Correlation between copy number variation genes (focal) and selected clinical features
Overview
Introduction

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

Summary

Testing the association between subtypes identified by 43 different clustering approaches and 3 clinical features across 146 patients, 2 significant findings detected with Q value < 0.25.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 1(1q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 2(3q26.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 3(7p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 4(8p11.22) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 5(8q21.13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 6(10q21.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 7(12q24.32) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 8(14q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 10(Xp22.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 11(Xp21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 12(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 13(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 14(Xq21.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 15(Xq25) mutation analysis'. These subtypes correlate to 'AGE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 16(Xq25) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 17(Xq27.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 1(1p31.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 2(1p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 3(1q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 4(1q42.13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 5(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 6(2q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 7(3p13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 8(3q29) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 9(4q28.1) mutation analysis'. These subtypes correlate to 'AGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 10(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 11(5q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 12(6q15) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 13(7q36.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 14(8p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 15(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 16(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 17(11q23.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 18(12p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 19(13q14.13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 20(16q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 21(16q24.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 22(17p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 23(17q21.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 24(18q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 25(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 26(21q22.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 27(21q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between subtypes identified by 43 different clustering approaches and 3 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE RADIATIONS
RADIATION
REGIMENINDICATION
Statistical Tests logrank test t-test Fisher's exact test
Amp Peak 1(1q21 3) 1
(1.00) 		0.835
(1.00) 		1
(1.00)
Amp Peak 2(3q26 2) 1
(1.00) 		0.128
(1.00) 		1
(1.00)
Amp Peak 3(7p15 3) 1
(1.00) 		0.454
(1.00) 		0.258
(1.00)
Amp Peak 4(8p11 22) 1
(1.00) 		0.379
(1.00) 		1
(1.00)
Amp Peak 5(8q21 13) 1
(1.00) 		0.0354
(1.00) 		0.33
(1.00)
Amp Peak 6(10q21 2) 1
(1.00) 		0.215
(1.00) 		1
(1.00)
Amp Peak 7(12q24 32) 1
(1.00) 		0.988
(1.00) 		0.221
(1.00)
Amp Peak 8(14q21 1) 1
(1.00) 		0.0144
(1.00) 		0.192
(1.00)
Amp Peak 10(Xp22 11) 1
(1.00) 		0.25
(1.00) 		1
(1.00)
Amp Peak 11(Xp21 1) 1
(1.00) 		0.125
(1.00) 		1
(1.00)
Amp Peak 12(Xq21 1) 1
(1.00) 		0.731
(1.00) 		1
(1.00)
Amp Peak 13(Xq21 1) 1
(1.00) 		0.334
(1.00) 		1
(1.00)
Amp Peak 14(Xq21 31) 1
(1.00) 		0.235
(1.00) 		1
(1.00)
Amp Peak 15(Xq25) 1
(1.00) 		7.25e-09
(9.36e-07) 		1
(1.00)
Amp Peak 16(Xq25) 1
(1.00) 		0.724
(1.00) 		1
(1.00)
Amp Peak 17(Xq27 1) 1
(1.00) 		0.295
(1.00) 		1
(1.00)
Del Peak 1(1p31 3) 1
(1.00) 		0.787
(1.00) 		1
(1.00)
Del Peak 2(1p21 3) 1
(1.00) 		0.998
(1.00) 		1
(1.00)
Del Peak 3(1q23 1) 1
(1.00) 		0.643
(1.00) 		1
(1.00)
Del Peak 4(1q42 13) 1
(1.00) 		0.156
(1.00) 		1
(1.00)
Del Peak 5(2q22 1) 1
(1.00) 		0.0945
(1.00) 		1
(1.00)
Del Peak 6(2q22 3) 1
(1.00) 		0.149
(1.00) 		1
(1.00)
Del Peak 7(3p13) 1
(1.00) 		0.319
(1.00) 		0.0396
(1.00)
Del Peak 8(3q29) 1
(1.00) 		0.347
(1.00) 		1
(1.00)
Del Peak 9(4q28 1) 1
(1.00) 		0.000488
(0.0624) 		1
(1.00)
Del Peak 10(5q11 2) 1
(1.00) 		0.0689
(1.00) 		1
(1.00)
Del Peak 11(5q21 1) 1
(1.00) 		0.0196
(1.00) 		0.586
(1.00)
Del Peak 12(6q15) 1
(1.00) 		0.0337
(1.00) 		0.168
(1.00)
Del Peak 13(7q36 1) 1
(1.00) 		0.0663
(1.00) 		1
(1.00)
Del Peak 14(8p21 3) 1
(1.00) 		0.231
(1.00) 		1
(1.00)
Del Peak 15(8p11 21) 1
(1.00) 		0.0851
(1.00) 		0.176
(1.00)
Del Peak 16(10q23 31) 1
(1.00) 		0.975
(1.00) 		0.653
(1.00)
Del Peak 17(11q23 2) 1
(1.00) 		0.635
(1.00) 		1
(1.00)
Del Peak 18(12p13 2) 1
(1.00) 		0.768
(1.00) 		1
(1.00)
Del Peak 19(13q14 13) 1
(1.00) 		0.00565
(0.717) 		0.184
(1.00)
Del Peak 20(16q22 3) 1
(1.00) 		0.0237
(1.00) 		0.324
(1.00)
Del Peak 21(16q24 1) 1
(1.00) 		0.123
(1.00) 		1
(1.00)
Del Peak 22(17p13 1) 1
(1.00) 		0.447
(1.00) 		1
(1.00)
Del Peak 23(17q21 31) 1
(1.00) 		0.675
(1.00) 		1
(1.00)
Del Peak 24(18q22 1) 1
(1.00) 		0.659
(1.00) 		1
(1.00)
Del Peak 25(18q23) 1
(1.00) 		0.0888
(1.00) 		0.631
(1.00)
Del Peak 26(21q22 2) 1
(1.00) 		0.858
(1.00) 		0.331
(1.00)
Del Peak 27(21q22 3) 1
(1.00) 		0.689
(1.00) 		0.18
(1.00)
Clustering Approach #1: 'Amp Peak 1(1q21.3) mutation analysis'

