Agent skill

bio-clinical-databases-msi-detection

Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill msi-detection --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 19 KB
Bundled scripts: yes
Path: skills/bioskills/msi-detection/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

Review
written from the skill's own SKILL.md · Aug 5, 2026

What it does

Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

How it works

  • Version compatibility notes reference MSIsensor-pro 1.2+ and other tools; provides commands for various workflows:
    • Tumor-only: msisensor-pro msi -d microsatellites.list -t tumor.bam -o msi_out -b 16
    • Baseline generation: msisensor-pro scan -d /reference/GRCh38.fa -o microsatellites.list -p 1 -m 5; msisensor-pro baseline -d microsatellites.list -i normal_samples.list -o baseline.list -b 16; then msisensor-pro pro with --baseline baseline.list
    • Paired tumor-normal: msisensor msi -d microsatellites.list -n normal.bam -t tumor.bam -o msi_paired_out -b 16
    • MANTIS (paired): mantis.py -t tumor.bam -n normal.bam -b microsatellite_targets.bed --threads 8 -o mantis_output
  • Provides specific CLI examples, output formats, and threshold guidance (e.g., %_unstable, 20-30% as panel-driven MSI-H threshold; FoCR and FDA references).
  • Includes multiple classification routines in Python sketches: classify_msi and workflows for Lynch screening and ICI decisions, tying MSI-H and dMMR to eligibility and noting that TMB-H is not additive per Sha 2020.
  • Contains per-operation failure modes, reconciliation patterns, and a set of quantitative thresholds with sources.

When to use it

  • Use for FDA pembrolizumab MSI-H pan-tumor eligibility assessment; screening for Lynch syndrome; differentiating MSI-H from POLE-exo hypermutators; and when combining MSI with TMB-H across tumor types.

What it can touch

  • CLI tools: MSIsensor-pro, MSIsensor, MSIsensor-ct, MANTIS, MSIngs, MSIPanel, ngsMSI, MSIDetect, and related scripts. It references commands and files such as msisensor-pro, microsatellites.list, tumor.bam, normal.bam, baseline.list, msi_output.txt, and msi_output_all.

Caveats

  • Licensing: NOASSERTION. Version compatibility and panel calibration are emphasized; thresholds are panel-specific and may vary. Warnings include potential discordance between IHC and MSI results, panel size effects, and ctDNA fraction limitations for cfDNA MSI calls.
From the SKILL.md

## Version Compatibility Reference examples tested with: MSIsensor-pro 1.2+, MSIsensor 0.6+, MSIngs 1.0+, MANTIS 1.0.5+, samtools 1.19+, mSINGS 5.6+, pandas 2.2+, cyvcf2 0.30+. FDA pembrolizumab MSI-H / dMMR pan-tumor approval is from 2017 (Le 2015 *NEJM*; KEYNOTE-016/164/158); approval extended to colorectal first-line in 2020. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. MSIsensor-pro replaces MSIsensor for tumor-only assays; MSIsensor-ct is the bTMB-equivalent for ctDNA panels. # MSI Detection; The Companion ICI Biomarker to TMB **'Detect MSI status from this somatic sequencing data'** -> Profile microsatellite instability across canonical loci (Bethesda 5 panel + extended NGS-derived sites); classify MSI-H / MSS / MSI-L per Bethesda / FDA / KEYNOTE convention. - CLI (recommended tumor-only): `msisensor-pro msi -d microsatellites.list -t tumor.bam -o msi_out -b 16` - CLI (paired tumo

What's inside
Steps it walks through
  1. Version Compatibility
  2. The Regulatory and Trial Landscape
  3. MSI vs dMMR vs TMB-H: The Conceptual Hierarchy
  4. Tool Taxonomy
  5. Decision Tree by Scenario
  6. Bethesda Panel and Modern NGS-Derived Loci
  7. Standard Workflow: MSIsensor-pro Tumor-Only
  8. Paired Tumor-Normal MSIsensor
  9. MANTIS Step-wise Difference
  10. MSI-H Classification Logic
  11. Per-Operation Failure Modes
  12. Reconciliation: When Sources Disagree
  13. Quantitative Thresholds and Conventions
  14. Common Errors
Ships with 2 files
  • examples/msi_detection.sh
  • usage-guide.md
Commands it runs
Generate microsatellite list from reference genome (one-time)
msisensor-pro scan -d /reference/GRCh38.fa -o microsatellites.list -p 1 -m 5
Generate baseline from N normal control samples (one-time per panel)
msisensor-pro baseline -d microsatellites.list -i normal_samples.list -o baseline.list -b 16
Score tumor sample. The `-i sample_id` flag is uncommon: in typical msisensor-pro
usage the sample identifier is derived from the BAM file -- verify the flag set
against `msisensor-pro pro --help` for the installed release.
msisensor-pro pro \
Critical column: %_unstable. Threshold MSI-H typically >= 20-30% depending on panel.
msisensor msi \
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About this skill
What does the bio-clinical-databases-msi-detection skill do?

Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), MSIngs, MANTIS, MSIPanel, MSIDetect, and ngsMSI for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill msi-detection --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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