A genotype calling algorithm for the Illumina BeadArray platform
Open accessAbstract
Motivation: Large-scale genotyping relies on the use of unsupervised automated calling algorithms to assign genotypes to hybridization data. A number of such calling algorithms have been recently established for the Affymetrix GeneChip genotyping technology. Here, we present a fast and accurate genotype calling algorithm for the Illumina BeadArray genotyping platforms. As the technology moves towards assaying millions of genetic polymorphisms simultaneously, there is a need for an integrated and easy-to-use software for calling genotypes. Results: We have introduced a model-based genotype calling algorithm which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm. By incorporating the process of perturbation analysis, we can obtain a quality metric measuring the stability of the assigned genotype calls. We show that this quality metric can be used to identify SNPs with low call rates and accuracy. Availability: The C++ executable for the algorithm described here is available by request from the authors. Contact: teo@well.ox.ac.uk or tgc@well.ox.ac.uk
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Stringent QC filters were applied separately to each of the 8 groups to remove poorly performing samples.
“As we used genotype data from multiple sources, it was important to apply stringent QC filters, as differential genotyping error rates between groups could result in spurious associations when the data are combined 50, 51.These filters were applied separately to each of these 8 groups to remove poorly performing samples using tools implemented in PLINK v1.0552.”
From Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease (2009) · cites this paper as [50]
The Results describe filtering poorly performing SNPs by call rate, and Methods §2.7 describes excluding unreliable SNP calls. Neither section reports applying QC filters separately to eight groups or removing poorly performing samples. In the citing sentence, the citation to this paper is attached to the preceding rationale about differential genotyping errors, not to the statement about the eight groups. (LLM, conf=0.77)
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- Authors
- Teo, Y. Y., Inouye, M., Small, K. S., Gwilliam, R., Deloukas, P., Kwiatkowski, D. P., & Clark, T. G.
- Affiliations
- Centre for Human Genetics (GB)
- 1 Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN and 2Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Corresponding author
- Teo, Yik Y.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-09-10
- Volume
- 23
- Issue
- 20
- Pages
- 2741-2746
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2666488
- OpenAlex
- W2119004823
- Cited by
- 216
- References
- 2
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 3 · 2023: 1 · 2022: 4 · 2021: 7 · 2020: 8 · 2019: 9 · 2018: 6 · 2017: 9 · 2016: 13 · 2015: 14 · 2014: 21 · 2013: 19 · 2012: 25
- FWCI
- 8.75
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Foundation for the National Institutes of Health
- Bill and Melinda Gates Foundation
- Wellcome Trust (077011, 082370)
- Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- genotype calling, SNP genotyping, perturbation analysis
- MeSH terms
- Algorithms, Chromosome Mapping, Genotype, Cluster Analysis, In Situ Hybridization, Fluorescence, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide
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