• Manuals

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• Introduction
• Ingenuity Variant Analysis
• Ingenuity Variant Analysis for Hereditary Diseases
  • Genetic disease pipelines
  • Pipeline description and supported input
• Workflows
  • Identify and Interpret Causal Variants in a Trio using IVA (WGS)
  • Identify and Interpret Causal Variants in a Trio using IVA (WES)
  • Identify Somatic Variants from a Single cfDNA Sample using IVA (WES)
• Analysis using the plugin and the IVA web interface
• Add Information from Allele Frequency Community
• Remove Variants Found in Allele Frequency Community
• Changing Allele Frequency Community opt-in settings
• Install and uninstall plugins
  • Install
  • Uninstall

Pipeline description and supported input

For each genetic disease pipeline, only certain sample input combinations are supported, and running an analysis with an unsupported sample input combination may output wrong results. Make sure to review filter cascade settings in Ingenuity Variant Analysis if you are running an unsupported analysis. For example, if all four analyses are run on a sample trio with one affected parent, then only the results from the dominant and recessive homozygous analyses are supported.

Dominant inheritance pattern

Best practice filter cascade to identify variants present in affected parents and transmitted to the proband and affected siblings in a dominant inheritance pattern. When one parent is set to affected, variants present in the unaffected parent will be excluded. Setting both parents to unaffected will be interpreted as if the affected status of the parents is unknown, and transmitted heterozygous variants from both parents will then be reported. Note that de novo variants are only reported by the dedicated analysis described in the paragraph below.

Supported input:

• Proband affected + Mother unaffected + Father unaffected
• Proband affected + Mother unaffected + Father affected
• Proband affected + Mother affected + Father unaffected

This disease is caused by a de novo mutation

Best practice filter cascade for identification of disease associated variants in the proband that are not present in any parent.

Supported input:

• Proband affected + Mother unaffected + Father unaffected

This disease is caused by a recessive compound heterozygous variant

Best practice filter cascade to identify recessive heterozygous variants present in the unaffected parents and transmitted to the proband in a compound heterozygous pattern, thus impacting both alleles of a gene associated with genetic disease.

Supported input:

• Proband affected + Mother unaffected + Father unaffected

This disease is caused by a recessive homozygous variant

Best practice filter cascade for identification of recessive variants present in both parents and transmitted to the proband, resulting in a homozygous variant that impacts both alleles of a gene associated with genetic disease.

Supported input:

• Proband affected + Mother unaffected + Father unaffected
• Proband affected + Mother unaffected + Father affected
• Proband affected + Mother affected + Father unaffected

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