Some Capabilities for Model-Based and Model-Free Linkage Analysis using the Program Package S.A.G.E. (Statistical Analysis for Genetic Epidemiology)

Abstract

For both model-free and model-based linkage analysis the S.A.G.E. (Statistical Analysis for Genetic Epidemiology) program package has some unique capabilities in analyzing both continuous traits and binary traits with variable age of onset. Here we highlight model-based linkage analysis of a quantitative trait (plasma dopamine β hydroxylase) that is known to be largely determined by monogenic inheritance, using a prior segregation analysis to produce the best fitting model for the trait. For a binary trait with variable age of onset (schizophrenia), we illustrate how using age of onset information to obtain a quantitative susceptibility trait leads to more statistically significant linkage signals, suggesting better power.

Familial Correlation of Retinal Vascular Caliber in Singapore Chinese

“…(Statistical Analysis for Genetic Epidemiology; Statistical Solutions, Ltd., Cork, Ireland) computer software program package. [26][27][28][29] To obtain estimates of familial correlations adjusted for covariates, phenotypic residuals from regression models were used as input. Linear regressions were performed using STATA software, version 12.1 (STATA Corp., College Station, TX), with each phenotype as a dependent variable and covariates as independent variables.…”

PLXNA4 is associated with Alzheimer disease and modulates tau phosphorylation

“…20, 21 Propensity scores were obtained for unaffected family members using the AGEON program in S.A.G.E. (v6.2) 22 as the probability of getting disease conditioned on affection status and censoring age of their parents. Affection status for AD cases (probability=1) was retained in the model.…”

Model‐Free Tests for Genetic Linkage

“…program AGEON obtains maximum likelihood estimates of the parameters that determine "susceptibility" to disease as a function of age, producing a quantitative susceptibility trait for each individual that can be used as the trait data in SIBPAL (Dawson et al, 1990).Using the S.A.G.E. program AGEON to obtain estimates for the susceptibility to disease this way, and using these estimates as the trait values in SIBPAL, may lead to more power (Schnell et al, 2011).…”