Correlation between copy number variation genes and selected clinical features

Overview

Introduction

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

Summary

Testing the association between copy number variation of 70 peak regions and 7 clinical features across 554 patients, 12 significant findings detected with Q value < 0.25.

Amp Peak 2(1q21.3) cnvs correlated to 'AGE'.
Amp Peak 3(1q42.2) cnvs correlated to 'AGE'.
Amp Peak 12(8p11.21) cnvs correlated to 'AGE'.
Amp Peak 14(10p15.3) cnvs correlated to 'AGE'.
Amp Peak 17(12p13.33) cnvs correlated to 'AGE'.
Amp Peak 18(12p12.1) cnvs correlated to 'AGE'.
Amp Peak 24(19q12) cnvs correlated to 'AGE'.
Amp Peak 25(19q13.2) cnvs correlated to 'AGE'.
Amp Peak 27(20q11.21) cnvs correlated to 'AGE'.
Amp Peak 28(20q13.33) cnvs correlated to 'AGE'.
Del Peak 16(9q21.11) cnvs correlated to 'AGE'.
Del Peak 30(16q23.1) cnvs correlated to 'AGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 70 regions and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.


		Clinical Features	Time to Death	AGE	PRIMARY SITE OF DISEASE	KARNOFSKY PERFORMANCE SCORE	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION	NEOADJUVANT THERAPY
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Amp Peak 2(1q21 3)	348 (63%)	206	0.277 (1.00)	5.85e-06 (0.00284)	0.128 (1.00)	0.408 (1.00)	0.767 (1.00)	1 (1.00)	0.737 (1.00)
Amp Peak 3(1q42 2)	298 (54%)	256	0.322 (1.00)	0.000505 (0.242)	0.252 (1.00)	0.736 (1.00)	0.175 (1.00)	0.598 (1.00)	1 (1.00)
Amp Peak 12(8p11 21)	197 (36%)	357	0.353 (1.00)	0.000433 (0.208)	0.121 (1.00)	0.662 (1.00)	0.314 (1.00)	0.289 (1.00)	0.91 (1.00)
Amp Peak 14(10p15 3)	238 (43%)	316	0.14 (1.00)	0.000341 (0.164)	0.154 (1.00)	0.923 (1.00)	0.228 (1.00)	0.58 (1.00)	0.124 (1.00)
Amp Peak 17(12p13 33)	309 (56%)	245	0.74 (1.00)	5.41e-07 (0.000264)	0.756 (1.00)	0.735 (1.00)	0.0944 (1.00)	1 (1.00)	0.0496 (1.00)
Amp Peak 18(12p12 1)	294 (53%)	260	0.0836 (1.00)	2.08e-08 (1.02e-05)	0.251 (1.00)	0.335 (1.00)	0.0316 (1.00)	0.603 (1.00)	0.0637 (1.00)
Amp Peak 24(19q12)	307 (55%)	247	0.566 (1.00)	1.66e-05 (0.00802)	0.161 (1.00)	0.51 (1.00)	0.102 (1.00)	1 (1.00)	0.0283 (1.00)
Amp Peak 25(19q13 2)	233 (42%)	321	0.0172 (1.00)	5.74e-06 (0.0028)	0.15 (1.00)	0.989 (1.00)	0.646 (1.00)	0.575 (1.00)	0.0779 (1.00)
Amp Peak 27(20q11 21)	324 (58%)	230	0.0954 (1.00)	1.12e-07 (5.47e-05)	1 (1.00)	0.264 (1.00)	0.0809 (1.00)	1 (1.00)	0.0272 (1.00)
Amp Peak 28(20q13 33)	385 (69%)	169	0.319 (1.00)	1.21e-05 (0.00585)	1 (1.00)	0.752 (1.00)	0.538 (1.00)	1 (1.00)	0.195 (1.00)
