Cervical Squamous Cell Carcinoma: Correlation between copy number variation genes (focal) and selected clinical features<BR>(primary solid tumor cohort)

Cervical Squamous Cell Carcinoma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 51 arm-level results and 10 clinical features across 34 patients, no significant finding detected with Q value < 0.25.

No arm-level cnvs related to clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level results and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.


		Clinical Features	Time to Death	AGE	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	NUMBERPACKYEARSSMOKED	TOBACCOSMOKINGHISTORYINDICATOR	DISTANT METASTASIS	LYMPH NODE METASTASIS	NUMBER OF LYMPH NODES	TUMOR STAGECODE
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test	t-test	t-test	Fisher's exact test	Fisher's exact test	t-test	t-test
Amp Peak 1(1q21 3)	24 (71%)	10	0.298 (1.00)	0.581 (1.00)	0.746 (1.00)	1 (1.00)	0.287 (1.00)	0.792 (1.00)	0.675 (1.00)	0.687 (1.00)	0.35 (1.00)
Amp Peak 2(1q44)	22 (65%)	12	0.35 (1.00)	0.368 (1.00)	0.598 (1.00)	0.705 (1.00)	0.287 (1.00)	0.953 (1.00)	1 (1.00)	1 (1.00)	0.503 (1.00)
Amp Peak 3(2p24 3)	10 (29%)	24	0.0352 (1.00)	0.238 (1.00)	0.532 (1.00)	1 (1.00)	0.646 (1.00)	0.544 (1.00)	1 (1.00)	1 (1.00)	0.654 (1.00)
Amp Peak 4(2q32 3)	4 (12%)	30	0.395 (1.00)	0.198 (1.00)	1 (1.00)	1 (1.00)		0.693 (1.00)	1 (1.00)	1 (1.00)	0.774 (1.00)
Amp Peak 5(3q26 2)	27 (79%)	7	0.423 (1.00)	0.525 (1.00)	0.28 (1.00)	1 (1.00)	0.682 (1.00)	0.608 (1.00)	0.287 (1.00)	0.641 (1.00)	0.566 (1.00)
Amp Peak 6(3q28)	27 (79%)	7	0.423 (1.00)	0.525 (1.00)	0.28 (1.00)	1 (1.00)	0.682 (1.00)	0.608 (1.00)	0.287 (1.00)	0.641 (1.00)	0.566 (1.00)
Amp Peak 7(4q12)	5 (15%)	29	0.857 (1.00)	0.148 (1.00)	1 (1.00)	0.3 (1.00)		0.321 (1.00)	0.22 (1.00)	0.537 (1.00)	0.593 (1.00)
Amp Peak 8(6p21 33)	10 (29%)	24	0.959 (1.00)	0.138 (1.00)	0.193 (1.00)	1 (1.00)	0.612 (1.00)	0.891 (1.00)	1 (1.00)	0.417 (1.00)	0.872 (1.00)
Amp Peak 9(6q12)	4 (12%)	30	0.285 (1.00)	0.388 (1.00)	1 (1.00)	0.58 (1.00)		0.671 (1.00)	1 (1.00)	0.611 (1.00)	0.914 (1.00)
Amp Peak 10(8q24 21)	16 (47%)	18	0.988 (1.00)	0.748 (1.00)	1 (1.00)	0.477 (1.00)	0.783 (1.00)	0.186 (1.00)	0.427 (1.00)	1 (1.00)	1 (1.00)
Amp Peak 11(8q24 21)	16 (47%)	18	0.305 (1.00)	0.911 (1.00)	1 (1.00)	0.477 (1.00)	0.783 (1.00)	0.729 (1.00)	0.427 (1.00)	0.45 (1.00)	0.68 (1.00)
Amp Peak 12(9p24 1)	7 (21%)	27	0.129 (1.00)	0.122 (1.00)	0.67 (1.00)	0.384 (1.00)		0.805 (1.00)	1 (1.00)	0.372 (1.00)	0.634 (1.00)
Amp Peak 13(11q13 3)	4 (12%)	30	0.423 (1.00)	0.28 (1.00)	1 (1.00)	0.58 (1.00)		0.589 (1.00)	0.532 (1.00)	0.52 (1.00)
Amp Peak 14(11q22 1)	7 (21%)	27	0.9 (1.00)	0.00543 (1.00)	1 (1.00)	1 (1.00)		0.528 (1.00)	0.633 (1.00)	0.372 (1.00)	0.154 (1.00)
