Scenario 2: Genetic Analysis Case Study on MAPK1 gene

Scenario 2: Genetic Analysis Case Study on MAPK1 gene#

A Girl Diagnosed with Noonan-like Syndrome#

A girl was diagnosed affected by a Noonan-like syndrome, but she was negative after analysis of an extended panel for Rasopathies. Following Whole Exome Sequencing (WES), a de novo likely pathogenic mutation was found in the MAPK1 gene.

Research Questions#

Question 1: Mutation Prevalence#

Are there any other individuals with the same mutation or allelic variant?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?individual ?individualLabel
WHERE {
  # Identify the mutation of interest
  ?mutation rdf:type sio:SIO_000115 ;
            rdfs:label "MAPK1_mutation"@en .

  # Find individuals with the same mutation
  ?individual rdf:type sio:SIO_000498 ;  # Individual
              sio:denotes ?mutation ;
              rdfs:label ?individualLabel .

  # Ensure the labels are in English
  FILTER(LANG(?individualLabel) = "en") .
}

Question 2: Phenotype and Natural History#

What is their phenotype and natural history of the disease?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>

SELECT ?individual ?phenotype ?natural_history
WHERE {
  ?individual sio:SIO_000115 ?variant ;
              sio:SIO_000628 ?phenotype ;
              sio:SIO_000628 ?natural_history .
  ?variant rdfs:label "MAPK1 gene mutation" .
  ?phenotype rdfs:label ?phenotype_label .
  ?natural_history rdfs:label ?natural_history_label .
}
ORDER BY ?individual

Question 3: Variant Frequency in Populations#

What is the variant frequency across different populations?

Work in Progress: This query is still under development and may not yet provide complete or accurate results. It serves as a foundation for further refinement and enhancement. 
PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?population ?populationLabel ?mutation ?mutationLabel ?frequency ?frequencyLabel
WHERE {
  # Identify the mutation of interest
  ?mutation rdf:type sio:SIO_000115 ;  # Identifier
            rdfs:label "MAPK1 gene mutation"@en ;
            sio:denotes ?gene .

  # Find populations with this mutation
  ?observation rdf:type sio:SIO_000498 ;  # Observation
               sio:has-input ?mutation ;
               sio:has-output ?frequency ;
               sio:has-agent ?population .

  # Get the labels for the mutation, frequency, and population
  ?mutation rdfs:label ?mutationLabel .
  ?frequency rdf:type sio:SIO_001367 ;  # Frequency
             rdfs:label ?frequencyLabel .
  ?population rdf:type sio:SIO_000015 ;  # Population
              rdfs:label ?populationLabel .

  # Ensure the labels are in English
  FILTER(LANG(?mutationLabel) = "en") .
  FILTER(LANG(?frequencyLabel) = "en") .
  FILTER(LANG(?populationLabel) = "en") .
}
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