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ExamplesMutation Queries

Mutation Queries

Examples of mutation frequency analyses.

Basic Mutation Frequency

Calculate how often a gene is mutated in a specific cancer type.

Percentage Format

What percentage of glioblastoma patients have IDH1 mutations?

What you’ll get:

  • Bar chart showing mutation rate
  • Percentage with confidence interval
  • Total sample count
  • Breakdown by mutation type (if applicable)

Rate Format

What's the TP53 mutation rate in colorectal cancer?

Same analysis, different phrasing.

Specific Mutations

Hotspot Mutations

How common is BRAF V600E in melanoma?
What's the frequency of EGFR L858R in lung adenocarcinoma?
Is KRAS G12D common in pancreatic cancer?

Hotspot queries search for specific amino acid changes in the mutation data.

Mutation Classes

What percentage of colorectal cancer has KRAS mutations?
How common are PIK3CA mutations in breast cancer?

These return all mutation types affecting the gene.

Cancer-Specific Examples

Glioblastoma

What percentage of GBM has IDH1 mutations?
Is PTEN mutated in glioblastoma?
How common are EGFR amplifications in GBM?

IDH1 mutations distinguish primary GBM from secondary GBM (arising from lower-grade glioma).

Melanoma

What's the BRAF mutation rate in melanoma?
How common is BRAF V600E in skin melanoma?
Is NRAS mutated in BRAF-wildtype melanoma?

Lung Cancer

What percentage of lung adenocarcinoma has EGFR mutations?
How common is KRAS G12C in LUAD?
Is ALK rearranged in lung cancer?

Colorectal Cancer

What's the KRAS mutation rate in colorectal cancer?
How common are BRAF mutations in MSI-H colorectal tumors?
Is APC mutated in most colorectal cancers?

Breast Cancer

What percentage of breast cancer has PIK3CA mutations?
How common are TP53 mutations in triple-negative breast cancer?
Is BRCA1 mutated in hereditary breast cancer cases?

Comparing Mutation Rates

Between Cancer Types

Is TP53 mutated more often in LUSC than LUAD?
Compare KRAS mutation rates between pancreatic and colorectal cancer

Comparison queries for mutations are in beta. Results show rates side-by-side.

Understanding Mutation Data

Data Source

BioQuery uses TCGA MC3 somatic mutation calls:

  • Curated, validated mutations
  • Multiple callers with consensus filtering
  • Excludes germline variants

Mutation Types Included

TypeDescriptionExample
MissenseAmino acid substitutionBRAF V600E
NonsensePremature stop codonAPC R1450*
FrameshiftReading frame disruptionBRCA1 185delAG
Splice siteAffects mRNA splicingTP53 splice
In-frame indelPreserves reading frameEGFR exon 19 del

What’s NOT Included

  • Copy number alterations (amplifications, deletions)
  • Structural variants (translocations, inversions)
  • Germline variants
  • Promoter mutations

Common Questions

”Why is the mutation rate lower than expected?”

  • TCGA uses stringent filters
  • Only high-confidence somatic calls included
  • Some databases include germline or low-quality calls

”Can I query copy number?”

Copy number analysis is planned for a future release. Currently, only point mutations and indels are supported.

”What about fusion genes?”

Fusion gene queries (e.g., BCR-ABL, EML4-ALK) are coming soon.

Expression QueriesSurvival Queries