Correlate_Clinical_vs_CustomEvents

Thyroid Adenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlate_Clinical_vs_CustomEvents. Broad Institute of MIT and Harvard. doi:10.7908/C1B856C7

Overview

Introduction

This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.

Summary

Testing the association between mutation status of 6 genes and 14 clinical features across 229 patients, 3 significant findings detected with P value < 0.05 and Q value < 0.25.

FUSION RET mutation correlated to 'AGE'.
MUTATION MUT HRAS mutation correlated to 'AGE' and 'DISTANT.METASTASIS'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 6 genes and 14 clinical features. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 3 significant findings detected.


		Clinical Features	AGE	GENDER	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RADIATIONEXPOSURE	DISTANT METASTASIS	EXTRATHYROIDAL EXTENSION	LYMPH NODE METASTASIS	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	TUMOR STAGECODE	NEOPLASM DISEASESTAGE	MULTIFOCALITY	TUMOR SIZE
	nMutated (%)	nWild-Type	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	t-test	t-test	Chi-square test	Fisher's exact test	t-test
MUTATION MUT HRAS	0 (NaN%)	0	0.00121 (0.0918)	1 (1.00)	0.338 (1.00)	0.599 (1.00)	1 (1.00)	0.00304 (0.225)	0.384 (1.00)	0.0227 (1.00)	0.754 (1.00)	0.5 (1.00)		0.247 (1.00)	0.745 (1.00)	0.993 (1.00)
FUSION RET	0 (NaN%)	0	0.00143 (0.107)	0.177 (1.00)	0.714 (1.00)	0.426 (1.00)	1 (1.00)	1 (1.00)	0.721 (1.00)	0.452 (1.00)	0.309 (1.00)	0.303 (1.00)		0.144 (1.00)	1 (1.00)	0.816 (1.00)
FUSION PAX8	0 (NaN%)	0	0.848 (1.00)	0.255 (1.00)	0.0274 (1.00)	1 (1.00)	1 (1.00)	0.759 (1.00)	0.712 (1.00)	0.607 (1.00)	0.726 (1.00)	0.801 (1.00)		0.757 (1.00)	0.243 (1.00)	0.0518 (1.00)
FUSION BRAF	0 (NaN%)	0	0.372 (1.00)	0.553 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.595 (1.00)	1 (1.00)	0.725 (1.00)	1 (1.00)			0.618 (1.00)	0.585 (1.00)
MUTATION MUT BRAF	0 (NaN%)	0	0.507 (1.00)	0.591 (1.00)	0.0757 (1.00)	0.212 (1.00)	1 (1.00)	0.445 (1.00)	0.696 (1.00)	0.315 (1.00)	0.0292 (1.00)	0.867 (1.00)		0.268 (1.00)	1 (1.00)	0.0303 (1.00)
MUTATION MUT NRAS	0 (NaN%)	0	0.0416 (1.00)	0.287 (1.00)	0.219 (1.00)	0.0582 (1.00)	1 (1.00)	0.399 (1.00)	1 (1.00)	0.0291 (1.00)	0.766 (1.00)	0.469 (1.00)		0.16 (1.00)	1 (1.00)	0.638 (1.00)

'FUSION RET' versus 'AGE'

P value = 0.00143 (t-test), Q value = 0.11

Table S1. Gene #1: 'FUSION RET' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	171	47.5 (15.5)
subtype0	161	48.2 (15.6)
subtype1	10	36.1 (8.6)

Figure S1. Get High-res Image Gene #1: 'FUSION RET' versus Clinical Feature #1: 'AGE'

'FUSION RET' versus 'GENDER'

P value = 0.177 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'FUSION RET' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	118	53
subtype0	109	52
subtype1	9	1

'FUSION RET' versus 'HISTOLOGICAL.TYPE'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'FUSION RET' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	16	87	50	18
subtype0	16	81	46	18
subtype1	0	6	4	0

'FUSION RET' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.426 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'FUSION RET' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	9	162
subtype0	8	153
subtype1	1	9

'FUSION RET' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'FUSION RET' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	143	8
subtype0	134	8
subtype1	9	0

