Learning to use

Phenome Analyzer FAQs

A more complete list of features is found on the Features page

What does the software do?

The fundamental tasks performed by the DDSS are as follows:

  • Computes differential diagnosis – the ranked list of candidate diseases a patient might have based on the findings (symptoms, signs and test results) you enter.
  • Suggests useful findings based on the evolving differential diagnosis.
  • Provides contextual links to other resources, including articles, images, etc.
  • Reveals the logic so you can assess if you believe it. Compares the entered findings to those in the selected disease. 

Where do I start?

You must enter the age and chromosomal sex of the patient to get started.  It gets entered on the Initial screen.  Then you must add your first finding, by going to search and typing the finding into the green search box or one of the core lists on the same page, and then commenting on the finding’s presence or absence by pulling down the menu.  Next to each finding is a pull-down menu with a “?”.  This is where you specify onset or absence, and “add the finding to the patient’s phenotype”. 

Does it matter which finding I add first?

To maximize efficiency, start with the most unusual finding.

Why does the software focus on the time-course of findings?  

The database has the time course of each finding in each disease.  By specifying the time course in your patient, you get a better differential diagnosis.

Why specify Pertinent negatives? 

Diagnoses of exclusion and pertinent negatives are a critical part of rare disease diagnosis.

Where do findings “go” once I add them?

The findings you have added are collected on the Phenotype tab under Dx.

How do I erase a finding I previously added?  

Go to Dx/Phenotype and under the presence button, click “unspecified”.

How do I enter test results?

Go to Dx/Add tests for suggestions of useful tests or use search under the magnifying glass.  For some specialties there are collections of key tests in the core lists under search.

Where do I enter Family history?

On the Initial screen, click family history to get the menu to specify if others in the family are affected, if known.

If common diseases have already been ruled out, how do I reduce the common diseases in the differential diagnosis?

On the initial screen, specifying Primary, secondary or tertiary allows you to adjust for the incidence of the disease, and is useful for when a patient has already had many conditions ruled out or where the disease may be newly described and the incidence not well known.

What if I want to only look at diseases that include an unusual or striking finding?

Occasionally, a finding is so striking or so intense you want to be sure the Differential Diagnosis only considers diseases with that finding.  Next to where you specify presence or absence, you can require a finding.  Findings marked with an asterisk are required.  Leaving a finding not required means the DDSS will consider the possibility that any particular finding is incidental to the diagnosis.

What do I do if I want to read more about a finding or disease?

Click the button of the name of the finding or the disease and then click “Tips” up on the black bar to go to related resources about the finding or disease.  

How do I check synonyms of a finding or disease?

Hover over the name of the finding or diseases to see synonyms.

Does the software use machine-learning?

To be able to reveal the logic, the software avoids using machine learning-based artificial intelligence.  The database is built through manual curation by expert clinicians.  Machine learning is lousy at unlearning, while our understanding of medicine continues to change and many subtle facts about rare diseases have never been written down and are only known to specialists, so there are no training sets from which the machine could learn.

What do the colors mean?

  • Blue is used for diseases
  • Green is used for findings
  • Orange is used for genomes

What is the difference between “usefulness” and “pertinence”?

The two concepts are related.

  1. Usefulness is prospective, meaning what additional information would most change the differential diagnosis. 
  2. Pertinence is retrospective, meaning a measure of how much this finding has driven the differential diagnosis.

What file format can the software read to load the patient?

You can load the text string or the PDF Patient Summary, or even the HTML version of the Patient Summary that you may have saved from the old version of the software.

How do I update my name and title that appears in the Patient Summary?

From any page on the SimulConsult Web site other than the page running the software, hover over the My Account menu, then choose “Account details”.

Is there a “rule out” feature?

Yes.  Once you select a disease as active by clicking on it, two options will appear in the the Add findings tab and Add tests tab: “Usefulness in all diseases” and “Rule in or out selected disease”.

What is the difference between the Profile of the Finding and of a Disease?

  1. The Profile of a Finding shows the frequency and onset of that finding in each disease, displayed in declining frequency at the patient age. 
  2. The Profile of a Disease shows the Findings in the selected disease displayed in declining frequency at the patient age.

How do I find the app in the app store?

There is no need to install an app to run on mobile platforms. The diagnostic tool runs from the same URL as it does on personal computers.

What do the colors mean in the software?

Diseases are blue.
Findings are green (signs, symptoms, lab results).
The current age period is black. Later is purple. Earlier is brown. Gone is gray.

How is the dominant versus recessive character of an X-linked disease handled?

In simpler times, it was common to refer to an X-linked disease as dominant or recessive. Now, it is recognized that many X-linked diseases have a mixture of the two types of expression. A good example is X-linked adrenoleukodystrophy, where the leukodystrophy is dominant and the adrenal deficiency is recessive (losing half of myelin cells is enough to block axonal transmission but losing half of hormone-producing cells is less problematic).

The diagnostic software applies both recessive and dominant models to X-linked diseases, according to the recessive versus dominant character of the disease. For some diseases, there are separate listings for forms of the disease in males and females.

Can the software be used in prenatal settings?

SimulConsult has lots of material on prenatal findings, curated from many sources, including the Woodward “Diagnostic Imaging: Obstetrics” and Benacerraf “Ultrasound of Fetal Syndromes” textbooks.  There is a bundle “Prenatal ultrasound” that combines information in that test and puts it in order of usefulness (green shading), as shown in the image below for a 0 day old boy with nuchal thickness on prenatal ultrasound already entered as a required finding (using the box that appears to the left of the presence box). 

Prenatal diagnosis