Amp Peak 15(13q22 1)	4 (12%)	30	0.634 (1.00)	0.981 (1.00)	0.243 (1.00)	1 (1.00)		0.345 (1.00)	1 (1.00)	0.537 (1.00)	0.593 (1.00)
Amp Peak 16(14q24 1)	7 (21%)	27	0.285 (1.00)	0.715 (1.00)	0.19 (1.00)	0.384 (1.00)		0.555 (1.00)	1 (1.00)	0.641 (1.00)	0.527 (1.00)
Amp Peak 17(15q26 3)	10 (29%)	24	0.829 (1.00)	0.441 (1.00)	1 (1.00)	0.437 (1.00)		0.676 (1.00)	0.675 (1.00)	0.672 (1.00)	0.271 (1.00)
Amp Peak 18(16p13 2)	8 (24%)	26	0.317 (1.00)	0.206 (1.00)	0.242 (1.00)	1 (1.00)		0.645 (1.00)	0.642 (1.00)	1 (1.00)	0.704 (1.00)
Amp Peak 19(16p13 13)	8 (24%)	26	0.552 (1.00)	0.112 (1.00)	0.0374 (1.00)	1 (1.00)		0.388 (1.00)	0.158 (1.00)	1 (1.00)	0.704 (1.00)
Amp Peak 20(17q12)	5 (15%)	29	0.932 (1.00)	0.89 (1.00)	0.331 (1.00)	1 (1.00)		0.589 (1.00)	0.153 (1.00)	0.327 (1.00)	0.613 (1.00)
Amp Peak 21(17q25 1)	10 (29%)	24	0.28 (1.00)	0.914 (1.00)	0.0477 (1.00)	1 (1.00)	0.783 (1.00)	0.24 (1.00)	1 (1.00)	0.225 (1.00)	0.367 (1.00)
Amp Peak 22(19q13 31)	11 (32%)	23	0.149 (1.00)	0.9 (1.00)	0.577 (1.00)	0.016 (1.00)	0.985 (1.00)	0.524 (1.00)	0.396 (1.00)	0.687 (1.00)	0.692 (1.00)
Amp Peak 23(20q11 21)	19 (56%)	15	0.0234 (1.00)	0.373 (1.00)	0.813 (1.00)	0.475 (1.00)	0.113 (1.00)	0.293 (1.00)	0.454 (1.00)	0.142 (1.00)	0.54 (1.00)
Amp Peak 24(Xq28)	7 (21%)	27	0.241 (1.00)	0.691 (1.00)	0.67 (1.00)	1 (1.00)		0.645 (1.00)	0.158 (1.00)	1 (1.00)	0.89 (1.00)
Del Peak 1(1p36 23)	6 (18%)	28	0.916 (1.00)	0.242 (1.00)	0.146 (1.00)	1 (1.00)	0.277 (1.00)	0.728 (1.00)	0.633 (1.00)	1 (1.00)	0.8 (1.00)
Del Peak 2(1p13 1)	7 (21%)	27	0.719 (1.00)	0.329 (1.00)	1 (1.00)	0.656 (1.00)		0.235 (1.00)	0.633 (1.00)	1 (1.00)	0.917 (1.00)
Del Peak 3(2q22 1)	4 (12%)	30	0.747 (1.00)	0.569 (1.00)	1 (1.00)	0.0889 (1.00)		0.888 (1.00)	0.532 (1.00)	1 (1.00)	0.718 (1.00)
Del Peak 4(2q37 1)	14 (41%)	20	0.0924 (1.00)	0.0168 (1.00)	1 (1.00)	0.295 (1.00)	0.0503 (1.00)	0.206 (1.00)	1 (1.00)	0.442 (1.00)	0.463 (1.00)
Del Peak 5(3p11 1)	17 (50%)	17	0.68 (1.00)	0.559 (1.00)	0.398 (1.00)	1 (1.00)	0.534 (1.00)	0.354 (1.00)	0.7 (1.00)	0.257 (1.00)	0.0769 (1.00)
Del Peak 6(4q22 1)	8 (24%)	26	0.559 (1.00)	0.535 (1.00)	0.707 (1.00)	1 (1.00)	0.881 (1.00)	0.86 (1.00)	1 (1.00)	0.372 (1.00)	0.164 (1.00)
Del Peak 7(4q35 2)	12 (35%)	22	0.0897 (1.00)	0.529 (1.00)	0.769 (1.00)	1 (1.00)	0.838 (1.00)	0.769 (1.00)	0.675 (1.00)	0.702 (1.00)	0.441 (1.00)
Del Peak 8(5q14 3)	16 (47%)	18	0.327 (1.00)	0.135 (1.00)	0.66 (1.00)	0.477 (1.00)	0.627 (1.00)	0.977 (1.00)	0.688 (1.00)	0.707 (1.00)	0.171 (1.00)
Del Peak 9(6p24 3)	6 (18%)	28	0.986 (1.00)	0.324 (1.00)	0.42 (1.00)	0.638 (1.00)		0.263 (1.00)	1 (1.00)	0.0472 (1.00)	0.165 (1.00)
Del Peak 11(6q26)	8 (24%)	26	0.602 (1.00)	0.114 (1.00)	0.707 (1.00)	0.227 (1.00)		0.696 (1.00)	0.642 (1.00)	0.372 (1.00)	0.634 (1.00)
