Bladder Urothelial Carcinoma: Mutation Analysis (MutSig vS2N)
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 vS2N was used to generate the results found in this report.

  • Working with individual set: BLCA

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
Results
Significantly Mutated Genes

Column Descriptions:

  • N = number of sequenced bases in this gene across the individual set

  • nnon = number of (nonsilent) mutations in this gene across the individual set

  • nnull = number of (nonsilent) null mutations in this gene across the individual set

  • nflank = number of noncoding mutations from this gene's flanking region, across the individual set

  • nsil = number of silent mutations in this gene across the individual set

  • p = p-value (overall)

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

Table 1.  Get Full Table A Ranked List of Significantly Mutated Genes. Number of significant genes found: 21. Number of genes displayed: 35. Click on a gene name to display its stick figure depicting the distribution of mutations and mutation types across the chosen gene (this feature may not be available for all significant genes).

gene N nflank nsil nnon nnull p q
TP53 3528 0 1 14 3 0 0
KDM6A 12769 1 2 6 6 2.5e-132 2.3e-128
ARID1A 16296 0 1 8 5 8.2e-54 5.2e-50
ASXL2 12589 0 0 6 2 2.4e-18 1.1e-14
FLG 30575 0 1 8 0 1.4e-15 5.1e-12
HRNR 15146 0 0 6 0 2.3e-15 7.1e-12
TTN 357098 1 3 34 4 2.6e-14 6.9e-11
RPAP1 10651 0 0 5 0 1.9e-11 4.6e-08
FBXW7 8047 0 0 6 2 4.2e-11 8.9e-08
MLL 36311 0 1 9 2 1.2e-10 2.3e-07
GOLGB1 34742 0 2 12 3 1.7e-10 2.9e-07
ADAMTS12 15260 0 1 4 0 8.8e-10 1.4e-06
DCC 13602 0 1 5 0 4.1e-09 5.9e-06
MLL2 34764 0 0 6 6 2.5e-08 0.000034
MACF1 85714 2 0 10 2 1.2e-07 0.00015
PRX 9460 0 0 9 1 1.8e-07 0.00021
ABCA10 17600 1 0 5 2 4.6e-07 0.00051
HCN1 8148 1 1 5 3 1.9e-06 0.002
SPTA1 24718 0 0 5 0 0.000024 0.024
APOB 49173 0 0 6 0 0.000031 0.029
TPR 26207 1 1 5 0 0.000044 0.039
BCLAF1 9083 0 0 5 1 0.00026 0.23
HMCN1 55209 3 0 9 2 0.00028 0.23
DNAH5 49325 0 1 7 1 0.00032 0.25
SACS 47870 0 2 6 2 0.00091 0.69
OTUD7A 4967 0 0 4 0 0.0012 0.87
XPR1 7476 0 1 5 2 0.0014 1
SPATS2 5365 0 0 4 1 0.0019 1
KPNA3 5639 1 0 4 1 0.0026 1
NFE2L2 6020 0 0 4 0 0.004 1
MLL3 45342 0 0 7 2 0.0066 1
ERCC2 7666 0 0 4 0 0.012 1
SYNE1 91835 0 3 8 1 0.012 1
FGA 8013 0 0 4 0 0.015 1
CUL1 8607 0 0 4 0 0.02 1
TP53

Figure S1.  This figure depicts the distribution of mutations and mutation types across the TP53 significant gene.

KDM6A

Figure S2.  This figure depicts the distribution of mutations and mutation types across the KDM6A significant gene.

ARID1A

Figure S3.  This figure depicts the distribution of mutations and mutation types across the ARID1A significant gene.

ASXL2

Figure S4.  This figure depicts the distribution of mutations and mutation types across the ASXL2 significant gene.

FLG

Figure S5.  This figure depicts the distribution of mutations and mutation types across the FLG significant gene.

HRNR

Figure S6.  This figure depicts the distribution of mutations and mutation types across the HRNR significant gene.

TTN

Figure S7.  This figure depicts the distribution of mutations and mutation types across the TTN significant gene.

RPAP1

Figure S8.  This figure depicts the distribution of mutations and mutation types across the RPAP1 significant gene.

FBXW7

Figure S9.  This figure depicts the distribution of mutations and mutation types across the FBXW7 significant gene.

MLL

Figure S10.  This figure depicts the distribution of mutations and mutation types across the MLL significant gene.

GOLGB1

Figure S11.  This figure depicts the distribution of mutations and mutation types across the GOLGB1 significant gene.

ADAMTS12

Figure S12.  This figure depicts the distribution of mutations and mutation types across the ADAMTS12 significant gene.

DCC

Figure S13.  This figure depicts the distribution of mutations and mutation types across the DCC significant gene.

MLL2

Figure S14.  This figure depicts the distribution of mutations and mutation types across the MLL2 significant gene.

MACF1

Figure S15.  This figure depicts the distribution of mutations and mutation types across the MACF1 significant gene.

PRX

Figure S16.  This figure depicts the distribution of mutations and mutation types across the PRX significant gene.

ABCA10

Figure S17.  This figure depicts the distribution of mutations and mutation types across the ABCA10 significant gene.

HCN1

Figure S18.  This figure depicts the distribution of mutations and mutation types across the HCN1 significant gene.

SPTA1

Figure S19.  This figure depicts the distribution of mutations and mutation types across the SPTA1 significant gene.

APOB

Figure S20.  This figure depicts the distribution of mutations and mutation types across the APOB significant gene.

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)