Bladder Urothelial Carinoma: Mutation Analysis (MutSig)

Maintained by Dan DiCara (Broad Institute)

Overview

Introduction

This report serves to describe the mutational landscape and properties of a given individual set, as well as rank genes and genesets according to mutational significance. MutSig v1.5 was used to generate the results found in this report.

Working with individual set: BLCA.

Number of patients in set: 28

Input

The input for this pipeline is a set of individuals with the following files associated for each:

1. An annotated .maf file describing the mutations called for the respective individual, and their properties.

2. A .wig file that contains information about the coverage of the sample.

Summary

Significantly mutated genes (q ≤ 0.1): 9

Mutations seen in COSMIC: 0

Significantly mutated genes in COSMIC territory: 0

Genes with clustered mutations (&le 3 aa apart): 0

Significantly mutated genesets: 33

Significantly mutated genesets: (excluding sig. mutated genes): 2

Results

Breakdown of Mutations by Type

Table 1. Get Full Table Table representing breakdown of mutations by type.

type	count
Frame_Shift_Del	103
Frame_Shift_Ins	48
In_Frame_Del	29
In_Frame_Ins	5
Missense_Mutation	3424
Nonsense_Mutation	305
Nonstop_Mutation	6
Silent	1300
Splice_Site	84
Translation_Start_Site	7
Total	5311

Breakdown of Mutation Rates by Category Type

Table 2. Get Full Table A breakdown of mutation rates per category discovered for this individual set.

category	n	N	rate	rate_per_mb	relative_rate
A->T	743	415320976	1.8e-06	1.8	0.38
*Np(A/T)->nonflip	1427	459226432	3.1e-06	3.1	0.66
*Np(C/G)->nonflip	838	392937804	2.1e-06	2.1	0.45
C->G	423	436843260	9.7e-07	0.97	0.21
indel+null	566	852164264	6.6e-07	0.66	0.14
double_null	14	852164264	1.6e-08	0.016	0.0035
Total	4011	852164264	4.7e-06	4.7	1

Target Coverage for Each Individual

The x axis represents the samples. The y axis represents the exons, one row per exon, and they are sorted by average coverage across samples. For exons with exactly the same average coverage, they are sorted next by the %GC of the exon. (The secondary sort is especially useful for the zero-coverage exons at the bottom).

Figure 1.

Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples

Figure 2.

Significantly Mutated Genes

Table 3. Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 9. Number of genes displayed: 35

