FastMap

FastMap performs rapid eQTL mapping in homozygous inbred populations by organizing single nucleotide polymorphisms (SNPs) into a Hamming distance-based tree to enable efficient single-marker and m-SNP haplotype association mapping with permutation-based significance testing for gene expression traits.

Key Features:

• Hamming Distance-Based Tree Structure: SNPs are organized into a tree based on Hamming distance to structure computations and exploit similarities between markers.
• Parent-Result Reuse Optimization: Each SNP's association calculation reuses its parent SNP's results to minimize arithmetic operations and reduce redundant computation.
• Single-Marker and Haplotype Mapping: Supports single marker association mapping and haplotype association mapping over an m-SNP window.
• Permutation-Based Significance Testing: Incorporates permutation testing to assess statistical significance and control for multiple testing in large-scale datasets.
• Scalability for High-Density Data: Handles datasets with up to 100,000 transcripts and between 100,000 and 1,000,000 genetic markers typical of high-density genotype data.
• Designed for Homozygous Inbred Data: Leverages binary allele calls common in homozygous inbred populations to improve computational efficiency.

Scientific Applications:

• eQTL mapping in inbred populations: Mapping expression quantitative trait loci in inbred mouse populations and other homozygous organisms where binary allele calls are prevalent.
• Identification of regulatory loci: Identifying genomic loci that regulate transcript expression by associating high-density genotype data with gene expression profiles.
• Genetic basis of complex traits: Investigating the genetic regulation underlying complex traits and disease-related expression changes.

Methodology:

SNPs are organized into a Hamming distance-based tree, each SNP association calculation reuses its parent node's results to reduce arithmetic operations, the program performs single-marker and m-SNP haplotype association mapping, and significance is assessed by permutation-based testing.