ALG: Automated Genotype Calling of Luminex Assays

Mathieu Bourgey,Daniel Sinnett,Mathieu Lariviere,Chantal Richer,Pablo Villoslada

doi:10.1371/journal.pone.0019368

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 available for non-commercial use either at http://alg.sourceforge.net or by request to mathieu.bourgey@umontreal.ca

Highlights

A single nucleotide polymorphism (SNP) is a DNA sequence variation that occurs at a single nucleotide position in the genome
In response to the need for additional Luminex genotype calling software, we have developed the Automated Luminex Genotyping (ALG) software package that allows for extensive genotype calling from Luminex assays using either a friendly graphical user interface (GUI) or a command line interface in R
ALG was used to genotyped a set of 95 SNPs in a cohort consisting of 300 childhood acute lymphoblastic leukemia patients and 329 healthy controls from the province of Quebec

Summary

Introduction

A single nucleotide polymorphism (SNP) is a DNA sequence variation that occurs at a single nucleotide position in the genome. ALG is semi-automated, requiring no prior manual inspection of the microassay Luminex data, and provides numerical measures of confidence for each SNP called, as well as an effective graphical plot (Figure 2) of the data clustering for visualization, optimization or troubleshooting purposes.

Results

Conclusion