rank	gene	description	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	p	q
1	TP53	tumor protein p53	35896	12	9	12	0	4	4	1	0	3	3.5e-14	6.4e-10
2	KDM6A		117040	6	6	6	2	0	0	0	0	6	2.8e-07	0.0025
3	HLA-A	major histocompatibility complex, class I, A	31640	3	3	3	0	0	0	1	0	2	0.000012	0.053
4	ELF3	E74-like factor 3 (ets domain transcription factor, epithelial-specific )	32144	3	3	3	0	0	0	0	1	2	0.000013	0.053
5	XPR1	xenotropic and polytropic retrovirus receptor	60228	4	4	4	1	0	0	1	1	2	0.000015	0.053
6	ARID1A	AT rich interactive domain 1A (SWI-like)	164864	6	5	6	1	1	0	0	0	5	0.000024	0.071
7	OR2T35	olfactory receptor, family 2, subfamily T, member 35	12964	2	2	1	0	0	0	0	0	2	0.000038	0.097
8	ERCC2	excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)	61460	4	4	4	0	0	1	1	2	0	0.000045	0.1
9	FBXW7	F-box and WD repeat domain containing 7	72352	5	4	4	0	0	4	0	0	1	0.000097	0.19
10	C20orf20	chromosome 20 open reading frame 20	13524	2	2	2	1	0	0	0	2	0	0.00016	0.3
11	NAA25		82684	4	4	4	0	1	0	1	1	1	0.00019	0.31
12	LETMD1	LETM1 domain containing 1	31332	3	3	3	0	1	0	1	1	0	0.00022	0.33
13	CREBBP	CREB binding protein (Rubinstein-Taybi syndrome)	201964	5	5	5	1	1	0	1	0	3	0.00024	0.33
14	HCRT	hypocretin (orexin) neuropeptide precursor	4060	1	1	1	0	0	0	0	0	1	0.00027	0.35
15	FAM57A	family with sequence similarity 57, member A	17388	2	2	2	0	0	0	2	0	0	0.00036	0.4
16	CUL1	cullin 1	67620	3	3	2	0	1	0	2	0	0	0.00038	0.4
17	RIMS3	regulating synaptic membrane exocytosis 3	26572	2	2	2	0	0	0	2	0	0	0.00039	0.4
18	MTERFD2	MTERF domain containing 2	31836	3	3	3	0	0	3	0	0	0	0.0004	0.4
19	GTF3C3	general transcription factor IIIC, polypeptide 3, 102kDa	76524	3	3	3	0	0	1	0	1	1	0.00043	0.41
20	ACN9	ACN9 homolog (S. cerevisiae)	10808	2	2	2	1	0	2	0	0	0	0.00046	0.42
21	IL34		20188	2	2	2	0	1	0	1	0	0	0.00052	0.43
22	OTUD7A	OTU domain containing 7A	57260	3	3	3	0	0	2	0	1	0	0.00054	0.43
23	CSNK1E	casein kinase 1, epsilon	33992	2	2	2	0	0	0	1	0	1	0.00058	0.43
24	C7orf36	chromosome 7 open reading frame 36	19404	2	2	2	0	0	1	1	0	0	0.00058	0.43
25	BCLAF1	BCL2-associated transcription factor 1	78596	4	3	4	0	0	1	0	2	1	0.00067	0.46
26	ORC3L	origin recognition complex, subunit 3-like (yeast)	62132	3	3	3	0	0	1	1	1	0	0.00068	0.46
27	CAT	catalase	45780	3	3	3	0	0	1	2	0	0	0.00071	0.46
28	GPS2	G protein pathway suppressor 2	27468	2	2	2	0	0	1	0	0	1	0.00073	0.46
29	CDH22	cadherin-like 22	55244	3	3	3	0	2	1	0	0	0	0.00076	0.46
30	NFE2L2	nuclear factor (erythroid-derived 2)-like 2	50092	3	3	3	0	1	1	1	0	0	0.0008	0.46
31	TMCO2	transmembrane and coiled-coil domains 2	15596	2	2	1	0	0	0	0	0	2	0.00083	0.46
32	PAK3	p21 (CDKN1A)-activated kinase 3	48692	3	3	3	0	0	2	0	1	0	0.00085	0.46
33	LASP1	LIM and SH3 protein 1	19656	2	2	2	0	0	0	0	1	1	0.00087	0.46
34	CD200	CD200 molecule	25116	2	2	2	0	0	1	1	0	0	0.0009	0.46
35	HOXB4	homeobox B4	18256	2	2	2	0	1	1	0	0	0	0.00094	0.46

Note:

N - number of sequenced bases in this gene across the individual set.

n - number of (nonsilent) mutations in this gene across the individual set.

npat - number of patients (individuals) with at least one nonsilent mutation.

nsite - number of unique sites having a non-silent mutation.

nsil - number of silent mutations in this gene across the individual set.

n1 - number of nonsilent mutations of type: A->T .

n2 - number of nonsilent mutations of type: *Np(A/T)->nonflip .

n3 - number of nonsilent mutations of type: *Np(C/G)->nonflip .

n4 - number of nonsilent mutations of type: C->G .

n5 - number of nonsilent mutations of type: indel+null .

null - mutation category that includes nonsense, frameshift, splice-site mutations

p_classic = p-value for the observed amount of nonsilent mutations being elevated in this gene

p_ns_s = p-value for the observed nonsilent/silent ratio being elevated in this gene

p = p-value (overall)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

COSMIC analyses

In this analysis, COSMIC is used as a filter to increase power by restricting the territory of each gene. Cosmic version: v48.

