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alg automated genotype calling of luminex assaysalg自动化luminex化验基因型的职业
ALG: Automated Genotype Calling of Luminex Assays
1 1 1 1,2
Mathieu Bourgey , Mathieu Lariviere , Chantal Richer , Daniel Sinnett *
1 Sainte-Justine Hospital Research Center, University of Montreal, Montreal, Quebec, Canada, 2 Department of Pediatrics, Faculty of Medicine, University of Montreal,
Montreal, Quebec, Canada
Abstract
Single nucleotide polymorphisms (SNPs) are the most commonly used polymorphic markers in genetics studies. Among the
different platforms for SNP genotyping, Luminex is one of the less exploited mainly due to the lack of a robust (semi-
automated and replicable) freely available genotype calling software. Here we describe a clustering algorithm that provides
automated SNP calls for Luminex genotyping assays. We genotyped 3 SNPs in a cohort of 330 childhood leukemia patients,
200 parents of patient and 325 healthy individuals and used the Automated Luminex Genotyping (ALG) algorithm for SNP
calling. ALG genotypes were called twice to test for reproducibility and were compared to sequencing data to test for
accuracy. Globally, this analysis demonstrates the accuracy (99.6%) of the method, its reproducibility (99.8%) and the low
level of no genotyping calls (3.4%). The high efficiency of the method proves that ALG is a suitable alternative to the current
commercial software. ALG is semi-automated, and provides numerical measures of confidence for each SNP called, as well
as an effective graphical plot. Moreover ALG can be used either through a graphical user interface, requiring no specific
informatics knowledge, or through command line with access to the open source code. The ALG software has been
implemented in R and is freely av
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