'FUSION RET' versus 'DISTANT.METASTASIS'

P value = 1 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'FUSION RET' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	70	3	97
subtype0	66	3	91
subtype1	4	0	6

'FUSION RET' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'FUSION RET' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	122
subtype0	37	2	114
subtype1	1	0	8

'FUSION RET' versus 'LYMPH.NODE.METASTASIS'

P value = 0.452 (Chi-square test), Q value = 1

Table S8. Gene #1: 'FUSION RET' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	84	7	35	24	21
subtype0	81	6	33	21	20
subtype1	3	1	2	3	1

'FUSION RET' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S9. Gene #1: 'FUSION RET' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	131	14	12
subtype0	124	12	12
subtype1	7	2	0

'FUSION RET' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.303 (t-test), Q value = 1

Table S10. Gene #1: 'FUSION RET' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	135	2.7 (4.8)
subtype0	127	2.5 (4.3)
subtype1	8	6.1 (9.3)

'FUSION RET' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.144 (Chi-square test), Q value = 1

Table S11. Gene #1: 'FUSION RET' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	91	25	38	13	3
subtype0	82	25	38	12	3
subtype1	9	0	0	1	0

'FUSION RET' versus 'MULTIFOCALITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S12. Gene #1: 'FUSION RET' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	90	72
subtype0	86	69
subtype1	4	3

'FUSION RET' versus 'TUMOR.SIZE'

P value = 0.816 (t-test), Q value = 1

Table S13. Gene #1: 'FUSION RET' versus Clinical Feature #14: 'TUMOR.SIZE'

	nPatients	Mean (Std.Dev)
ALL	147	2.9 (1.5)
subtype0	141	2.9 (1.5)
subtype1	6	3.0 (1.6)

'FUSION PAX8' versus 'AGE'

P value = 0.848 (t-test), Q value = 1

Table S14. Gene #2: 'FUSION PAX8' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	171	47.5 (15.5)
subtype0	163	47.4 (15.6)
subtype1	8	48.5 (15.1)

'FUSION PAX8' versus 'GENDER'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'FUSION PAX8' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	118	53
subtype0	114	49
subtype1	4	4

'FUSION PAX8' versus 'HISTOLOGICAL.TYPE'

P value = 0.0274 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'FUSION PAX8' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	16	87	50	18
subtype0	16	86	44	17
subtype1	0	1	6	1

Figure S2. Get High-res Image Gene #2: 'FUSION PAX8' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'FUSION PAX8' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1 (Fisher's exact test), Q value = 1

Table S17. Gene #2: 'FUSION PAX8' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	9	162
subtype0	9	154
subtype1	0	8

'FUSION PAX8' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S18. Gene #2: 'FUSION PAX8' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	143	8
subtype0	136	8
subtype1	7	0

'FUSION PAX8' versus 'DISTANT.METASTASIS'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S19. Gene #2: 'FUSION PAX8' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	70	3	97
subtype0	66	3	93
subtype1	4	0	4

'FUSION PAX8' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S20. Gene #2: 'FUSION PAX8' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	122
subtype0	37	2	115
subtype1	1	0	7

'FUSION PAX8' versus 'LYMPH.NODE.METASTASIS'

P value = 0.607 (Chi-square test), Q value = 1

Table S21. Gene #2: 'FUSION PAX8' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	84	7	35	24	21
subtype0	80	7	33	24	19
subtype1	4	0	2	0	2

'FUSION PAX8' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S22. Gene #2: 'FUSION PAX8' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	131	14	12
subtype0	125	13	12
subtype1	6	1	0

'FUSION PAX8' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.801 (t-test), Q value = 1

Table S23. Gene #2: 'FUSION PAX8' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	135	2.7 (4.8)
subtype0	132	2.7 (4.8)
subtype1	3	2.3 (2.1)

'FUSION PAX8' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.757 (Chi-square test), Q value = 1

Table S24. Gene #2: 'FUSION PAX8' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	91	25	38	13	3
subtype0	86	23	37	13	3
subtype1	5	2	1	0	0

'FUSION PAX8' versus 'MULTIFOCALITY'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S25. Gene #2: 'FUSION PAX8' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	90	72
subtype0	88	67
subtype1	2	5