Table 4. Get Full Table Significantly mutated genes (COSMIC territory only). To access the database please go to: COSMIC. Number of significant genes found: 0. Number of genes displayed: 10

rank	gene	description	n	p	q
1	A4GNT	alpha-1,4-N-acetylglucosaminyltransferase	0	1	1
2	AACS	acetoacetyl-CoA synthetase	0	1	1
3	ABCA9	ATP-binding cassette, sub-family A (ABC1), member 9	1	1	1
4	ABCC10	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1	1	1
5	ABCF2	ATP-binding cassette, sub-family F (GCN20), member 2	0	1	1
6	ABHD2	abhydrolase domain containing 2	0	1	1
7	ABHD4	abhydrolase domain containing 4	0	1	1
8	ACADS	acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain	0	1	1
9	ACOT11	acyl-CoA thioesterase 11	0	1	1
10	ACRBP	acrosin binding protein	0	1	1

Note:

n - number of (nonsilent) mutations in this gene across the individual set.

cos = number of unique mutated sites in this gene in COSMIC

n_cos = overlap between n and cos.

N_cos = number of individuals times cos.

cos_ev = total evidence: number of reports in COSMIC for mutations seen in this gene.

p = p-value for seeing the observed amount of overlap in this gene)

q = q-value, False Discovery Rate (Benjamini-Hochberg procedure)

Clustered Mutations

Table 5. Get Full Table Genes with Clustered Mutations

num	gene	desc	n	mindist
1762	MXRA5	matrix-remodelling associated 5	2	48
1	A2M	alpha-2-macroglobulin	2	Inf
4	ABCA10	ATP-binding cassette, sub-family A (ABC1), member 10	3	Inf
6	ABCA13	ATP-binding cassette, sub-family A (ABC1), member 13	2	Inf
10	ABCA8	ATP-binding cassette, sub-family A (ABC1), member 8	3	Inf
17	ABCC9	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	2	Inf
32	ACN9	ACN9 homolog (S. cerevisiae)	2	Inf
38	ACTA2	actin, alpha 2, smooth muscle, aorta	2	Inf
41	ACTN4	actinin, alpha 4	3	Inf
50	ADAMTS12	ADAM metallopeptidase with thrombospondin type 1 motif, 12	4	Inf

Note:

n - number of mutations in this gene in the individual set.

mindist - distance (in aa) between closest pair of mutations in this gene

npairs3 - how many pairs of mutations are within 3 aa of each other.

npairs12 - how many pairs of mutations are within 12 aa of each other.