Table S1.  Description of clustering approach #1: 'Amp Peak 1(1q21.3) mutation analysis'

Cluster Labels AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
Number of samples 9 137
Clustering Approach #2: 'Amp Peak 2(3q26.2) mutation analysis'

Table S2.  Description of clustering approach #2: 'Amp Peak 2(3q26.2) mutation analysis'

Cluster Labels AMP PEAK 2(3Q26.2) MUTATED AMP PEAK 2(3Q26.2) WILD-TYPE
Number of samples 23 123
Clustering Approach #3: 'Amp Peak 3(7p15.3) mutation analysis'

Table S3.  Description of clustering approach #3: 'Amp Peak 3(7p15.3) mutation analysis'

Cluster Labels AMP PEAK 3(7P15.3) MUTATED AMP PEAK 3(7P15.3) WILD-TYPE
Number of samples 29 117
Clustering Approach #4: 'Amp Peak 4(8p11.22) mutation analysis'

Table S4.  Description of clustering approach #4: 'Amp Peak 4(8p11.22) mutation analysis'

Cluster Labels AMP PEAK 4(8P11.22) MUTATED AMP PEAK 4(8P11.22) WILD-TYPE
Number of samples 15 131
Clustering Approach #5: 'Amp Peak 5(8q21.13) mutation analysis'

Table S5.  Description of clustering approach #5: 'Amp Peak 5(8q21.13) mutation analysis'

Cluster Labels AMP PEAK 5(8Q21.13) MUTATED AMP PEAK 5(8Q21.13) WILD-TYPE
Number of samples 37 109
Clustering Approach #6: 'Amp Peak 6(10q21.2) mutation analysis'

Table S6.  Description of clustering approach #6: 'Amp Peak 6(10q21.2) mutation analysis'

Cluster Labels AMP PEAK 6(10Q21.2) MUTATED AMP PEAK 6(10Q21.2) WILD-TYPE
Number of samples 7 139
Clustering Approach #7: 'Amp Peak 7(12q24.32) mutation analysis'

Table S7.  Description of clustering approach #7: 'Amp Peak 7(12q24.32) mutation analysis'

Cluster Labels AMP PEAK 7(12Q24.32) MUTATED AMP PEAK 7(12Q24.32) WILD-TYPE
Number of samples 7 139
Clustering Approach #8: 'Amp Peak 8(14q21.1) mutation analysis'

Table S8.  Description of clustering approach #8: 'Amp Peak 8(14q21.1) mutation analysis'

Cluster Labels AMP PEAK 8(14Q21.1) MUTATED AMP PEAK 8(14Q21.1) WILD-TYPE
Number of samples 6 140
Clustering Approach #9: 'Amp Peak 10(Xp22.11) mutation analysis'

