Mutation Assessor
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C12R3Q03
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C12R3Q03
Overview
Introduction

This report serves to summarize the functional impact of missense mutations in each gene as determined by Mutation Assessor[1].

Summary

- High Functional Impact Missense Mutations: 155

- Medium Functional Impact Missense Mutations: 469

- Low Functional Impact Missense Mutations: 412

- Neutral Functional Impact Mutations: 326

Results
Functional Impact by Gene

Table 1. Get Full Table A gene-level breakdown of missense mutation functional impact, ordered by MutSig rank. Includes missense mutation counts broken down by level of functional impact (high, medium, low, neutral), median functional impact score and level, and most common level(s) of functional impact (mode) per gene.

Gene | MutSig Rank | High Functional Impact Count | Medium Functional Impact Count | Low Functional Impact Count | Neutral Functional Impact Count | Median Functional Impact Score | Median Functional Impact Level | Mode Functional Impact Level
--- | --- | --- | --- | --- | --- | --- | --- | ---
DNMT3A | 1 | 0 | 39 | 2 | 2 | 2.520 | medium | medium
U2AF1 | 2 | 7 | 1 | 0 | 0 | 3.820 | high | high
FLT3 | 3 | 0 | 0 | 13 | 4 | 1.040 | low | low
IDH2 | 4 | 20 | 0 | 0 | 0 | 3.890 | high | high
IDH1 | 5 | 19 | 0 | 0 | 0 | 4.540 | high | high
NPM1 | 6 | 0 | 1 | 0 | 0 | 2.175 | medium | medium
NRAS | 7 | 5 | 10 | 0 | 0 | 3.325 | medium | medium
WT1 | 8 | 0 | 1 | 1 | 0 | 1.740 | low | medium/low
RUNX1 | 9 | 0 | 9 | 0 | 0 | 3.085 | medium | medium
SMG1 | 10 | 1 | 1 | 1 | 0 | 2.200 | medium | high/medium/low

Methods & Data
Input

1. LAML-TB.maf.annotated

2. LAML-TB.sig_genes.txt

3. Mutation Assessor Scores Release 2:

- hg18

- hg19

A lookup is done against the relevant Mutation Assessor Scores table for each missense mutation in a given MAF file, and available functional impact score and level are appended as two new columns to generate LAML-TB.maf.annotated. These are summarized in Table 1, sorted by MutSig rank.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Boris Reva, Yevgeniy Antipin, and Chris Sander, Predicting the functional impact of protein mutations: application to cancer genomics, Nucl. Acids Res. 39(17):e118 (2011)
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