Geneset Analyses

Table 6. Get Full Table A Ranked List of Significantly Mutated Genesets. (Source: MSigDB GSEA Cannonical Pathway Set).Number of significant genesets found: 33. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	PMLPATHWAY	Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis.	CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1	13	CREBBP(5), DAXX(1), PML(2), RARA(1), RB1(1), SP100(1), TNFRSF1B(1), TP53(12)	823508	24	15	24	1	6	7	3	1	7	0	1.7e-08	1e-05
2	SA_G1_AND_S_PHASES	Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition.	ARF1, ARF3, CCND1, CDK2, CDK4, CDKN1A, CDKN1B, CDKN2A, CFL1, E2F1, E2F2, MDM2, NXT1, PRB1, TP53	15	CCND1(1), CDKN1A(2), E2F2(1), TP53(12)	343280	16	11	16	0	5	5	2	1	3	0	3.9e-08	0.000012
3	P53PATHWAY	p53 induces cell cycle arrest or apoptosis under conditions of DNA damage.	APAF1, ATM, BAX, BCL2, CCND1, CCNE1, CDK2, CDK4, CDKN1A, E2F1, GADD45A, MDM2, PCNA, RB1, TIMP3, TP53	16	ATM(3), BAX(1), CCND1(1), CDKN1A(2), RB1(1), TP53(12)	778904	20	14	20	2	6	6	2	1	5	0	1.4e-07	0.000024
4	TERTPATHWAY	hTERC, the RNA subunit of telomerase, and hTERT, the catalytic protein subunit, are required for telomerase activity and are overexpressed in many cancers.	HDAC1, MAX, MYC, SP1, SP3, TP53, WT1, ZNF42	7	SP3(1), TP53(12)	298060	13	10	13	1	5	4	1	0	3	0	1.6e-07	0.000024
5	RBPATHWAY	The ATM protein kinase recognizes DNA damage and blocks cell cycle progression by phosphorylating chk1 and p53, which normally inhibits Rb to allow G1/S transitions.	ATM, CDC2, CDC25A, CDC25B, CDC25C, CDK2, CDK4, CHEK1, MYT1, RB1, TP53, WEE1, YWHAH	12	ATM(3), RB1(1), TP53(12), WEE1(1)	748720	17	13	17	1	5	5	2	0	5	0	3.9e-07	0.000048
6	HISTONE_METHYLTRANSFERASE	Genes with HMT activity	AOF2, KDM6A, ASH1L, ASH2L, C17orf79, CARM1, CTCFL, DOT1L, EED, EHMT1, EHMT2, EZH1, EZH2, FBXL10, FBXL11, FBXO11, HCFC1, HSF4, JMJD1A, JMJD1B, JMJD2A, JMJD2B, JMJD2C, JMJD2D, JMJD3, JMJD4, JMJD6, MEN1, MLL, MLL2, MLL3, MLL4, MLL5, NSD1, OGT, PAXIP1, PPP1CA, PPP1CB, PPP1CC, PRDM2, PRDM6, PRDM7, PRDM9, PRMT1, PRMT5, PRMT6, PRMT7, PRMT8, RBBP5, SATB1, SETD1A, SETD1B, SETD2, SETD7, SETD8, SETDB1, SETDB2, SETMAR, SMYD3, STK38, SUV39H1, SUV39H2, SUV420H1, SUV420H2, SUZ12, WHSC1, WHSC1L1	55	ASH1L(3), CARM1(1), CTCFL(1), DOT1L(5), EZH1(2), HCFC1(1), KDM6A(6), MLL(6), MLL2(5), MLL3(7), MLL4(2), NSD1(1), OGT(1), PPP1CA(3), PRDM2(1), PRMT6(1), SETD1A(1), SETD2(3), SETD8(1), STK38(1), SUV420H1(2), WHSC1(2)	5165860	56	24	55	8	9	13	12	4	14	4	2.2e-06	0.00022
7	P53HYPOXIAPATHWAY	Hypoxia induces p53 accumulation and consequent apoptosis with p53-mediated cell cycle arrest, which is present under conditions of DNA damage.	ABCB1, AKT1, ATM, BAX, CDKN1A, CPB2, CSNK1A1, CSNK1D, FHL2, GADD45A, HIC1, HIF1A, HSPA1A, HSPCA, IGFBP3, MAPK8, MDM2, NFKBIB, NQO1, TP53	19	ATM(3), BAX(1), CDKN1A(2), MAPK8(2), TP53(12)	892864	20	13	20	1	6	6	2	2	4	0	6.8e-06	0.0006
8	G1PATHWAY	CDK4/6-cyclin D and CDK2-cyclin E phosphorylate Rb, which allows the transcription of genes needed for the G1/S cell cycle transition.	ABL1, ATM, ATR, CCNA1, CCND1, CCNE1, CDC2, CDC25A, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, DHFR, E2F1, GSK3B, HDAC1, MADH3, MADH4, RB1, SKP2, TFDP1, TGFB1, TGFB2, TGFB3, TP53	25	ABL1(1), ATM(3), ATR(2), CCND1(1), CDK6(1), CDKN1A(2), RB1(1), TP53(12)	1271004	23	15	23	0	7	7	4	1	4	0	0.000011	0.00088
9	TIDPATHWAY	On ligand binding, interferon gamma receptors stimulate JAK2 kinase to phosphorylate STAT transcription factors, which promote expression of interferon responsive genes.	DNAJA3, HSPA1A, IFNG, IFNGR1, IFNGR2, IKBKB, JAK2, LIN7A, NFKB1, NFKBIA, RB1, RELA, TIP-1, TNF, TNFRSF1A, TNFRSF1B, TP53, USH1C, WT1	18	IFNGR2(1), JAK2(1), RB1(1), RELA(1), TNFRSF1B(1), TP53(12), USH1C(1)	798532	18	12	18	0	5	6	2	1	4	0	0.000015	0.001
10	RNAPATHWAY	dsRNA-activated protein kinase phosphorylates elF2a, which generally inhibits translation, and activates NF-kB to provoke inflammation.	CHUK, DNAJC3, EIF2S1, EIF2S2, MAP3K14, NFKB1, NFKBIA, PRKR, RELA, TP53	9	RELA(1), TP53(12)	430948	13	9	13	0	4	5	1	0	3	0	2e-05	0.0011

