Mendelian

Mendelian implements heuristic variant filtering as an R-package for whole-exome sequencing variant datasets to identify candidate disease-causing variants across species.

Key Features:

• Versatility Across Species: Species-independent operation allowing analysis of datasets from diverse organisms beyond traditional model species.
• Support for Multiple Inheritance Models: Accommodates recessive and dominant inheritance models with variable degrees of penetrance and detectability.
• Trios Analysis: Supports analysis of trio data (two parents and one offspring) to evaluate inherited variant transmission.
• Database Filtering and Annotation: Filters against variant databases and supports variant annotation to distinguish common polymorphisms from potentially pathogenic variants.
• Parallel Computation Support: Leverages parallel computation to accelerate processing of large whole-exome sequencing variant datasets.

Scientific Applications:

• Human intellectual disability: Reanalysis of whole-exome sequencing data related to intellectual disability to identify relevant genetic variants.
• Canine coat color genetics: Identification of mutations responsible for coat color in dogs from whole-exome sequencing data without prior mapping.

Methodology:

Sequential heuristic filters are applied to large variant datasets, integrating database filtering and variant annotation; the implementation supports analysis of trio data and models of recessive and dominant inheritance with variable penetrance and detectability and can leverage parallel computation.