Del Peak 16(9q21 11)	268 (48%)	286	0.634 (1.00)	6.17e-06 (0.00299)	0.0541 (1.00)	0.634 (1.00)	0.00397 (1.00)	1 (1.00)	0.232 (1.00)
Del Peak 30(16q23 1)	431 (78%)	123	0.153 (1.00)	9.06e-05 (0.0437)	0.635 (1.00)	0.0778 (1.00)	0.124 (1.00)	1 (1.00)	0.194 (1.00)
Amp Peak 1(1p34 3)	277 (50%)	277	0.0388 (1.00)	0.012 (1.00)	1 (1.00)	0.985 (1.00)	0.888 (1.00)	0.249 (1.00)	0.744 (1.00)
Amp Peak 4(2p23 2)	231 (42%)	323	0.948 (1.00)	0.076 (1.00)	0.763 (1.00)	0.988 (1.00)	0.384 (1.00)	1 (1.00)	1 (1.00)
Amp Peak 5(2q31 2)	244 (44%)	310	0.192 (1.00)	0.011 (1.00)	0.756 (1.00)	0.693 (1.00)	0.00638 (1.00)	0.0848 (1.00)	0.827 (1.00)
Amp Peak 6(3q26 2)	460 (83%)	94	0.978 (1.00)	0.000932 (0.444)	0.526 (1.00)	0.00131 (0.623)	0.0534 (1.00)	1 (1.00)	0.772 (1.00)
Amp Peak 7(4p16 3)	152 (27%)	402	0.474 (1.00)	0.607 (1.00)	0.724 (1.00)	0.0728 (1.00)	0.834 (1.00)	1 (1.00)	0.329 (1.00)
Amp Peak 8(4q13 3)	105 (19%)	449	0.212 (1.00)	0.196 (1.00)	0.57 (1.00)	0.42 (1.00)	0.395 (1.00)	1 (1.00)	0.491 (1.00)
Amp Peak 9(5p15 33)	293 (53%)	261	0.0479 (1.00)	0.00215 (1.00)	0.751 (1.00)	0.798 (1.00)	0.295 (1.00)	0.604 (1.00)	0.446 (1.00)
Amp Peak 10(6p22 3)	283 (51%)	271	0.147 (1.00)	0.00682 (1.00)	1 (1.00)	0.545 (1.00)	0.0513 (1.00)	0.616 (1.00)	1 (1.00)
Amp Peak 11(7q36 3)	297 (54%)	257	0.314 (1.00)	0.801 (1.00)	1 (1.00)	0.1 (1.00)	0.74 (1.00)	0.599 (1.00)	0.744 (1.00)
Amp Peak 13(8q24 21)	435 (79%)	119	0.526 (1.00)	0.0927 (1.00)	1 (1.00)	0.628 (1.00)	0.182 (1.00)	0.517 (1.00)	0.508 (1.00)
Amp Peak 15(10q22 3)	173 (31%)	381	0.499 (1.00)	0.205 (1.00)	0.0925 (1.00)	0.989 (1.00)	0.736 (1.00)	1 (1.00)	0.559 (1.00)
Amp Peak 16(11q14 1)	245 (44%)	309	0.322 (1.00)	0.382 (1.00)	0.256 (1.00)	0.474 (1.00)	0.0503 (1.00)	1 (1.00)	0.191 (1.00)
Amp Peak 19(14q11 2)	140 (25%)	414	0.778 (1.00)	0.0596 (1.00)	0.123 (1.00)	0.378 (1.00)	0.0918 (1.00)	1 (1.00)	0.381 (1.00)
Amp Peak 20(15q26 3)	153 (28%)	401	0.067 (1.00)	0.304 (1.00)	0.727 (1.00)	0.42 (1.00)	0.143 (1.00)	0.565 (1.00)	0.0103 (1.00)
Amp Peak 21(17q25 3)	203 (37%)	351	0.0254 (1.00)	0.861 (1.00)	1 (1.00)	0.685 (1.00)	0.382 (1.00)	1 (1.00)	0.177 (1.00)
Amp Peak 22(18q11 2)	134 (24%)	420	0.997 (1.00)	0.0401 (1.00)	0.113 (1.00)	0.18 (1.00)	0.854 (1.00)	0.565 (1.00)	0.253 (1.00)
Amp Peak 23(19p13 12)	301 (54%)	253	0.219 (1.00)	0.0833 (1.00)	0.46 (1.00)	0.597 (1.00)	0.115 (1.00)	0.595 (1.00)	0.19 (1.00)
Amp Peak 26(20p13)	300 (54%)	254	0.299 (1.00)	0.00953 (1.00)	0.753 (1.00)	0.11 (1.00)	0.00212 (1.00)	1 (1.00)	1 (1.00)
