Correlation between mutation rate and clinical features

Liver Hepatocellular Carcinoma (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C19W0DCQ

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 12 clinical features across 187 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one variables.

1 variable correlated to 'AGE'.

MUTATIONRATE_SILENT

1 variable correlated to 'GENDER'.

MUTATIONRATE_SILENT

No variables correlated to 'Time to Death', 'AGE_mutation.rate', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'HISTOLOGICAL.TYPE', 'COMPLETENESS.OF.RESECTION', '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=0
AGE	Spearman correlation test	N=1	older	N=1	younger	N=0
AGE	Linear Regression Analysis	N=0
NEOPLASM DISEASESTAGE	Kruskal-Wallis test	N=0
PATHOLOGY T STAGE	Spearman correlation test	N=0
PATHOLOGY N STAGE	Wilcoxon test	N=0
PATHOLOGY M STAGE	Kruskal-Wallis test	N=0
GENDER	Wilcoxon test	N=1	male	N=1	female	N=0
HISTOLOGICAL TYPE	Kruskal-Wallis test	N=0
COMPLETENESS OF RESECTION	Kruskal-Wallis test	N=0
RACE	Kruskal-Wallis test	N=0
ETHNICITY	Wilcoxon 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)	0-113 (median=15.7)
	censored	N = 99
	death	N = 73

	Significant variables	N = 0

Clinical variable #2: 'AGE'

One variable related to 'AGE'.

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


AGE	Mean (SD)	60.45 (14)
	Significant variables	N = 1
	pos. correlated	1
	neg. correlated	0

List of one variable associated with 'AGE'

Table S3. Get Full Table List of one variable significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
MUTATIONRATE_SILENT	0.1444	0.04986	0.0997

Clinical variable #3: 'AGE'

No variable related to 'AGE'.

Table S4. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	60.45 (14)
	Significant variables	N = 0

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	74
	STAGE II	43
	STAGE III	2
	STAGE IIIA	40
	STAGE IIIB	7
	STAGE IIIC	6
	STAGE IV	1
	STAGE IVA	1
	STAGE IVB	2

	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)	1.97 (0.96)
		N
	1	77
	2	48
	3	49
	4	11

	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	Labels	N
	class0	118
	class1	3

	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	138
	M1	3
	MX	46

	Significant variables	N = 0

Clinical variable #8: 'GENDER'

One variable related to 'GENDER'.

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


GENDER	Labels	N
	FEMALE	68
	MALE	119

	Significant variables	N = 1
	Higher in MALE	1
	Higher in FEMALE	0

List of one variable associated with 'GENDER'

Table S10. Get Full Table List of one variable differentially expressed by 'GENDER'. 0 significant gene(s) located in sex chromosomes is(are) filtered out.

	W(pos if higher in 'MALE')	wilcoxontestP	Q	AUC
MUTATIONRATE_SILENT	4809	0.03223	0.0645	0.5943

Clinical variable #9: 'HISTOLOGICAL.TYPE'

No variable related to 'HISTOLOGICAL.TYPE'.

Table S11. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	FIBROLAMELLAR CARCINOMA	1
	HEPATOCELLULAR CARCINOMA	183
	HEPATOCHOLANGIOCARCINOMA (MIXED)	3

	Significant variables	N = 0

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	155
	R1	10
	RX	16

	Significant variables	N = 0

Clinical variable #11: 'RACE'

No variable related to 'RACE'.

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


RACE	Labels	N
	AMERICAN INDIAN OR ALASKA NATIVE	1
	ASIAN	51
	BLACK OR AFRICAN AMERICAN	14
	WHITE	113

	Significant variables	N = 0

Clinical variable #12: 'ETHNICITY'

No variable related to 'ETHNICITY'.

Table S14. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	5
	NOT HISPANIC OR LATINO	168

	Significant variables	N = 0

Methods & Data

Input

Expresson data file = LIHC-TP.patients.counts_and_rates.txt
Clinical data file = LIHC-TP.merged_data.txt
Number of patients = 187
Number of variables = 2
Number of clinical features = 12

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.

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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