Table S9.  Description of clustering approach #9: 'Amp Peak 10(Xp22.11) mutation analysis'

Cluster Labels AMP PEAK 10(XP22.11) MUTATED AMP PEAK 10(XP22.11) WILD-TYPE
Number of samples 4 142
Clustering Approach #10: 'Amp Peak 11(Xp21.1) mutation analysis'

Table S10.  Description of clustering approach #10: 'Amp Peak 11(Xp21.1) mutation analysis'

Cluster Labels AMP PEAK 11(XP21.1) MUTATED AMP PEAK 11(XP21.1) WILD-TYPE
Number of samples 4 142
Clustering Approach #11: 'Amp Peak 12(Xq21.1) mutation analysis'

Table S11.  Description of clustering approach #11: 'Amp Peak 12(Xq21.1) mutation analysis'

Cluster Labels AMP PEAK 12(XQ21.1) MUTATED AMP PEAK 12(XQ21.1) WILD-TYPE
Number of samples 7 139
Clustering Approach #12: 'Amp Peak 13(Xq21.1) mutation analysis'

Table S12.  Description of clustering approach #12: 'Amp Peak 13(Xq21.1) mutation analysis'

Cluster Labels AMP PEAK 13(XQ21.1) MUTATED AMP PEAK 13(XQ21.1) WILD-TYPE
Number of samples 5 141
Clustering Approach #13: 'Amp Peak 14(Xq21.31) mutation analysis'

Table S13.  Description of clustering approach #13: 'Amp Peak 14(Xq21.31) mutation analysis'

Cluster Labels AMP PEAK 14(XQ21.31) MUTATED AMP PEAK 14(XQ21.31) WILD-TYPE
Number of samples 5 141
Clustering Approach #14: 'Amp Peak 15(Xq25) mutation analysis'

Table S14.  Description of clustering approach #14: 'Amp Peak 15(Xq25) mutation analysis'

Cluster Labels AMP PEAK 15(XQ25) MUTATED AMP PEAK 15(XQ25) WILD-TYPE
Number of samples 3 143
'Amp Peak 15(Xq25) mutation analysis' versus 'AGE'

P value = 7.25e-09 (t-test), Q value = 9.4e-07

Table S15.  Clustering Approach #14: 'Amp Peak 15(Xq25) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 146 60.4 (7.0)
AMP PEAK 15(XQ25) MUTATED 3 65.7 (0.6)
AMP PEAK 15(XQ25) WILD-TYPE 143 60.3 (7.0)

Figure S1.  Get High-res Image Clustering Approach #14: 'Amp Peak 15(Xq25) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #15: 'Amp Peak 16(Xq25) mutation analysis'

Table S16.  Description of clustering approach #15: 'Amp Peak 16(Xq25) mutation analysis'

Cluster Labels AMP PEAK 16(XQ25) MUTATED AMP PEAK 16(XQ25) WILD-TYPE
Number of samples 6 140
Clustering Approach #16: 'Amp Peak 17(Xq27.1) mutation analysis'

Table S17.  Description of clustering approach #16: 'Amp Peak 17(Xq27.1) mutation analysis'

Cluster Labels AMP PEAK 17(XQ27.1) MUTATED AMP PEAK 17(XQ27.1) WILD-TYPE
Number of samples 9 137
Clustering Approach #17: 'Del Peak 1(1p31.3) mutation analysis'

Table S18.  Description of clustering approach #17: 'Del Peak 1(1p31.3) mutation analysis'

Cluster Labels DEL PEAK 1(1P31.3) MUTATED DEL PEAK 1(1P31.3) WILD-TYPE
Number of samples 19 127
Clustering Approach #18: 'Del Peak 2(1p21.3) mutation analysis'

Table S19.  Description of clustering approach #18: 'Del Peak 2(1p21.3) mutation analysis'

Cluster Labels DEL PEAK 2(1P21.3) MUTATED DEL PEAK 2(1P21.3) WILD-TYPE
Number of samples 13 133
Clustering Approach #19: 'Del Peak 3(1q23.1) mutation analysis'

Table S20.  Description of clustering approach #19: 'Del Peak 3(1q23.1) mutation analysis'