Amp Peak 29(22q12 2)	89 (16%)	465	0.539 (1.00)	0.0215 (1.00)	1 (1.00)	0.419 (1.00)	0.438 (1.00)	1 (1.00)	0.883 (1.00)
Amp Peak 30(Xp11 23)	162 (29%)	392	0.154 (1.00)	0.0199 (1.00)	0.0773 (1.00)	0.275 (1.00)	0.362 (1.00)	0.56 (1.00)	0.72 (1.00)
Amp Peak 31(Xq28)	221 (40%)	333	0.393 (1.00)	0.962 (1.00)	0.769 (1.00)	0.654 (1.00)	0.00184 (0.874)	0.063 (1.00)	0.657 (1.00)
Del Peak 1(1p36 11)	261 (47%)	293	0.186 (1.00)	0.162 (1.00)	0.751 (1.00)	0.427 (1.00)	0.494 (1.00)	1 (1.00)	0.913 (1.00)
Del Peak 2(1q32 3)	89 (16%)	465	0.943 (1.00)	0.564 (1.00)	1 (1.00)	0.287 (1.00)	0.415 (1.00)	0.409 (1.00)	0.463 (1.00)
Del Peak 3(2p25 3)	117 (21%)	437	0.896 (1.00)	0.404 (1.00)	0.614 (1.00)	0.875 (1.00)	0.0566 (1.00)	0.51 (1.00)	0.69 (1.00)
Del Peak 4(2q22 1)	130 (23%)	424	0.211 (1.00)	0.464 (1.00)	0.658 (1.00)	0.595 (1.00)	0.345 (1.00)	1 (1.00)	0.055 (1.00)
Del Peak 5(2q37 3)	171 (31%)	383	0.619 (1.00)	0.0843 (1.00)	0.363 (1.00)	0.432 (1.00)	0.806 (1.00)	0.227 (1.00)	0.41 (1.00)
Del Peak 6(3p26 2)	204 (37%)	350	0.838 (1.00)	0.00357 (1.00)	0.127 (1.00)	0.246 (1.00)	0.132 (1.00)	0.0495 (1.00)	0.735 (1.00)
Del Peak 7(4q22 1)	370 (67%)	184	0.468 (1.00)	0.967 (1.00)	1 (1.00)	0.925 (1.00)	0.0443 (1.00)	1 (1.00)	0.165 (1.00)
Del Peak 8(4q34 3)	401 (72%)	153	0.827 (1.00)	0.339 (1.00)	0.727 (1.00)	0.171 (1.00)	0.809 (1.00)	0.565 (1.00)	0.33 (1.00)
Del Peak 9(5q11 2)	330 (60%)	224	0.764 (1.00)	0.676 (1.00)	0.767 (1.00)	0.325 (1.00)	0.236 (1.00)	0.569 (1.00)	0.096 (1.00)
Del Peak 10(5q13 2)	393 (71%)	161	0.272 (1.00)	0.965 (1.00)	0.748 (1.00)	0.216 (1.00)	0.866 (1.00)	0.204 (1.00)	0.119 (1.00)
Del Peak 11(6q27)	367 (66%)	187	0.322 (1.00)	0.000581 (0.278)	1 (1.00)	0.508 (1.00)	0.372 (1.00)	1 (1.00)	0.73 (1.00)
Del Peak 12(7p22 1)	241 (44%)	313	0.0833 (1.00)	0.035 (1.00)	0.758 (1.00)	0.497 (1.00)	0.971 (1.00)	1 (1.00)	1 (1.00)
Del Peak 13(8p23 3)	372 (67%)	182	0.243 (1.00)	0.0512 (1.00)	1 (1.00)	0.95 (1.00)	0.901 (1.00)	1 (1.00)	0.489 (1.00)
Del Peak 14(8p21 2)	388 (70%)	166	0.647 (1.00)	0.0716 (1.00)	1 (1.00)	0.647 (1.00)	0.535 (1.00)	1 (1.00)	1 (1.00)
Del Peak 15(9p24 3)	246 (44%)	308	0.982 (1.00)	0.021 (1.00)	0.45 (1.00)	0.928 (1.00)	0.4 (1.00)	0.587 (1.00)	0.325 (1.00)
Del Peak 17(9q34 13)	330 (60%)	224	0.827 (1.00)	0.0326 (1.00)	0.767 (1.00)	0.623 (1.00)	0.865 (1.00)	0.276 (1.00)	0.912 (1.00)
Del Peak 18(10p15 3)	111 (20%)	443	0.437 (1.00)	0.865 (1.00)	0.592 (1.00)	0.809 (1.00)	0.362 (1.00)	0.489 (1.00)	1 (1.00)
