Statistical Programming Core Miller School of Medicine

Contact Information

For more information or to request a quote, contact us. We welcome all inquiries and look forward to serving your research needs.

Phone: 305-243-5248 Email

The Statistical Programming Core is led by Michael Schmidt Ph.D., with expertise in commercial software development, and QA engineering methods. Dr. Schmidt is involved in the software development and in the implementation of automated testing procedures for new statistical methods. His areas of interest include genetic simulations software, analysis programs and parallel processing. He was instrumental in the development of our in-house software’s and methods, which are maintained by the division and made easily accessible to the genetic research community.

SIMLA Simulation Software
PDT Analysis Program v 5.1
Combined Association in the Presence of Linkage (CAPL)
Extended Multifactor Dimensionality Reduction (EMDR), MDR-PDT and MDR-phenomics

SIMLA Simulation Software

SIMLA is a SIMulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.1 is a major upgrade to version 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

The SIBLINK program performs linkage analysis on affected sib-pairs.

PDT Analysis Program v 5.1

The Pedigree Disequilibrium Test (PDT) analysis program allows the user to test for linkage and association in general pedigree data. In addition to allele- and genotype- specific analysis of individual markers, PDT version 5.1 adds the ability to perform genotype – specific analysis over marker sets (Solaris, Linux, Windows). The extension versions allow for genotype association analysis (geno-PDT) and multi-locus effect estimate 9multi-locus geno-PDT).

Combined Association in the Presence of Linkage (CAPL)

CAPL is a C++ program that provides a novel test for association in the presence of linkage using general pedigree data and accounts for population stratification. The CAPL takes advantage of modern multicore hardware architecture. Recently a function for analysis of X-linked markers was added.

Extended Multifactor Dimensionality Reduction (EMDR, MDR-PDT and MDR-phenomics)

EMDR and MDR-PDT are extensions of MDR, which is a model-free non-parametric method for identifying and characterizing gene-gene effect influencing complex diseases. These methods are more powerful for detecting high order gene-gene or gene-environment interactions in both family-based and case-control studies than traditional parametric methods.

MDR-Phenomics was developed to test for high-order interaction with the consideration of genetic heterogeneity. It inherits the advantages from MDR that no assumptions of genetic models are required and that high dimensionality can be processed by reductions. It also improves the power by integration of phenotypic covariate analysis.

SIMLA Simulation Software

SIMLA is a SIMulation program that generates data sets of families for use in linkage and association studies. SIMLA_3.1 is a major upgrade to version 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

The SIBLINK program performs linkage analysis on affected sib-pairs.
PDT Analysis Program v 5.1

The Pedigree Disequilibrium Test (PDT) analysis program allows the user to test for linkage and association in general pedigree data. In addition to allele- and genotype- specific analysis of individual markers, PDT version 5.1 adds the ability to perform genotype – specific analysis over marker sets (Solaris, Linux, Windows). The extension versions allow for genotype association analysis (geno-PDT) and multi-locus effect estimate 9multi-locus geno-PDT).
Combined Association in the Presence of Linkage (CAPL)

CAPL is a C++ program that provides a novel test for association in the presence of linkage using general pedigree data and accounts for population stratification. The CAPL takes advantage of modern multicore hardware architecture. Recently a function for analysis of X-linked markers was added.
Extended Multifactor Dimensionality Reduction (EMDR, MDR-PDT and MDR-phenomics)

EMDR and MDR-PDT are extensions of MDR, which is a model-free non-parametric method for identifying and characterizing gene-gene effect influencing complex diseases. These methods are more powerful for detecting high order gene-gene or gene-environment interactions in both family-based and case-control studies than traditional parametric methods.

MDR-Phenomics was developed to test for high-order interaction with the consideration of genetic heterogeneity. It inherits the advantages from MDR that no assumptions of genetic models are required and that high dimensionality can be processed by reductions. It also improves the power by integration of phenotypic covariate analysis.