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Genomics. 2008 Jun;91(6):544-7. doi: 10.1016/j.ygeno.2008.02.001. Epub 2008 Apr 2.

LINKGEN: a new algorithm to process data in genetic linkage studies.

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1
Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Tessália Vieira de Camargo, Cidade Universitária Zeferino Vaz, Campinas SP, Brazil.

Abstract

Genetic linkage studies using whole genome scans are useful approaches for identifying genes related to human diseases. In general, these studies require genotyping of a large number of markers, which are used in statistical analysis. Recent technology has allowed easy genotyping of a large number of markers in less time; therefore, interface programs are required for manipulation of these large data sets. We present a new algorithm, which processes input data in LINKAGE format from data analyzed by automated genotyping systems. The algorithm was implemented in PERL script and R environment. Validation was performed with genotyped data from 127 individuals and 720 microsatellite markers of two whole genome scans. Our results showed a significant decrease in data processing time. In addition, this algorithm provides unbiased allele frequency estimation used for linkage analysis. LINKGEN is a freely available online tool and allows easier, faster, and reliable manipulation of large genotyping data sets.

PMID:
18378114
DOI:
10.1016/j.ygeno.2008.02.001
[Indexed for MEDLINE]
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