Del Peak 19(10q23 31)	214 (39%)	340	0.309 (1.00)	0.928 (1.00)	1 (1.00)	0.393 (1.00)	0.628 (1.00)	0.562 (1.00)	0.0742 (1.00)
Del Peak 20(10q26 3)	187 (34%)	367	0.0788 (1.00)	0.889 (1.00)	0.799 (1.00)	0.77 (1.00)	0.344 (1.00)	1 (1.00)	0.252 (1.00)
Del Peak 21(11p15 5)	329 (59%)	225	0.0452 (1.00)	0.628 (1.00)	0.0268 (1.00)	0.267 (1.00)	0.684 (1.00)	1 (1.00)	0.58 (1.00)
Del Peak 22(11q25)	192 (35%)	362	0.551 (1.00)	0.101 (1.00)	0.225 (1.00)	0.631 (1.00)	0.0768 (1.00)	0.277 (1.00)	0.568 (1.00)
Del Peak 23(12q23 1)	189 (34%)	365	0.304 (1.00)	0.0113 (1.00)	0.797 (1.00)	0.4 (1.00)	0.265 (1.00)	1 (1.00)	0.108 (1.00)
Del Peak 24(12q24 33)	208 (38%)	346	0.614 (1.00)	0.0929 (1.00)	0.13 (1.00)	0.652 (1.00)	0.549 (1.00)	0.295 (1.00)	0.117 (1.00)
Del Peak 25(13q14 2)	344 (62%)	210	0.078 (1.00)	0.526 (1.00)	0.778 (1.00)	0.592 (1.00)	0.77 (1.00)	0.56 (1.00)	0.219 (1.00)
Del Peak 26(14q23 2)	291 (53%)	263	0.703 (1.00)	0.503 (1.00)	0.475 (1.00)	0.0423 (1.00)	0.319 (1.00)	0.106 (1.00)	0.514 (1.00)
Del Peak 27(15q15 1)	348 (63%)	206	0.712 (1.00)	0.00444 (1.00)	0.412 (1.00)	0.253 (1.00)	0.0294 (1.00)	0.298 (1.00)	0.433 (1.00)
Del Peak 28(16p13 3)	293 (53%)	261	0.927 (1.00)	0.941 (1.00)	0.751 (1.00)	0.578 (1.00)	0.209 (1.00)	0.604 (1.00)	0.913 (1.00)
Del Peak 29(16q22 1)	439 (79%)	115	0.625 (1.00)	0.00557 (1.00)	0.192 (1.00)	0.275 (1.00)	0.537 (1.00)	1 (1.00)	0.789 (1.00)
Del Peak 31(17p12)	468 (84%)	86	0.813 (1.00)	0.995 (1.00)	0.492 (1.00)	0.73 (1.00)	0.011 (1.00)	1 (1.00)	1 (1.00)
Del Peak 32(17q11 2)	452 (82%)	102	0.729 (1.00)	0.0307 (1.00)	0.0662 (1.00)	0.686 (1.00)	0.246 (1.00)	1 (1.00)	0.0673 (1.00)
Del Peak 33(18q23)	361 (65%)	193	0.701 (1.00)	0.834 (1.00)	0.227 (1.00)	0.544 (1.00)	0.705 (1.00)	1 (1.00)	0.138 (1.00)
Del Peak 34(19p13 3)	485 (88%)	69	0.244 (1.00)	0.0111 (1.00)	1 (1.00)	0.00833 (1.00)	0.0673 (1.00)	1 (1.00)	0.742 (1.00)
Del Peak 35(19q13 33)	288 (52%)	266	0.641 (1.00)	0.391 (1.00)	1 (1.00)	0.311 (1.00)	0.358 (1.00)	0.25 (1.00)	0.327 (1.00)
Del Peak 36(19q13 43)	274 (49%)	280	0.419 (1.00)	0.0381 (1.00)	1 (1.00)	0.283 (1.00)	0.264 (1.00)	1 (1.00)	0.233 (1.00)
Del Peak 37(21q22 3)	214 (39%)	340	0.556 (1.00)	0.323 (1.00)	0.774 (1.00)	0.665 (1.00)	0.126 (1.00)	1 (1.00)	0.577 (1.00)
Del Peak 38(22q13 32)	478 (86%)	76	0.747 (1.00)	0.744 (1.00)	0.447 (1.00)	0.752 (1.00)	0.565 (1.00)	1 (1.00)	0.874 (1.00)
Del Peak 39(Xp21 1)	354 (64%)	200	0.808 (1.00)	0.342 (1.00)	1 (1.00)	0.987 (1.00)	0.671 (1.00)	0.557 (1.00)	0.311 (1.00)

