QTL-ALL

QTL-ALL performs quantitative trait locus (QTL) linkage analysis for nuclear family datasets, emphasizing score statistics for ascertained samples such as concordant and discordant sibling pairs.

Key Features:

• QTL linkage statistics: Calculates a diverse array of QTL linkage statistics, including LOD scores.
• Score statistic methodology: Implements score statistics tailored for ascertained samples (concordant and discordant sibling pairs).
• Data format support: Supports sib-pair and sibship data formats.
• Two-dimensional genome-wide strategy: Enables two-dimensional (pairwise) genome-wide linkage analysis.
• Polygenic effect detection: Facilitates identification of polygenic effects that contribute to complex traits.

Scientific Applications:

• Genome-wide linkage scans: Applied in genome-wide linkage scans for complex phenotypes.
• Type 2 diabetes mellitus (T2DM) studies: Used in an analysis of T2DM in 238 sib-pairs from American Samoa to investigate genetic variation and locus pairs including 11q22, 21q21, and 9q21.
• Adult height linkage: Detected linkage for variation in adult height on chromosome 9q31.
• Locus-pair discovery: Identified locus pairs (e.g., 11q22 and 21q21; 9q21 and 11q22) with maximum LOD scores exceeding 2.00 in a two-dimensional genome-wide scan.
• Candidate gene and pathway selection: Aids selection of candidate genes and molecular pathways by highlighting linked loci and polygenic effects.

Methodology:

Computes QTL linkage statistics and LOD scores, implements score statistic methodology for ascertained sibling pairs, accepts sib-pair and sibship formats, and performs two-dimensional genome-wide (pairwise) linkage analyses.