RESEARCH & SCIENCE

Research & Science

From genome to phenotype — the complete equine genomics analysis pipeline

Research Methodology

From raw sequencing data to actionable insights — a complete equine genomics analysis pipeline

WGS Sequencing

Illumina NovaSeq platform, 150bp paired-end sequencing, average 30X coverage depth

Variant Calling

GATK 4.x best practices pipeline, SNP/Indel/SV detection across all variant types with stringent QC

Functional Annotation

VEP transcript annotation + SIFT/PolyPhen-2 dual-algorithm missense prediction + structural variant annotation

Causal Inference

Multi-omics evidence integration from GWAS + WGS, Tier A/B/C causal stratification, regulatory network construction

Phenotype Prediction

NCDS v3.4 model-driven precise prediction from genotype to athletic aptitude and hereditary disease risk

Core Algorithm

NCDS v3.4 — Neuro-Centric Differentiable System

🧠 Tri-Modular Architecture

NCDS v3.4 integrates three biological dimensions: Neural Regulation (34 genes), Skeletal Development (38 genes), and Growth & Development (30 genes) — a systematic 102-gene functional architecture with 90% core gene validation rate.

Neural module: signal transduction, synaptic plasticity, neuromuscular junction
Skeletal module: muscle fiber type, energy metabolism, muscle contraction
Developmental module: growth factors, hormonal regulation, nutrient metabolism

📊 Athletic Scoring Engine

7 athletic scoring engines covering all performance assessment scenarios, calibrated against 400+ breed baseline data for precise prediction across Sprint, Endurance, Dressage, Jumping, and Racing dimensions.

Sprint Index — explosive power assessment
Endurance Index — aerobic capacity evaluation
Dressage Index — coordination and collection
Jumping Index — power-to-weight ratio
Racing Index — composite performance metric

Data Pipeline Architecture

JumpChain™ whole-genome variant database construction workflow

🗄️ Reference Genome

EquCab 3.0 (GCF_002863925.1)
Equine reference genome led by UC Davis. Contains 31 chromosomes (30 auto + X), total length ~2.7Gb, N50 > 85Mb.

📋 Variant Calling Pipeline

BWA-MEM2 alignment → GATK HaplotypeCaller → VQSR quality control → BCFtools joint calling. Supports SNP/Indel and 5 structural variant types.

🏷️ Annotation Pipeline

Ensembl VEP v110 annotation → SIFT prediction → PolyPhen-2 scoring → CADD integrated scoring → causal evidence level annotation (Tier A/B/C).

982

Data Tables

41,896

Gene Annotations

40.15M

Variant Positions

22 GB

Database Size

49,697

Causal Variants

852K

VEP Transcripts