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AUTOGSCAN: Powerful Tools for Automated Genome-Wide Linkage and Linkage Disequilibrium Analysis

Published online by Cambridge University Press:  21 February 2012

Tero Hiekkalinna ,
Joseph D. Terwilliger ,
Sampo Sammalisto ,
Leena Peltonen  and
Markus Perola
Tero Hiekkalinna
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland.
Joseph D. Terwilliger
Affiliation:
Finnish Genome Center, University of Helsinki, Helsinki, Finland; Columbia Genome Center, Department of Psychiatry and Department of Genetics and Development, Columbia University, New York, United States of America; Division of Molecular Genetics, New York State Psychiatric Institute, New York, United States of America.
Sampo Sammalisto
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland; Department of Medical Genetics, University of Helsinki, Helsinki, Finland.
Leena Peltonen*
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, California, United States of America; Department of Medical Genetics, University of Helsinki, Helsinki, Finland. [email protected]
Markus Perola
Affiliation:
Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland; Department of Medical Genetics, University of Helsinki, Helsinki, Finland.
*
*Address for correspondence: Leena Peltonen, MD, PhD, Academy Professor, National Public Health Institute, Department of Molecular Medicine, PO Box 104, 00251 Helsinki, Finland.

Abstract

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Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense.

Type
Articles
Information
Twin Research and Human Genetics , Volume 8 , Issue 1 , 01 February 2005 , pp. 16 - 21
Copyright
Copyright © Cambridge University Press 2005