Learning to use

Genome-Phenome Analyzer: How the genome capabilities work

Combining an annotated variant table with patient findings to arrive at a differential diagnosis is labor intensive and costly when done manually.  SimulConsult’s integrated Genome-Phenome Analyzer reduces the time involved dramatically and uses a hypothesis-independent approach to the analysis that promotes accuracy.

How does the Analyzer work?

It combines the power of the following 2 inputs:

  • Clinical findings and lab tests input by the user, providing phenotype information to be compared to the phenome. 
  • Annotated genomic variants, providing genotype information to be compared to the genome. 

Combining the genome and phenome perspectives using a “pertinence” metric allows for a hypothesis-independent approach that is more powerful and efficient than doing the approaches manually or sequentially.

How long does the Analyzer take?

The software analysis takes seconds and the whole process takes less than 10 minutes for a typical patient – saving hours of time.  Full trio (proband, mother, father) support is included, with novelty and compound heterozygote analysis.

What is distinctive about SimulConsult?

The approach is distinctive in being hypothesis-independent in not requiring assumptions about mode of inheritance, number of genes involved, or which clinical findings are most relevant.  In some clinical situations it is possible to construct a short list of genes that are relevant (e.g., for centronuclear myopathy) but it many other situations the clinical picture is less pathognomonic and a more robust clinical analysis is needed.

This is enabled by a curated, evidence-based, computational database of diseases and findings is combined with a Bayesian approach (no evoking strengths) to enable it to reason from pertinent positives and negatives. This approach allows use of timing of onset and disappearance information about individual findings, along with family history, and taking cost into consideration in test recommendations.  More details about the approach and the efficacy are in a study published in the Journal of Child Neurology (free PubMed Central and PDF versions).

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