Table 7. Get Full Table A Ranked List of Significantly Mutated Genesets (Excluding Significantly Mutated Genes). Number of significant genesets found: 2. Number of genesets displayed: 10

rank	geneset	description	genes	N_genes	mut_tally	N	n	npat	nsite	nsil	n1	n2	n3	n4	n5	n6	p	q
1	HISTONE_METHYLTRANSFERASE	Genes with HMT activity	AOF2, KDM6A, ASH1L, ASH2L, C17orf79, CARM1, CTCFL, DOT1L, EED, EHMT1, EHMT2, EZH1, EZH2, FBXL10, FBXL11, FBXO11, HCFC1, HSF4, JMJD1A, JMJD1B, JMJD2A, JMJD2B, JMJD2C, JMJD2D, JMJD3, JMJD4, JMJD6, MEN1, MLL, MLL2, MLL3, MLL4, MLL5, NSD1, OGT, PAXIP1, PPP1CA, PPP1CB, PPP1CC, PRDM2, PRDM6, PRDM7, PRDM9, PRMT1, PRMT5, PRMT6, PRMT7, PRMT8, RBBP5, SATB1, SETD1A, SETD1B, SETD2, SETD7, SETD8, SETDB1, SETDB2, SETMAR, SMYD3, STK38, SUV39H1, SUV39H2, SUV420H1, SUV420H2, SUZ12, WHSC1, WHSC1L1	54	ASH1L(3), CARM1(1), CTCFL(1), DOT1L(5), EZH1(2), HCFC1(1), MLL(6), MLL2(5), MLL3(7), MLL4(2), NSD1(1), OGT(1), PPP1CA(3), PRDM2(1), PRMT6(1), SETD1A(1), SETD2(3), SETD8(1), STK38(1), SUV420H1(2), WHSC1(2)	5048820	50	23	49	6	9	13	12	4	8	4	0.000049	0.018
2	FBW7PATHWAY	Cyclin E interacts with cell cycle checkpoint kinase cdk2 to allow transcription of genes required for S phase, including transcription of additional cyclin E.	CCNE1, CDC34, CDK2, CUL1, E2F1, FBXW7, RB1, SKP1A, TFDP1	8	CUL1(3), FBXW7(5), RB1(1)	361480	9	7	7	0	1	4	2	0	2	0	0.000058	0.018
3	HSA00680_METHANE_METABOLISM	Genes involved in methane metabolism	ADH5, CAT, EPX, LPO, MPO, MTHFR, PRDX6, SHMT1, SHMT2, TPO	10	CAT(3), MPO(1), MTHFR(1), PRDX6(1), TPO(2)	496552	8	8	8	1	1	4	2	0	1	0	0.00065	0.13
4	PMLPATHWAY	Ring-shaped PML nuclear bodies regulate transcription and are required co-activators in p53- and DAXX-mediated apoptosis.	CREBBP, DAXX, HRAS, PAX3, PML, PRAM-1, RARA, RB1, SIRT1, SP100, TNF, TNFRSF1A, TNFRSF1B, TNFRSF6, TNFSF6, TP53, UBL1	12	CREBBP(5), DAXX(1), PML(2), RARA(1), RB1(1), SP100(1), TNFRSF1B(1)	787612	12	9	12	1	2	3	2	1	4	0	0.00094	0.15
5	SODDPATHWAY	Some members of the tumor necrosis factor receptor family have cytoplasmic death domains that promote apoptosis when active and are repressed by silencers called SODDs.	BAG4, BIRC3, CASP8, FADD, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TRADD, TRAF2	10	BAG4(1), CASP8(2), FADD(1), RIPK1(1), TNFRSF1B(1), TRAF2(1)	369068	7	6	7	1	0	5	0	2	0	0	0.0014	0.15