'FUSION PAX8' versus 'TUMOR.SIZE'

P value = 0.0518 (t-test), Q value = 1

Table S26. Gene #2: 'FUSION PAX8' versus Clinical Feature #14: 'TUMOR.SIZE'

	nPatients	Mean (Std.Dev)
ALL	147	2.9 (1.5)
subtype0	140	2.8 (1.6)
subtype1	7	3.7 (0.9)

'FUSION BRAF' versus 'AGE'

P value = 0.372 (t-test), Q value = 1

Table S27. Gene #3: 'FUSION BRAF' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	171	47.5 (15.5)
subtype0	168	47.6 (15.6)
subtype1	3	39.0 (13.1)

'FUSION BRAF' versus 'GENDER'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S28. Gene #3: 'FUSION BRAF' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	118	53
subtype0	115	53
subtype1	3	0

'FUSION BRAF' versus 'HISTOLOGICAL.TYPE'

P value = 1 (Fisher's exact test), Q value = 1

Table S29. Gene #3: 'FUSION BRAF' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	16	87	50	18
subtype0	16	85	49	18
subtype1	0	2	1	0

'FUSION BRAF' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1 (Fisher's exact test), Q value = 1

Table S30. Gene #3: 'FUSION BRAF' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	9	162
subtype0	9	159
subtype1	0	3

'FUSION BRAF' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S31. Gene #3: 'FUSION BRAF' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	143	8
subtype0	140	8
subtype1	3	0

'FUSION BRAF' versus 'DISTANT.METASTASIS'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S32. Gene #3: 'FUSION BRAF' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	70	3	97
subtype0	68	3	96
subtype1	2	0	1

'FUSION BRAF' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 1 (Fisher's exact test), Q value = 1

Table S33. Gene #3: 'FUSION BRAF' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	122
subtype0	38	2	119
subtype1	0	0	3

'FUSION BRAF' versus 'LYMPH.NODE.METASTASIS'

P value = 0.725 (Chi-square test), Q value = 1

Table S34. Gene #3: 'FUSION BRAF' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	84	7	35	24	21
subtype0	83	7	34	24	20
subtype1	1	0	1	0	1

'FUSION BRAF' versus 'COMPLETENESS.OF.RESECTION'

P value = 1 (Fisher's exact test), Q value = 1

Table S35. Gene #3: 'FUSION BRAF' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	131	14	12
subtype0	128	14	12
subtype1	3	0	0

'FUSION BRAF' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.618 (Chi-square test), Q value = 1

Table S36. Gene #3: 'FUSION BRAF' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	91	25	38	13	3
subtype0	88	25	38	13	3
subtype1	3	0	0	0	0

'FUSION BRAF' versus 'MULTIFOCALITY'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S37. Gene #3: 'FUSION BRAF' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	90	72
subtype0	89	70
subtype1	1	2

'MUTATION MUT BRAF' versus 'AGE'

P value = 0.507 (t-test), Q value = 1

Table S38. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	136	46.0 (15.4)
subtype0	115	45.7 (15.7)
subtype1	21	47.9 (13.4)

'MUTATION MUT BRAF' versus 'GENDER'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	100	36
subtype0	83	32
subtype1	17	4

'MUTATION MUT BRAF' versus 'HISTOLOGICAL.TYPE'

P value = 0.0757 (Fisher's exact test), Q value = 1

Table S40. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	1	84	34	17
subtype0	1	72	25	17
subtype1	0	12	9	0

'MUTATION MUT BRAF' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.212 (Fisher's exact test), Q value = 1

Table S41. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	12	124
subtype0	12	103
subtype1	0	21

'MUTATION MUT BRAF' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S42. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	114	6
subtype0	99	6
subtype1	15	0

'MUTATION MUT BRAF' versus 'DISTANT.METASTASIS'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S43. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	59	1	75
subtype0	52	1	61
subtype1	7	0	14

'MUTATION MUT BRAF' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S44. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	93
subtype0	34	2	78
subtype1	4	0	15

'MUTATION MUT BRAF' versus 'LYMPH.NODE.METASTASIS'