Cluster Labels DEL PEAK 3(1Q23.1) MUTATED DEL PEAK 3(1Q23.1) WILD-TYPE
Number of samples 5 141
Clustering Approach #20: 'Del Peak 4(1q42.13) mutation analysis'

Table S21.  Description of clustering approach #20: 'Del Peak 4(1q42.13) mutation analysis'

Cluster Labels DEL PEAK 4(1Q42.13) MUTATED DEL PEAK 4(1Q42.13) WILD-TYPE
Number of samples 14 132
Clustering Approach #21: 'Del Peak 5(2q22.1) mutation analysis'

Table S22.  Description of clustering approach #21: 'Del Peak 5(2q22.1) mutation analysis'

Cluster Labels DEL PEAK 5(2Q22.1) MUTATED DEL PEAK 5(2Q22.1) WILD-TYPE
Number of samples 19 127
Clustering Approach #22: 'Del Peak 6(2q22.3) mutation analysis'

Table S23.  Description of clustering approach #22: 'Del Peak 6(2q22.3) mutation analysis'

Cluster Labels DEL PEAK 6(2Q22.3) MUTATED DEL PEAK 6(2Q22.3) WILD-TYPE
Number of samples 18 128
Clustering Approach #23: 'Del Peak 7(3p13) mutation analysis'

Table S24.  Description of clustering approach #23: 'Del Peak 7(3p13) mutation analysis'

Cluster Labels DEL PEAK 7(3P13) MUTATED DEL PEAK 7(3P13) WILD-TYPE
Number of samples 26 120
Clustering Approach #24: 'Del Peak 8(3q29) mutation analysis'

Table S25.  Description of clustering approach #24: 'Del Peak 8(3q29) mutation analysis'

Cluster Labels DEL PEAK 8(3Q29) MUTATED DEL PEAK 8(3Q29) WILD-TYPE
Number of samples 9 137
Clustering Approach #25: 'Del Peak 9(4q28.1) mutation analysis'

Table S26.  Description of clustering approach #25: 'Del Peak 9(4q28.1) mutation analysis'

Cluster Labels DEL PEAK 9(4Q28.1) MUTATED DEL PEAK 9(4Q28.1) WILD-TYPE
Number of samples 11 135
'Del Peak 9(4q28.1) mutation analysis' versus 'AGE'

P value = 0.000488 (t-test), Q value = 0.062

Table S27.  Clustering Approach #25: 'Del Peak 9(4q28.1) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 146 60.4 (7.0)
DEL PEAK 9(4Q28.1) MUTATED 11 65.5 (3.7)
DEL PEAK 9(4Q28.1) WILD-TYPE 135 60.0 (7.0)

Figure S2.  Get High-res Image Clustering Approach #25: 'Del Peak 9(4q28.1) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #26: 'Del Peak 10(5q11.2) mutation analysis'

Table S28.  Description of clustering approach #26: 'Del Peak 10(5q11.2) mutation analysis'

Cluster Labels DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
Number of samples 23 123
Clustering Approach #27: 'Del Peak 11(5q21.1) mutation analysis'

Table S29.  Description of clustering approach #27: 'Del Peak 11(5q21.1) mutation analysis'

Cluster Labels DEL PEAK 11(5Q21.1) MUTATED DEL PEAK 11(5Q21.1) WILD-TYPE
Number of samples 26 120
Clustering Approach #28: 'Del Peak 12(6q15) mutation analysis'

Table S30.  Description of clustering approach #28: 'Del Peak 12(6q15) mutation analysis'

Cluster Labels DEL PEAK 12(6Q15) MUTATED DEL PEAK 12(6Q15) WILD-TYPE
Number of samples 49 97
Clustering Approach #29: 'Del Peak 13(7q36.1) mutation analysis'

Table S31.  Description of clustering approach #29: 'Del Peak 13(7q36.1) mutation analysis'

Cluster Labels DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
Number of samples 5 141
Clustering Approach #30: 'Del Peak 14(8p21.3) mutation analysis'

Table S32.  Description of clustering approach #30: 'Del Peak 14(8p21.3) mutation analysis'

Cluster Labels DEL PEAK 14(8P21.3) MUTATED DEL PEAK 14(8P21.3) WILD-TYPE
Number of samples 87 59
Clustering Approach #31: 'Del Peak 15(8p11.21) mutation analysis'

Table S33.  Description of clustering approach #31: 'Del Peak 15(8p11.21) mutation analysis'

