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🖐 Howdy!

✨ 소개

  • cbioportal dataset의 mutational signature의 양상을 확인할 수 있습니다.
  • Signature 비교에는 COSMIC Mutational Signatures (v3.2 - March 2021)을 사용했습니다.


🔨 추가할 사항

  • 아직 Missing된 Project가 있습니다. (추가 예정)
    • TumorSeq Allele과 Ref Allele이 같은 경우 예외처리해야함
  • 암종별 분류
  • 암종별 + 프로젝트 별 분류
  • Signature Clustering (by sample?)

📝Methods

  1. Download dataset from cbioportal.
  2. Mutational signature information is downloaded from COSMIC.
  3. Mutation context theorem was done using SigProfilerMatrixGenerator, and similar signatures were found using deconstuctSigs.
  4. For visualization, R (plotly library) was used.

Row

📈 Overview

Test

Single Base Substitution (SBS)

Column

Mutation Signture

The signature weight was averaged by collecting only samples with a mutation count of 50 or more in each project.

Only signature weights greater than 0.01 appear.

Signature Aetiology

Signature Proposed Aetiology
SBS1 Spontaneous deamination of 5-methylcytosine (clock-like signature)
SBS2 Activity of APOBEC family of cytidine deaminases
SBS3 Defective homologous recombination DNA damage repair
SBS4 Tobacco smoking
SBS5 Unknown (clock-like signature)
SBS6 Defective DNA mismatch repair
SBS7a Ultraviolet light exposure
SBS7b Ultraviolet light exposure
SBS7c Ultraviolet light exposure
SBS7d Ultraviolet light exposure
SBS8 Unknown
SBS9 Polimerase eta somatic hypermutation activity
SBS10a Polymerase epsilon exonuclease domain mutations
SBS10b Polymerase epsilon exonuclease domain mutations
SBS10c Defective POLD1 proofreading
SBS10d Defective POLD1 proofreading
SBS11 Temozolomide treatment
SBS12 Unknown
SBS13 Activity of APOBEC family of cytidine deaminases
SBS14 Concurrent polymerase epsilon mutation and defective DNA mismatch repair
SBS15 Defective DNA mismatch repair
SBS16 Unknown
SBS17a Unknown
SBS17b Unknown
SBS18 Damage by reactive oxygen species
SBS19 Unknown
SBS20 Concurrent POLD1 mutations and defective DNA mismatch repair
SBS21 Defective DNA mismatch repair
SBS22 Aristolochic acid exposure
SBS23 Unknown
SBS24 Aflatoxin exposure
SBS25 Chemotherapy treatment
SBS26 Defective DNA mismatch repair
SBS28 Unknown
SBS29 Tobacco chewing
SBS30 Defective DNA base excision repair due to NTHL1 mutations
SBS31 Platinum chemotherapy treatment
SBS32 Azathioprine treatment
SBS33 Unknown
SBS34 Unknown
SBS35 Platinum chemotherapy treatment
SBS36 Defective DNA base excision repair due to MUTYH mutations
SBS37 Unknown
SBS38 Indirect effect of ultraviolet light
SBS39 Unknown
SBS40 Unknown
SBS41 Unknown
SBS42 Haloalkane exposure
SBS44 Defective DNA mismatch repair
SBS84 Activity of activation-induced cytidine deaminase (AID)
SBS85 Indirect effects of activation-induced cytidine deaminase (AID)
SBS86 Unknown chemotherapy treatment
SBS87 Thiopurine chemotherapy treatment
SBS88 Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)
SBS89 Unknown
SBS90 Duocarmycin exposure
SBS91 Unknown
SBS92 Tobacco smoking
SBS93 Unknown
SBS94 Unknown. Possible sequencing artefacts
SBS27 Possible sequencing artefacts
SBS43 Possible sequencing artefacts
SBS45 Possible sequencing artefacts
SBS46 Possible sequencing artefacts
SBS47 Possible sequencing artefacts
SBS48 Possible sequencing artefacts
SBS49 Possible sequencing artefacts
SBS50 Possible sequencing artefacts
SBS51 Possible sequencing artefacts
SBS52 Possible sequencing artefacts
SBS53 Possible sequencing artefacts
SBS54 Possible sequencing artefacts
SBS55 Possible sequencing artefacts
SBS56 Possible sequencing artefacts
SBS57 Possible sequencing artefacts
SBS58 Possible sequencing artefacts
SBS59 Possible sequencing artefacts
SBS60 Possible sequencing artefacts

Indel (ID)

Column

Mutation Signture

Only signature weights greater than 0.01 appear.

Signature Aetiology

Signature Proposed Aetiology
ID1 Slippage during DNA replication of the replicated DNA strand
ID2 Slippage during DNA replication of the replicated DNA strand
ID3 Tobacco smoking
ID4 Unknown
ID5 Unknown
ID6 Defective homologous recombination DNA damage repair
ID7 Defective DNA mismatch repair
ID8 Repair of DNA double strand breaks by NHEJ or mutations in TOP2A
ID9 Unknown
ID10 Unknown
ID11 Unknown
ID12 Unknown
ID13 Ultraviolet light exposure
ID14 Unknown
ID15 Unknown
ID16 Unknown
ID17 Mutations in topoisomerase TOP2A
ID18 Colibactin exposure (E.coli bacteria carrying pks pathogenicity island)

Double Base Substitution (DBS)

Column

Mutation Signture

Only signature weights greater than 0.01 appear.

Signature Aetiology

Signature Proposed Aetiology
DBS1 Ultraviolet light exposure
DBS2 Tobacco smoking and other mutagens (e.g. acetaldehyde)
DBS3 Polymerase epsilon exonuclease domain mutations
DBS4 Unknown
DBS5 Platinum chemotherapy treatment
DBS6 Unknown
DBS7 Defective DNA mismatch repair
DBS8 Unknown
DBS9 Unknown
DBS10 Defective DNA mismatch repair
DBS11 Unknown

📚Reference

  1. cbioportal Dataset Link

  2. COSMIC Mutational Signature Link

  3. deconstuctSigs Link

  4. SigProfilerMatrixGenerator Link