P value = 0.315 (Chi-square test), Q value = 1

Table S45. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	66	8	31	17	14
subtype0	53	8	29	14	11
subtype1	13	0	2	3	3

'MUTATION MUT BRAF' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.0292 (Fisher's exact test), Q value = 1

Table S46. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	112	11	6
subtype0	100	9	3
subtype1	12	2	3

Figure S3. Get High-res Image Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

'MUTATION MUT BRAF' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.867 (t-test), Q value = 1

Table S47. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	106	2.8 (4.8)
subtype0	90	2.9 (4.8)
subtype1	16	2.6 (5.1)

'MUTATION MUT BRAF' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.268 (Chi-square test), Q value = 1

Table S48. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	75	18	31	10	1
subtype0	65	12	27	9	1
subtype1	10	6	4	1	0

'MUTATION MUT BRAF' versus 'MULTIFOCALITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S49. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	64	68
subtype0	54	58
subtype1	10	10

'MUTATION MUT BRAF' versus 'TUMOR.SIZE'

P value = 0.0303 (t-test), Q value = 1

Table S50. Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #14: 'TUMOR.SIZE'

	nPatients	Mean (Std.Dev)
ALL	98	2.8 (1.4)
subtype0	88	2.8 (1.4)
subtype1	10	2.2 (0.7)

Figure S4. Get High-res Image Gene #4: 'MUTATION MUT BRAF' versus Clinical Feature #14: 'TUMOR.SIZE'

'MUTATION MUT NRAS' versus 'AGE'

P value = 0.0416 (t-test), Q value = 1

Table S51. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	136	46.0 (15.4)
subtype0	125	46.9 (15.2)
subtype1	11	36.2 (14.9)

Figure S5. Get High-res Image Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #1: 'AGE'

'MUTATION MUT NRAS' versus 'GENDER'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S52. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	100	36
subtype0	90	35
subtype1	10	1

'MUTATION MUT NRAS' versus 'HISTOLOGICAL.TYPE'

P value = 0.219 (Fisher's exact test), Q value = 1

Table S53. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	1	84	34	17
subtype0	1	74	33	17
subtype1	0	10	1	0

'MUTATION MUT NRAS' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.0582 (Fisher's exact test), Q value = 1

Table S54. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	12	124
subtype0	9	116
subtype1	3	8

'MUTATION MUT NRAS' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S55. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	114	6
subtype0	103	6
subtype1	11	0

'MUTATION MUT NRAS' versus 'DISTANT.METASTASIS'

P value = 0.399 (Fisher's exact test), Q value = 1

Table S56. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	59	1	75
subtype0	56	1	67
subtype1	3	0	8

'MUTATION MUT NRAS' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 1 (Fisher's exact test), Q value = 1

Table S57. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	93
subtype0	35	2	85
subtype1	3	0	8

'MUTATION MUT NRAS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.0291 (Chi-square test), Q value = 1

Table S58. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	66	8	31	17	14
subtype0	61	5	29	16	14
subtype1	5	3	2	1	0

Figure S6. Get High-res Image Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'MUTATION MUT NRAS' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S59. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	112	11	6
subtype0	101	11	6
subtype1	11	0	0

'MUTATION MUT NRAS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.469 (t-test), Q value = 1

Table S60. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	106	2.8 (4.8)
subtype0	97	2.7 (4.7)
subtype1	9	4.2 (5.9)

'MUTATION MUT NRAS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.16 (Chi-square test), Q value = 1

Table S61. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	75	18	31	10	1
subtype0	65	17	31	10	1
subtype1	10	1	0	0	0

'MUTATION MUT NRAS' versus 'MULTIFOCALITY'

P value = 1 (Fisher's exact test), Q value = 1

Table S62. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	64	68
subtype0	59	62
subtype1	5	6

'MUTATION MUT NRAS' versus 'TUMOR.SIZE'

P value = 0.638 (t-test), Q value = 1

Table S63. Gene #5: 'MUTATION MUT NRAS' versus Clinical Feature #14: 'TUMOR.SIZE'

	nPatients	Mean (Std.Dev)
ALL	98	2.8 (1.4)
subtype0	89	2.8 (1.4)
subtype1	9	2.6 (1.4)