'Amp Peak 2(1q21.3) mutation analysis' versus 'AGE'

P value = 5.85e-06 (t-test), Q value = 0.0028

Table S1. Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED	342	61.5 (11.1)
AMP PEAK 2(1Q21.3) WILD-TYPE	201	56.8 (11.9)

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 3(1q42.2) mutation analysis' versus 'AGE'

P value = 0.000505 (t-test), Q value = 0.24

Table S2. Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 3(1Q42.2) MUTATED	293	61.4 (11.3)
AMP PEAK 3(1Q42.2) WILD-TYPE	250	57.9 (11.7)

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(1q42.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 12(8p11.21) mutation analysis' versus 'AGE'

P value = 0.000433 (t-test), Q value = 0.21

Table S3. Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 12(8P11.21) MUTATED	193	62.1 (10.8)
AMP PEAK 12(8P11.21) WILD-TYPE	350	58.5 (11.9)

Figure S3. Get High-res Image Gene #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 14(10p15.3) mutation analysis' versus 'AGE'

P value = 0.000341 (t-test), Q value = 0.16

Table S4. Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED	234	61.8 (11.1)
AMP PEAK 14(10P15.3) WILD-TYPE	309	58.2 (11.8)

Figure S4. Get High-res Image Gene #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 17(12p13.33) mutation analysis' versus 'AGE'

P value = 5.41e-07 (t-test), Q value = 0.00026

Table S5. Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED	304	62.0 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE	239	56.9 (12.0)

Figure S5. Get High-res Image Gene #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 18(12p12.1) mutation analysis' versus 'AGE'

P value = 2.08e-08 (t-test), Q value = 1e-05

Table S6. Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED	287	62.4 (11.3)
AMP PEAK 18(12P12.1) WILD-TYPE	256	56.8 (11.3)

Figure S6. Get High-res Image Gene #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 24(19q12) mutation analysis' versus 'AGE'

P value = 1.66e-05 (t-test), Q value = 0.008

Table S7. Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 24(19Q12) MUTATED	302	61.7 (11.2)
AMP PEAK 24(19Q12) WILD-TYPE	241	57.4 (11.7)

Figure S7. Get High-res Image Gene #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 25(19q13.2) mutation analysis' versus 'AGE'

P value = 5.74e-06 (t-test), Q value = 0.0028

Table S8. Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 25(19Q13.2) MUTATED	229	62.4 (11.3)
AMP PEAK 25(19Q13.2) WILD-TYPE	314	57.9 (11.5)

Figure S8. Get High-res Image Gene #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 27(20q11.21) mutation analysis' versus 'AGE'

P value = 1.12e-07 (t-test), Q value = 5.5e-05

Table S9. Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 27(20Q11.21) MUTATED	317	62.0 (11.6)
AMP PEAK 27(20Q11.21) WILD-TYPE	226	56.7 (11.0)

Figure S9. Get High-res Image Gene #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 28(20q13.33) mutation analysis' versus 'AGE'

P value = 1.21e-05 (t-test), Q value = 0.0059

Table S10. Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
AMP PEAK 28(20Q13.33) MUTATED	377	61.2 (11.6)
AMP PEAK 28(20Q13.33) WILD-TYPE	166	56.5 (11.1)

Figure S10. Get High-res Image Gene #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 16(9q21.11) mutation analysis' versus 'AGE'

P value = 6.17e-06 (t-test), Q value = 0.003

Table S11. Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
DEL PEAK 16(9Q21.11) MUTATED	262	62.1 (11.6)
DEL PEAK 16(9Q21.11) WILD-TYPE	281	57.6 (11.3)

Figure S11. Get High-res Image Gene #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 30(16q23.1) mutation analysis' versus 'AGE'

P value = 9.06e-05 (t-test), Q value = 0.044

Table S12. Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	543	59.8 (11.6)
DEL PEAK 30(16Q23.1) MUTATED	425	60.8 (11.5)
DEL PEAK 30(16Q23.1) WILD-TYPE	118	56.1 (11.2)

Figure S12. Get High-res Image Gene #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #2: 'AGE'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Clinical data file = OV.clin.merged.picked.txt
Number of patients = 554
Number of copy number variation regions = 70
Number of selected clinical features = 7
Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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.

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)

[5] GISTIC_version2

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