Alohomora

Alohomora streamlines genome-wide linkage studies using high-density single nucleotide polymorphism (SNP) marker panels.

Key Features:

• Platform compatibility: Accepts genotype data from platforms such as the Affymetrix GeneChip(R) Human Mapping 10K Array and other high-density SNP arrays.
• Data conversion and quality control: Converts genotype data into formats compatible with common linkage analysis programs and applies rigorous quality-control routines.
• Versatile linkage analysis: Implements linkage scans for small and large family datasets across any genetic model.
• Customization: Allows use of different genetic maps and ethnicity-specific allele frequencies.
• Graphical outputs: Produces whole-genome multipoint LOD score graphics for entire datasets and for individual families.
• Implementation: Written in Perl.

Scientific Applications:

• Detection of linkage regions: Identifies genomic regions linked to heritable traits or diseases using dense SNP marker panels.
• Analysis of complex traits: Enables genome-wide linkage analysis of large-scale SNP data to investigate the genetic architecture of complex traits.

Methodology:

Genotype data from high-density SNP arrays are converted into formats for linkage analysis; standard quality-control routines are applied; linkage scans are performed with customizable parameters across genetic models and using population-specific allele frequencies and genetic maps; results are output as whole-genome multipoint LOD score graphics for datasets and individual families.