# Tertiary Analysis

[Emedgene](https://help.emg.illumina.com/) supports advanced interpretation of TruPath Genome data by integrating proximity‑aware, long‑range DRAGEN outputs into existing AI‑driven workflows. The platform enhances singleton interpretation through phasing, improves resolution in complex genomic regions such as STRs and homologous genes, and introduces more powerful filtering, phenotype‑driven prioritization, and visualization capabilities. Together, these updates increase interpretive confidence, reduce review time, and improve usability across genome and cytogenetic workflows.

#### TruPath Genome Interpretation

Supports AI‑assisted interpretation of long‑range TruPath Genome outputs while preserving existing analysis workflows.

* Ingests proximity‑aware DRAGEN outputs for SNVs, STRs, SVs, and paralog‑resolved variants
* Maintains compatibility with existing AI shortlisting and interpretation features
* Enables streamlined interpretation of TruPath‑specific outputs without workflow changes

#### SNV Phasing and Compound Heterozygous Resolution

Improves confidence in singleton interpretation by incorporating TruPath phasing information.

* Displays phase set and allele context (PS/GT) across Analysis Tools, Variant Page, and IGV
* Uses phasing to improve cis/trans determination for compound heterozygous variants
* Returns compound heterozygous results for singleton cases
* Prioritizes TruPath compound heterozygous variants in the AI shortlist
* Visualizes phased BAMs in IGV with phase‑set coloring and mismatch highlighting

#### STR and Paralog Resolution (MRJD) Support

Extends interpretation into complex and repetitive genomic regions using TruPath long‑range data.

* Supports extended STR length estimation into the kilobase range
* Preserves existing STR AI prioritization, filtering, and visualization workflows
* Supports MRJD interpretation with haplotype‑ and copy‑aware variants
* Enables analysis of homologous genes such as SMN1/2, PMS2, STRC, CYP2D6, and CYP21A2
* Visualizes MRJD‑specific BAMs directly in IGV

#### Structural Variant Interpretation Enhancements

Improves structural variant confidence and visualization using TruPath colocation signals.

* Reduces false‑positive inter‑chromosomal translocations and inversions
* Supports improved BND outputs and visualization
* Displays SV breakpoint confidence intervals and read‑support metrics
* Provides clearer assessment of SV quality and breakpoint precision

#### Advanced Filtering Capabilities

Enables complex, real‑world filtering strategies through logical operators and nesting.

* Supports AND, OR, and NOT operators
* Allows nested condition groups up to three levels deep
* Enables include/exclude logic at the individual filter level
* Supports numeric, interval, boolean, and multi‑select filter types
* Allows advanced filters to be saved, shared, locked, and managed like existing presets

#### Phenotype‑Driven Prioritization and AI Signals

Adds greater control over phenotype relevance while expanding AI‑derived variant annotations.

* Supports user‑defined phenotype hierarchy with adjustable weighting
* Allows phenotypes to be marked as Critical, Strong, Standard, Ignore, or Negative
* Reflects phenotype weighting in Phenomeld‑based gene prioritization scores
* Integrates PromoterAI scores for regulatory impact prediction of promoter variants
* Displays regulatory severity classifications that contribute to overall variant severity
* Keeps AI shortlist rankings unchanged by phenotype weighting

#### Visualization and IGV Workflow Improvements

Reduces manual effort and improves usability in variant visualization workflows.

* Persists IGV track selection and ordering per user and per organization
* Allows administrators to define default organization‑wide track configurations
* Supports popping out embedded IGV into a separate window for multi‑monitor workflows
* Adds visualization tracks for phased BAMs, segmental duplications, and SV confidence metrics