Cluster Labels DEL PEAK 15(8P11.21) MUTATED DEL PEAK 15(8P11.21) WILD-TYPE
Number of samples 47 99
Clustering Approach #32: 'Del Peak 16(10q23.31) mutation analysis'

Table S34.  Description of clustering approach #32: 'Del Peak 16(10q23.31) mutation analysis'

Cluster Labels DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
Number of samples 53 93
Clustering Approach #33: 'Del Peak 17(11q23.2) mutation analysis'

Table S35.  Description of clustering approach #33: 'Del Peak 17(11q23.2) mutation analysis'

Cluster Labels DEL PEAK 17(11Q23.2) MUTATED DEL PEAK 17(11Q23.2) WILD-TYPE
Number of samples 16 130
Clustering Approach #34: 'Del Peak 18(12p13.2) mutation analysis'

Table S36.  Description of clustering approach #34: 'Del Peak 18(12p13.2) mutation analysis'

Cluster Labels DEL PEAK 18(12P13.2) MUTATED DEL PEAK 18(12P13.2) WILD-TYPE
Number of samples 31 115
Clustering Approach #35: 'Del Peak 19(13q14.13) mutation analysis'

Table S37.  Description of clustering approach #35: 'Del Peak 19(13q14.13) mutation analysis'

Cluster Labels DEL PEAK 19(13Q14.13) MUTATED DEL PEAK 19(13Q14.13) WILD-TYPE
Number of samples 68 78
Clustering Approach #36: 'Del Peak 20(16q22.3) mutation analysis'

Table S38.  Description of clustering approach #36: 'Del Peak 20(16q22.3) mutation analysis'

Cluster Labels DEL PEAK 20(16Q22.3) MUTATED DEL PEAK 20(16Q22.3) WILD-TYPE
Number of samples 45 101
Clustering Approach #37: 'Del Peak 21(16q24.1) mutation analysis'

Table S39.  Description of clustering approach #37: 'Del Peak 21(16q24.1) mutation analysis'

Cluster Labels DEL PEAK 21(16Q24.1) MUTATED DEL PEAK 21(16Q24.1) WILD-TYPE
Number of samples 58 88
Clustering Approach #38: 'Del Peak 22(17p13.1) mutation analysis'

Table S40.  Description of clustering approach #38: 'Del Peak 22(17p13.1) mutation analysis'

Cluster Labels DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
Number of samples 39 107
Clustering Approach #39: 'Del Peak 23(17q21.31) mutation analysis'

Table S41.  Description of clustering approach #39: 'Del Peak 23(17q21.31) mutation analysis'

Cluster Labels DEL PEAK 23(17Q21.31) MUTATED DEL PEAK 23(17Q21.31) WILD-TYPE
Number of samples 26 120
Clustering Approach #40: 'Del Peak 24(18q22.1) mutation analysis'

Table S42.  Description of clustering approach #40: 'Del Peak 24(18q22.1) mutation analysis'

Cluster Labels DEL PEAK 24(18Q22.1) MUTATED DEL PEAK 24(18Q22.1) WILD-TYPE
Number of samples 37 109
Clustering Approach #41: 'Del Peak 25(18q23) mutation analysis'

Table S43.  Description of clustering approach #41: 'Del Peak 25(18q23) mutation analysis'

Cluster Labels DEL PEAK 25(18Q23) MUTATED DEL PEAK 25(18Q23) WILD-TYPE
Number of samples 43 103
Clustering Approach #42: 'Del Peak 26(21q22.2) mutation analysis'

Table S44.  Description of clustering approach #42: 'Del Peak 26(21q22.2) mutation analysis'

Cluster Labels DEL PEAK 26(21Q22.2) MUTATED DEL PEAK 26(21Q22.2) WILD-TYPE
Number of samples 48 98
Clustering Approach #43: 'Del Peak 27(21q22.3) mutation analysis'

Table S45.  Description of clustering approach #43: 'Del Peak 27(21q22.3) mutation analysis'

Cluster Labels DEL PEAK 27(21Q22.3) MUTATED DEL PEAK 27(21Q22.3) WILD-TYPE
Number of samples 46 100
Methods & Data
Input

  • Cluster data file = all_lesions.conf_99.cnv.cluster.txt

  • Clinical data file = PRAD-TP.clin.merged.picked.txt

  • Number of patients = 146

  • Number of clustering approaches = 43

  • Number of selected clinical features = 3

  • Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R

Fisher's exact test

For binary clinical features, 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)
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