'MUTATION MUT HRAS' versus 'AGE'

P value = 0.00121 (t-test), Q value = 0.092

Table S64. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #1: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	136	46.0 (15.4)
subtype0	126	46.9 (15.4)
subtype1	10	34.6 (8.6)

Figure S7. Get High-res Image Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #1: 'AGE'

'MUTATION MUT HRAS' versus 'GENDER'

P value = 1 (Fisher's exact test), Q value = 1

Table S65. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #2: 'GENDER'

nPatients	FEMALE	MALE
ALL	100	36
subtype0	92	34
subtype1	8	2

'MUTATION MUT HRAS' versus 'HISTOLOGICAL.TYPE'

P value = 0.338 (Fisher's exact test), Q value = 1

Table S66. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients	OTHER	THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL	THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED)	THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES)
ALL	1	84	34	17
subtype0	1	75	33	17
subtype1	0	9	1	0

'MUTATION MUT HRAS' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S67. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #4: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	12	124
subtype0	12	114
subtype1	0	10

'MUTATION MUT HRAS' versus 'RADIATIONEXPOSURE'

P value = 1 (Fisher's exact test), Q value = 1

Table S68. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #5: 'RADIATIONEXPOSURE'

nPatients	NO	YES
ALL	114	6
subtype0	104	6
subtype1	10	0

'MUTATION MUT HRAS' versus 'DISTANT.METASTASIS'

P value = 0.00304 (Fisher's exact test), Q value = 0.22

Table S69. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients	M0	M1	MX
ALL	59	1	75
subtype0	59	1	65
subtype1	0	0	10

Figure S8. Get High-res Image Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'MUTATION MUT HRAS' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S70. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #7: 'EXTRATHYROIDAL.EXTENSION'

nPatients	MINIMAL (T3)	MODERATE/ADVANCED (T4A)	NONE
ALL	38	2	93
subtype0	37	2	84
subtype1	1	0	9

'MUTATION MUT HRAS' versus 'LYMPH.NODE.METASTASIS'

P value = 0.0227 (Chi-square test), Q value = 1

Table S71. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients	N0	N1	N1A	N1B	NX
ALL	66	8	31	17	14
subtype0	64	8	26	17	11
subtype1	2	0	5	0	3

Figure S9. Get High-res Image Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'MUTATION MUT HRAS' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S72. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #9: 'COMPLETENESS.OF.RESECTION'

nPatients	R0	R1	RX
ALL	112	11	6
subtype0	102	11	6
subtype1	10	0	0

'MUTATION MUT HRAS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.5 (t-test), Q value = 1

Table S73. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	106	2.8 (4.8)
subtype0	99	2.9 (4.9)
subtype1	7	2.1 (2.4)

'MUTATION MUT HRAS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.247 (Chi-square test), Q value = 1

Table S74. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IVA	STAGE IVC
ALL	75	18	31	10	1
subtype0	66	18	30	10	1
subtype1	9	0	1	0	0

'MUTATION MUT HRAS' versus 'MULTIFOCALITY'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S75. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #13: 'MULTIFOCALITY'

nPatients	MULTIFOCAL	UNIFOCAL
ALL	64	68
subtype0	60	62
subtype1	4	6

'MUTATION MUT HRAS' versus 'TUMOR.SIZE'

P value = 0.993 (t-test), Q value = 1

Table S76. Gene #6: 'MUTATION MUT HRAS' versus Clinical Feature #14: 'TUMOR.SIZE'

	nPatients	Mean (Std.Dev)
ALL	98	2.8 (1.4)
subtype0	91	2.8 (1.4)
subtype1	7	2.8 (1.4)

Methods & Data

Input

Mutation data file = THCA-TP.mergedCustomEvents_for_correlateion.txt
Clinical data file = THCA-TP.clin.merged.picked.txt
Number of patients = 229
Number of significantly mutated genes = 6
Number of selected clinical features = 14
Exclude genes that fewer than K tumors have mutations, K = 3

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[2] 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)

[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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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