6	CERAMIDEPATHWAY	Ceramide is a lipid signaling molecule that can activate proliferative or apoptotic pathways, depending on signaling context, localization, and cell type.	BAD, BAX, BCL2, CASP8, CYCS, FADD, MAP2K1, MAP2K4, MAP3K1, MAPK1, MAPK3, MAPK8, NFKB1, NSMAF, PDCD8, RAF1, RELA, RIPK1, SMPD1, TNFRSF1A, TRADD, TRAF2	21	BAX(1), CASP8(2), FADD(1), MAP2K1(1), MAP3K1(1), MAPK8(2), NSMAF(1), RELA(1), RIPK1(1), SMPD1(1), TRAF2(1)	885640	13	10	13	3	3	6	1	2	1	0	0.0015	0.15
7	SETPATHWAY	Cytotoxic T cells release perforin, which to allow entry into target cells of granzyme B, which activates caspases, and granzyme A, which induces caspase-independent apoptosis.	ANP32A, APEX1, CREBBP, DFFA, DFFB, GZMA, GZMB, HMGB2, NME1, PRF1, SET	11	CREBBP(5), GZMB(1), PRF1(1)	449904	7	6	7	3	1	1	2	0	3	0	0.0019	0.17
8	HSA00940_PHENYLPROPANOID_BIOSYNTHESIS	Genes involved in phenylpropanoid biosynthesis	EPX, GBA, GBA3, LPO, MPO, PRDX6, TPO	7	GBA(1), GBA3(1), MPO(1), PRDX6(1), TPO(2)	362236	6	6	6	2	2	2	0	1	1	0	0.0023	0.18
9	METHANE_METABOLISM		ADH5, ATP6V0C, SHMT1, CAT, EPX, LPO, MPO, PRDX1, PRDX2, PRDX5, PRDX6, SHMT1, SHMT2, TPO	13	CAT(3), MPO(1), PRDX6(1), TPO(2)	505624	7	7	7	1	1	3	2	0	1	0	0.0032	0.19
10	RELAPATHWAY	Acetylated NF-kB proteins are immune to IkB regulation and promote transcription until the histone deacetylase HDAC3 deacetylates the RelA subunit of NF-kB.	CHUK, CREBBP, EP300, FADD, HDAC3, IKBKB, IKBKG, NFKB1, NFKBIA, RELA, RIPK1, TNF, TNFRSF1A, TNFRSF1B, TRADD, TRAF6	15	CREBBP(5), EP300(1), FADD(1), RELA(1), RIPK1(1), TNFRSF1B(1)	962360	10	9	10	2	1	4	1	1	3	0	0.0033	0.19

Methods & Data

Methods

In brief, we tabulate the number of mutations and the number of covered bases for each gene. The counts are broken down by mutation context category: four context categories that are discovered by MutSig, and one for indel and 'null' mutations, which include indels, nonsense mutations, splice-site mutations, and non-stop (read-through) mutations. For each gene, we calculate the probability of seeing the observed constellation of mutations, i.e. the product P1 x P2 x ... x Pm, or a more extreme one, given the background mutation rates calculated across the dataset.[1]

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] TCGA, Integrated genomic analyses of ovarian carcinoma, Nature 474:609 � 615 (2011)