Accurate and sensitive mutational signature analysis with MuSiCal, 06/25/2022
-> substitution. deletion, insertion, indel, structure variation, copy number of variation
-> mutional process
-> endogenous(replication error,reparie deficiencies,endogenous damage) exogenous(uv raiation, tobacco smoking, cancer treatment)
-> mutational signature analysis
-> which processes are active, how mnay mutationsl can be attribued to each process
-> when was each process active
-> 83 indel pattern
-> indel+SNP combination
-> TOP1 mutation ->
-> 1-20 to try ->optimization issue，r(number of signature)-> optional K number of clusters
-> How COSMIC pattern is created
-> assumption(homogenious) -> all TCGA samples -> signature
-> 20-30 samples, too small sample size is not useful for signature analysis
-> the current version is low, but next version will be faster
-> germine line mutation: topmed, blood
-> SBS maybe also a mixture for multiple signature/ tradeoff/
-> SBS7 ->SBS7a,SBS7b,SBS7c,SBS7d
-> Catalogue of Somatic Mutations in Cancer(COSMIC)
-> benchmark -> SBS1
-> PCAGW map to 96 samples, which are the most frequent signature
-> probability number/96 so that sum=1
-> CNV signature -> CNV variation related to BRCA1, and BRCA2
-> germline variation do not have affect to the risk of the cancer
Accurate and sensitive mutational signature analysis with MuSiCal, 06/25/2022
-> substitution. deletion, insertion, indel, structure variation, copy number of variation -> mutional process -> endogenous(replication error,reparie deficiencies,endogenous damage) exogenous(uv raiation, tobacco smoking, cancer treatment) -> mutational signature analysis -> which processes are active, how mnay mutationsl can be attribued to each process -> when was each process active -> 83 indel pattern -> indel+SNP combination -> TOP1 mutation -> -> 1-20 to try ->optimization issue，r(number of signature)-> optional K number of clusters -> How COSMIC pattern is created -> assumption(homogenious) -> all TCGA samples -> signature -> 20-30 samples, too small sample size is not useful for signature analysis -> the current version is low, but next version will be faster -> germine line mutation: topmed, blood -> SBS maybe also a mixture for multiple signature/ tradeoff/ -> SBS7 ->SBS7a,SBS7b,SBS7c,SBS7d
-> Catalogue of Somatic Mutations in Cancer(COSMIC) -> benchmark -> SBS1 -> PCAGW map to 96 samples, which are the most frequent signature -> probability number/96 so that sum=1 -> CNV signature -> CNV variation related to BRCA1, and BRCA2 -> germline variation do not have affect to the risk of the cancer