Skip to content

Genomic Foundation Engine

Stage 1 of the HCLS AI Factory Pipeline

The Genomic Foundation Engine transforms raw patient DNA (FASTQ) into 3.5 million annotated variant vectors in under 2 hours using NVIDIA Parabricks on DGX Spark. It creates the molecular foundation that all 11 intelligence agents build upon.

What It Does

Patient DNA → BWA-MEM2 alignment → DeepVariant variant calling → ClinVar/AlphaMissense annotation → BGE-small-en-v1.5 embeddings → Milvus genomic_evidence collection (3.5M vectors)

Key Numbers

Metric Value
Variants detected 11.7M per genome
Searchable variants 3.5M (after filtering + annotation)
Processing time 120-240 minutes (GPU) vs 24-48 hours (CPU)
ClinVar matches 35,616 per genome
AlphaMissense predictions 6,831 per genome
Reference genome GRCh38

How It Connects

The genomic_evidence collection is shared read-only with all 11 intelligence agents in the Precision Intelligence Network. Each agent queries this molecular foundation for domain-specific insights:

  • Precision Oncology Agent queries cancer-associated variants for MTB packet generation
  • CAR-T Intelligence Agent links genomic targets to cell therapy development
  • Imaging Intelligence Agent triggers genomic queries from Lung-RADS 4A+ findings
  • Pharmacogenomics Agent maps star alleles for genotype-guided dosing
  • Precision Biomarker Agent integrates genotype data with biomarker interpretation
  • Neurology Agent connects neurological variants to disease pathways
  • Cardiology Agent links cardiovascular genomics to risk scoring
  • Rare Disease Agent runs ACMG variant classification against genomic evidence
  • Clinical Trial Agent matches patient variants to trial eligibility criteria
  • Single-Cell Agent connects tumor heterogeneity findings to genomic context
  • Precision Autoimmune Agent correlates HLA associations with autoimmune risk

Pipeline Flow

FASTQ (raw sequences, ~100GB)
    |
    v
[BWA-MEM2 Alignment] ──── GPU-accelerated (20-45 min)
    |
    v
[DeepVariant Variant Calling] ──── CNN-based, >99% accuracy
    |
    v
VCF (11.7M variants)
    |
    v
[ClinVar Annotation] ──── 4.1M clinically annotated variants
    |
    v
[AlphaMissense Scoring] ──── 71M AI-predicted pathogenicity scores
    |
    v
[Quality Filtering] ──── PASS filter, annotation enrichment
    |
    v
[BGE-small-en-v1.5 Embedding] ──── 384-dim vectors
    |
    v
Milvus genomic_evidence (3.5M searchable vectors)

Technology

  • NVIDIA Parabricks 4.6 -- GPU-accelerated alignment and variant calling
  • BWA-MEM2 -- Short-read alignment (20-45 min on GPU)
  • DeepVariant -- CNN-based variant calling (>99% accuracy)
  • ClinVar -- 4.1M clinically annotated variants
  • AlphaMissense -- 71M AI-predicted pathogenicity scores
  • BGE-small-en-v1.5 -- 384-dimensional text embeddings
  • Milvus 2.4 -- Vector database with IVF_FLAT/COSINE indexing

Getting Started

Clinical Decision Support Disclaimer

The Genomic Foundation Engine is a research and clinical decision support tool. It is not FDA-cleared and is not intended as a standalone diagnostic device. All results should be reviewed by qualified healthcare professionals. Apache 2.0 License.