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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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cutoff-question #3

Open fengshuaisheng opened 4 years ago

fengshuaisheng commented 4 years ago

Hi, I have some questions while using the msisensor2, the description is "msi high: msi score >= 20%” in the offficial website (http://niulab.scgrid.cn/msisensor2/#services)， while I also found that the descripition "MSI_H: msiscore >= 10%, MSI_L: 3.5% =< msiscore < 10%; MSS: msiscore < 3.5%" in the msisensor V0.6 , so I wondering the cut-off value is how determined when analysing the Tumor-only data, and is there difference between WES, WGS or panel data ? by the way my data is is panel data(> 500 gene) thank you very much!!!

Beifang commented 4 years ago

MSIsensor2 is a new algorithm specially designed for matched-normal data free samples. We suggest "msi high: msi score >= 20%” for MSIsensor2. MSIsensor is our previous algorithm, which is specially designed for MSI detection using paired tumor and normal sequencing data. We suggest "MSI_H: msiscore >= 10%, MSI_L: 3.5% =< msiscore < 10%; MSS: msiscore < 3.5%" for MSIsensor. We can train a panel-specific model for you if you want.

fengshuaisheng commented 4 years ago

I got it, and thank you very much for your reply, while in the clinical application, the NGS panel sequencing is better applied than the WES because of the deep sequencing, many company panels (eg : IDT )have including the microsatellite associated genes( like MLH1, PMS2, MSH2 & MSH6), and also the MSIsensor was recommend by the "Consensus of Chinese experts on microsatellite instability detection" , So I expected the version of MSIsensor for appling in NGS panel dectection, which will really benifit for the researchers of clinician and others, thank you !!

Beifang commented 4 years ago

I just want to remind that both current MSIsensor and MSIsenor2 can be used for NGS panels. MLH1, PMS2, MSH2 & MSH6 are not necessary for MSIsensor and MSIsensor2 algorithm. What I was trying to say that we can train a panel-specific model for you if you just want to specify any particular microsatellites.

fengshuaisheng commented 4 years ago

Oh! I got it, I appreciate for your reply, and that's good works for MSI dectection, thank you and your teams very much!!!