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dc.contributor.authorRitchie, ME
dc.contributor.authorLiu, R
dc.contributor.authorCarvalho, BS
dc.contributor.authorIrizarry, RA
dc.date.available2016-03-03T01:18:06Z
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.available2011-03-08
dc.date.issued2011-03-08
dc.identifierpii: 1471-2105-12-68
dc.identifier.citationRitchie, M. E., Liu, R., Carvalho, B. S. & Irizarry, R. A. (2011). Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC BIOINFORMATICS, 12 (1), https://doi.org/10.1186/1471-2105-12-68.
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11343/59103
dc.description.abstractBACKGROUND: Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. RESULTS: In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics. CONCLUSIONS: CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.
dc.languageEnglish
dc.publisherBMC
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleComparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
dc.typeJournal Article
dc.identifier.doi10.1186/1471-2105-12-68
melbourne.affiliation.departmentMedicine, Dentistry & Health Sciences
melbourne.affiliation.departmentFlorey Department of Neuroscience and Mental Health
melbourne.affiliation.departmentMelbourne Medical School
melbourne.affiliation.departmentEducation Unit, MDHS
melbourne.affiliation.departmentRadiology
melbourne.affiliation.departmentMedicine (RMH)
melbourne.affiliation.departmentSchool of Biomedical Sciences
melbourne.affiliation.departmentAnatomy and Neuroscience
melbourne.affiliation.departmentCentre for Neuroscience
melbourne.affiliation.departmentPathology
melbourne.affiliation.departmentMedical Biology
melbourne.affiliation.departmentAgriculture and Food Systems
melbourne.source.titleBMC Bioinformatics
melbourne.source.volume12
melbourne.source.issue1
dc.rights.licenseCC BY
melbourne.elementsid332183
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063825
melbourne.contributor.authorRitchie, Matthew
melbourne.contributor.authorKilpatrick, Trevor
melbourne.contributor.authorPerreau, Victoria
melbourne.contributor.authorRubio, Justin
melbourne.contributor.authorField, Judith
melbourne.contributor.authorWILKINS, ELLA
melbourne.contributor.authorJENSEN, CATHY
melbourne.contributor.authorJOHNSON, LAURA
melbourne.contributor.authorButzkueven, Helmut
melbourne.contributor.authorWiley, James
melbourne.contributor.authorBahlo, Melanie
dc.identifier.eissn1471-2105
melbourne.accessrightsOpen Access


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