Del Peak 12(7q34)	7 (21%)	27	0.00723 (1.00)	0.811 (1.00)	1 (1.00)	0.178 (1.00)	0.838 (1.00)	0.608 (1.00)	1 (1.00)	1 (1.00)	0.458 (1.00)
Del Peak 13(10q23 31)	7 (21%)	27	0.108 (1.00)	0.903 (1.00)	1 (1.00)	0.656 (1.00)	0.77 (1.00)	0.0211 (1.00)	0.633 (1.00)	0.156 (1.00)	0.208 (1.00)
Del Peak 14(10q26 3)	6 (18%)	28	0.285 (1.00)	0.91 (1.00)	0.42 (1.00)	0.363 (1.00)	0.77 (1.00)	0.076 (1.00)	0.076 (1.00)	0.0472 (1.00)	0.115 (1.00)
Del Peak 15(11p15 1)	12 (35%)	22	0.87 (1.00)	0.938 (1.00)	0.598 (1.00)	1 (1.00)	0.881 (1.00)	0.953 (1.00)	0.694 (1.00)	0.238 (1.00)	0.0926 (1.00)
Del Peak 16(11q25)	23 (68%)	11	0.954 (1.00)	0.644 (1.00)	0.422 (1.00)	1 (1.00)	0.304 (1.00)	0.744 (1.00)	1 (1.00)	0.702 (1.00)	0.134 (1.00)
Del Peak 17(13q13 3)	13 (38%)	21	0.63 (1.00)	0.968 (1.00)	0.471 (1.00)	1 (1.00)	0.881 (1.00)	0.769 (1.00)	1 (1.00)	0.696 (1.00)	0.182 (1.00)
Del Peak 18(14q32 31)	3 (9%)	31	0.523 (1.00)	0.099 (1.00)	1 (1.00)	1 (1.00)		0.861 (1.00)	0.22 (1.00)	0.279 (1.00)	0.00565 (1.00)
Del Peak 19(15q15 1)	5 (15%)	29	0.986 (1.00)	0.529 (1.00)	1 (1.00)	1 (1.00)		0.447 (1.00)	0.568 (1.00)	1 (1.00)	0.443 (1.00)
Del Peak 20(16q11 2)	3 (9%)	31		0.734 (1.00)	1 (1.00)	0.535 (1.00)			1 (1.00)	0.52 (1.00)
Del Peak 21(16q23 1)	3 (9%)	31		0.893 (1.00)	0.0329 (1.00)	1 (1.00)			0.532 (1.00)	1 (1.00)
Del Peak 22(17p12)	12 (35%)	22	0.644 (1.00)	0.194 (1.00)	0.235 (1.00)	0.459 (1.00)	0.533 (1.00)	0.276 (1.00)	1 (1.00)	0.702 (1.00)	0.441 (1.00)
Del Peak 23(17q25 3)	8 (24%)	26	0.0882 (1.00)	0.307 (1.00)	0.707 (1.00)	1 (1.00)	0.373 (1.00)	0.86 (1.00)	1 (1.00)	0.641 (1.00)	0.527 (1.00)
Del Peak 24(19p13 3)	9 (26%)	25	0.447 (1.00)	0.612 (1.00)	0.278 (1.00)	0.111 (1.00)	0.764 (1.00)	0.837 (1.00)	1 (1.00)	1 (1.00)	0.566 (1.00)
Del Peak 25(20p12 1)	6 (18%)	28	0.296 (1.00)	0.804 (1.00)	0.224 (1.00)	0.145 (1.00)	0.733 (1.00)	0.728 (1.00)	0.287 (1.00)	1 (1.00)	0.8 (1.00)
Del Peak 26(21q21 1)	9 (26%)	25	0.337 (1.00)	0.605 (1.00)	0.492 (1.00)	0.0172 (1.00)		0.03 (1.00)	1 (1.00)	0.419 (1.00)	0.547 (1.00)
Del Peak 27(Xp11 3)	13 (38%)	21	0.844 (1.00)	0.187 (1.00)	0.789 (1.00)	0.262 (1.00)	0.0867 (1.00)	0.268 (1.00)	0.205 (1.00)	1 (1.00)	0.323 (1.00)
Del Peak 28(Xq21 33)	10 (29%)	24	0.00867 (1.00)	0.897 (1.00)	0.746 (1.00)	0.232 (1.00)	0.166 (1.00)	0.549 (1.00)	1 (1.00)	1 (1.00)	0.4 (1.00)

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = CESC-TP.clin.merged.picked.txt
Number of patients = 34
Number of significantly arm-level cnvs = 51
Number of selected clinical features = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

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

[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[4] 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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