FAVOR‑GPT Assistant Guide

FAVOR‑GPT is an AI chatbot powered by OpenAI’s GPT‑4 and DeepSeek R1. Use it to query genes, variants, rsIDs, regions, and database terms directly from the FAVOR UI.

Getting Started

  • Click Chat with FAVOR‑GPT (bottom-right).
  • Chat panel slides open with tips and examples.

Model Selection

Choose your model in the widget header:

  • GPT‑4o Mini (default, cost-effective, fast)
  • GPT‑4.1 Nano (cost-effective, fast)
  • DeepSeek R1 (multilingual, reasoning capabilities, slower)

Best Practices

  1. Be precise: supply exact gene symbols, rsIDs, or coordinates.
  2. Use supported formats: same as Main Search (e.g., BRCA1, rs123456, 2-200000-200500).
  3. Verify: AI responses may contain errors—cross‑check with FAVOR pages or API.

Example: Variant Pathogenicity

Provide variant_vcf or rsID (e.g., 19-44908822-C-T or rs7412).

User: “What is the pathogenicity of variant 19‑44908822‑C‑T?”

FAVOR‑GPT Response

The variant 19-44908822-C-T (rs7412) is a nonsynonymous SNV in the APOE gene. It has been annotated as
**pathogenic** for conditions like familial type 3 hyperlipoproteinemia and warfarin response. Population
frequency: allele count 39, allele number 264690 in Bravo.
Predicted impact:
- PolyPhen: probably damaging
- SIFT: deleterious
- CADD Phred: 27.8

Example: Term Definition

Ask for definitions of FAVOR-specific fields (e.g., BRAVO_AN).

User: “What is BRAVO_AN?”

FAVOR‑GPT Response

**BRAVO_AN** stands for Bravo Allele Number: the total number of alleles observed in the TOPMed Bravo
dataset (NHLBI TOPMed Consortium).

Limitations

  • Batch queries (e.g., >100 rsIDs) may time out.
  • Always validate critical data against the FAVOR API or UI.