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Missense Variant Triage Agent with OpenAI Agents SDK and Google Jules

In response to emerging missense functional prediction tools, genomic diagnostic labs require automated pipelines to classify novel variants. Build an autonomous triage agent using OpenAI Agents SDK integrated with Google Jules for automated code patch generation and Biopython validation. Achieve 92% classification accuracy on ClinVar benchmarking sets.

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What you are building

Build an automated missense variant triage workflow using OpenAI Agents SDK and Biopython for clinical genomic annotation.

How work is evaluated

Evaluation

Evaluates the agent's ability to classify missense variants and produce valid HGVS variant annotations.

Datasets

Public datasets, plus the private datasets you have access to.

How submissions are scored

Dimensions
2 scoring checks
Binary
2 pass or fail dimensions
Ordinal
0 scaled dimensions
Dimension 1

hgvs_syntax_check

Ensures HGVS transcript notation follows standard nomenclature.

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Dimension 2

classification_accuracy

Accuracy of pathogenic vs benign variant categorization • target: 0.92 • range: 0-1

Binary check

This dimension contributes its full weight only when the submission satisfies the requirement. Partial credit is not awarded.

Learning goals

  • Implement autonomous variant annotation tool workflows using OpenAI Agents SDK

  • Integrate Google Jules for automated execution of bioinformatics script updates

  • Parse and validate VCF and ClinVar data streams using Biopython

  • Evaluate variant pathogenicity scores using multi-agent verification checks

Resources

Dataset notes

Curated set of 500 missense single-nucleotide variants with gold-standard ClinVar pathogenicity labels and functional prediction scores.

Challenge setup

Evaluates the agent's ability to classify missense variants and produce valid HGVS variant annotations.

Challenge input

JSON containing a list of genomic variant objects with chromosome, position, ref, and alt alleles.

OpenAI Agents SDK

Required framework for building multi-turn tool-using agents.

Google Jules

Automated code modification and tool fixing during pipeline failure.

Evaluated output

JSON object with classified pathogenic status, score, and verified HGVS nomenclature string.

Evaluation checks
  • Ensures HGVS transcript notation follows standard nomenclature.
  • Accuracy of pathogenic vs benign variant categorization • target: 0.92 • range: 0-1
Configured evaluation evidence
  • Benchmark: ClinVar Variant Pathogenicity Benchmark
  • Classification Accuracy target: 0.92
  • 1 public reference case
Configured runtime
  • Python execution harness
  • Python sandbox (unavailable on Versalist)

Shows the first task, up to three tools, and up to three evidence items.

View technical recipe

Configured tools

Action Space
  • Google Jules · Required
  • OpenAI · Optional
  • Agno · Optional
Orchestration
  • Google Jules · Required
  • Agno · Optional

Evaluation contract

  • hgvs_syntax_check · Weight 1
  • classification_accuracy · Weight 1

Metrics

  • classification_accuracy · Target 0.92

Benchmarks

  • ClinVar Variant Pathogenicity Benchmark
  • biotech

Reference cases

  • 1 public reference case

Workflow tasks

  1. Task 1

    Input: JSON containing a list of genomic variant objects with chromosome, position, ref, and alt alleles.

    Output: JSON object with classified pathogenic status, score, and verified HGVS nomenclature string.

    Execution harness: Python

Evaluation tools

  • OpenAI Agents SDK · Agent Orchestration
  • Google Jules · AI Code Maintenance

Recipe freeze marker

No recipe freeze time is recorded.

Frequently Asked Questions about Missense Variant Triage Agent with OpenAI Agents SDK and Google Jules