontestP	Q	AUC
MUTATIONRATE_NONSYNONYMOUS	6874	0.01714	0.0343	0.5895
MUTATIONRATE_SILENT	7007	0.02984	0.0343	0.5815

Clinical variable #8: 'RACE'

No variable related to 'RACE'.

Table S12. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	1
	BLACK OR AFRICAN AMERICAN	12
	WHITE	265

	Significant variables	N = 0

Clinical variable #9: 'ETHNICITY'

No variable related to 'ETHNICITY'.

Table S13. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	14
	NOT HISPANIC OR LATINO	251

	Significant variables	N = 0

Methods & Data

Input

Expresson data file = LGG-TP.patients.counts_and_rates.txt
Clinical data file = LGG-TP.merged_data.txt
Number of patients = 282
Number of variables = 2
Number of clinical features = 9

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

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

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

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.

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)

[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)

Made with Nozzle