Abstract
Genome-wide association studies have been made possible because of advancements in the design of genotyping technologies to assay a million or more single nucleotide polymorphisms (SNPs) simultaneously. This has resulted in the introduction of automated and unsupervised statistical approaches for translating the probe hybridization intensities into the actual genotype calls. This chapter aims to provide an introduction to this process of genotype calling, highlighting in particular the design and approach used for the Illumina BeadArray platforms that are commonly used in large-scale genetic studies. The chapter also provides detailed instructions for preparing the input files required as well as the actual Linux commands and options to execute the ILLUMINUS software. Finally, it concludes with a brief exposition on the different outcomes from genotype calling and the use of perturbation analysis for identifying SNPs with erroneous genotype calls.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Di X, et al (2005) Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics 21: 1958–1963
Affymetrix Inc (2006) BRLMM: an improved genotype calling method for the GeneChip Human Mapping 500K Array Set http://media.affymetrix.com/support/technical/whitepapers/brlmm_whitepaper.pdf
Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678
Plagnol V, et al (2007) A method to address differential bias in genotyping in large-scale association studies. PLoS Genet 3: e74
Teo YY, et al (2007) A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics 23: 2741–2746
Illumina Inc (2005) Illumina GenCall data analysis software http://www.illumina.com/Documents/products/technotes/technote_gencall_data_analysis_software.pdf
Korn JM, et al (2008) Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 40: 1253–1260
Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Amer J Hum Genet 84: 210–223
Yu Z, et al (2009) Genotype determination for polymorphisms in linkage disequilibrium. BMC Bioinformatics 10: 63
Bolstad BM, et al (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193
Rabbee N, Speed TP (2006) A genotype calling algorithm for Affymetrix SNP arrays. Bioinformatics 22: 7–12
Carvalho B, et al (2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8: 485–499
Xiao Y, et al (2007) A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays. Bioinformatics 23: 1459–1467
Gunderson KL, et al (2006) Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 7: 641–648
Steemers FJ, et al (2006) Whole-genome genotyping with the single-base extension assay. Nat Methods 3: 31–33
Kermani BG (2005) Artificial intelligence and global normalization methods for genotyping. US Patent 20060224529
Teo YY, et al (2008) Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies. Ann Hum Genet 72: 368–374
Teo YY, et al (2007) On the usage of HWE for identifying genotyping errors. Ann Hum Genet 71: 701–703
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Teo, Y.Y. (2012). Genotype Calling for the Illumina Platform. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_29
Download citation
DOI: https://doi.org/10.1007/978-1-61779-555-8_29
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-554-1
Online ISBN: 978-1-61779-555-8
eBook Packages: Springer Protocols