How to use mTCTScan?

For the webserver visit mTCTScan.

Job submission

Input profile

Input cancer mutation profile, we currently support VCF file for hg19/grch37
mutation input

Mutation filtering

General parameters

Define the filtering parameters for cancer type, gene panel and allele frequency. Two allele frequency database are supported including 1000 Genomes project phase 3 and ExAC
general parameter

SnpEff parameters

We used SnpEff to annotate cancer mutations, and users can select and filter the undesired variant features
SnpEff parameter

Job tracking

mTCTScan supports job retrieving from two manners

Fixed job URL


Browser cookies in the Job menu


Prioritization result

Mutation prioritization

For each mutation at the transcript level, mTCTScan utilizes an evidence-based scoring strategy to prioritize the mutations associated with drug sensitivity.

First, mTCTScan uses a series of matching strategies to connect each mutation-affected transcript to our collected mutation-cancer drug association records, including Exact Match, Partial Match, Small-scale Overlap and Locus-based Overlap.

In order to retrieve all relevant evidences of different levels, mTCTScan would map every mutation to each of above categories.

Second, each association record contains a confidence level with five grades including

Then, for each mutation, by considering both the matching degree and the confidence level of association records, an evidence-based ensemble score would be calculated. According to this score, mTCTScan would rank all qualified mutations (mutations match with at least one record) in a table. User can click the Details button to get more information
mutation prioritization

Cancer drug classificaiton

For each drug/compound, mTCTScan would compare whether the mutations' impacts on drug sensitivity are consistent or conflicting across all associated mutations at the "Exact Match" and "Partial Match" levels. Based on the following criteria, drugs/compounds were divided into three categories

In addition, mTCTScan uses the number of associated mutations as the order to present drugs in each category.
cancer drug classification

Mutation annotations

mTCTScan reports all related mutation-affected gene transcripts.

Users can click each mutation record to expand the annotation panel.
expanded annotation

Eleven different annotation fields are provided, which include basic Mutation Information, Germline Allele Frequency (from 1000 Genomes project, ExAC, UK10K, ESP project), somatic recurrence rate from TCGAs, ICGC and COSMIC, clinical associated mutations from ClinVar, functional predictions including Nonsynonymous Functional Prediction, Splicing Functional Prediction and Non-coding Functional Prediction and base-wise Conservation.

For example, user can click ClinVar item to inspect detailed information

Mutation-cancer drug association

Association detail

For each mutation-affected transcript, user can check the Details Implication button to get all associated records
details implication

For each transcript, a lollipop-style diagram and tabs to display different levels of matched evidences are provided.

Moreover, for each association record, addition tabs are provided to display Mutation Association Summary, Drug & Therapy Information and Clinical Trial Information related to the drug.

Lollipop-style diagram

Lollipop-style mutation diagrams to visualize variant position in protein functional domain
Lollipop-style diagram

Different levels of matched evidences

For each query mutation, four levels of matching strategies were used to retrieve records from our database
evidence levels

Mutation Association Summary

association summary

Drug & Therapy Information

drug and therapy information

Clinical Trial Information

clinical trial information

Gene-Drug Information

For each mutation-affected transcript, mTCTScan also reports related drugs/compounds information based on the relationship between drugs and their gene targets. Also, clinical trial information related to these drugs are be provided.

Drug and therapy information

drug and therapy informaton in gene drug tab

Clinical trial information

clinical trial information in gene drug tab

Query by single mutation

mTCTScan also introduces a search engine for the query of associated drug response by a single mutation
single mutation query