Microsatellite Instability, Whole exome sequencing

Question

[vaish01kv]

How can Microsatellite instability be calculated using Whole exome sequencing, when microsatellite is comprised of tandem repeats etc,. and classified under non-coding regions?

Answer 1

[bruce.moran]

There was a good editorial on MSI in JCO PO a few years ago, alongside this paper which references the set of 2,359 microsatellites in or near the exome. So reason is that not all are in non-coding regions.

[vaish01kv]

How can MSI be calculated when there is no matched normal available?

[vaish01kv]

How to identify microsatellite markers in exome sequencing, to calculate MSI?

[bruce.moran]

Because microsatellites are so highly variable per individual, I think you will need matched normal to test MSI. Without matched normal you could investigate tumour mutational burden (TMB).

[vaish01kv]

Thank you so much for the information!

Answer 2

[Nicolas Rosewick]

You can check MSIsensor

paper : https://academic.oup.com/bioinformatics/article/30/7/1015/236553

tool : https://github.com/ding-lab/msisensor

[vaish01kv]

Thank you! But MSIsensor needs Matched normal for analysis. Is there any method where i can do it without normal sample?

[Nicolas Rosewick]

It can work in tumor-only mode . You just provide the tumor bam file. msisensor msi -d microsatellites.list -t tumor.bam -o output.tumor.prefix

[sruthi]

Hey Nicolas, I tried using this command and it says "please provide a valid format normal bam file!"

What should I do now? TIA

[Nicolas Rosewick]

Could you post the exact command you used. check on the github of msisensor. Maybe contact the other : https://github.com/ding-lab/msisensor

[sruthi]

Hey. The error is rectified. I had to give the whole path for the command to work. Thanks.

[sruthi]

Hey Nicolas, I get the following error while running msisensor:

[bam_index_load] fail to load BAM index. msisensor: bamreader.cpp:184:bool ReadInBamReads(const char*, const string&, unsigned int, unsignedint, std::vector<split_read>&, std::string): Assertion `idx' failed. Aborted (core dumped)

How should I work further? Thanks

[Nicolas Rosewick]

did you index your bam files before ie. samtools index alignment.bam

[sruthi]

Yes I did and all the files are in the same directory as well.

[Nicolas Rosewick]

do you have samtools in your PATH

[sruthi]

Yes I do. SAM tools is installed in my path.

Answer 3

[vivek.mathema]

has anyone tired the latest software OSTRFPD: Multifunctional tool for genome-wide short tandem repeat analysis for DNA, transcripts and amino acid sequences with integrated primer designer link: https://github.com/vivekmathema/OSTRFPD