Question: Microsatellite Instability (MSI)
0
gravatar for sruthi
12 months ago by
sruthi30
sruthi30 wrote:

Hi,

Could anyone suggest me free tools for calculating MSI for tumor samples alone?

TIA

sequencing next-gen • 581 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by sruthi30
2
gravatar for Nicolas Rosewick
12 months ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

You can use MSIsensor

Tumor only mode :

# first scan genome of interest 
msisensor scan -d reference.fa -o microsatellites.list
# Then use tumor bam file to detect MSI 
msisensor msi -d microsatellites.list -t tumor.bam -e bed.file -o output.tumor.prefix
ADD COMMENTlink written 12 months ago by Nicolas Rosewick8.8k

Hey Nicolas, Thanks for the reply. I have already used MSIsensor for 3 tumor samples. But I get 0 for "Number of sites with enough coverage" and "Number of somatic sites". How should I work further with MSIsensor?

ADD REPLYlink written 12 months ago by sruthi30

You should edit your question to add more informations regarding your data (which type : WGS, WES, targeted, etc... ). Without that I (and the community) would not be able to help you more.

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.8k

Yeah, sorry about that. I have used MSIsensor for 3 different tumor exome samples without matched normal and getting 0 as the value for "Number of sites with enough coverage" and "number of somatic sites (%)" for all the 3 samples. I need to know whether the value I'm getting is correct or am I missing out on something.

ADD REPLYlink written 12 months ago by sruthi30

Maybe check some sites in IGV to look if coverage is really low .. You could also reduce coverage thresold in msisensor mis with -c <int> coverage threshold for msi analysis, WXS: 20; WGS: 15, default=20

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.8k

I had set the coverage threshold to -c 20 but I still get the output as 0. Below is the code I've used, kindly let me know if I've done it the right way:

msisensor msi -d microsatellites.list -c 20 -i 1 -t tumor.bam -e bed.file -o output.tumor.prefix

And. I'll also check some sites with IGV.

ADD REPLYlink written 12 months ago by sruthi30

-c 20 is the default for WES. To decrease to min 10 of coverage try with -c 10

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.8k

I changed it to 10 and then increased the coverage as well. I'm still getting 0.

ADD REPLYlink written 12 months ago by sruthi30
0
gravatar for sruthi
12 months ago by
sruthi30
sruthi30 wrote:

Hi, Output of a tumor only case, is 2144 3491 15.01. I have a few queries regarding it.

1.From the sample output given on the github page, I understand that 15.01 is the % of "Number of somatic sites" and is the msi score as well. Is it msi-high or msi-low? 2. What is the cutoff score? Because it is mentioned that the cutoff values are calculated for various cancer types. 3.How do I get the MSI status?

TIA

ADD COMMENTlink modified 12 months ago • written 12 months ago by sruthi30

Figure 1 of the missensor paper seems explicit : https://academic.oup.com/bioinformatics/article/30/7/1015/236553 . As you have 15.01 % of somatic sites your sample should be MSI-H. The best would be to test on other samples ; and maybe on control samples (non-tumor) of the same tissue.

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.8k

Hey, Thanks for the article. I have read it. Let me explain from what I understood from the graph is, <10% would be msi-low and >10% is msi-high. Did I get it right?

ADD REPLYlink written 12 months ago by sruthi30

Yes indeed but should execute msisensor on all your samples and then check if you can see some stratification. Even better test it on control samples

ADD REPLYlink written 12 months ago by Nicolas Rosewick8.8k

Okay will do it. Thank you so much.

ADD REPLYlink written 12 months ago by sruthi30
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