Statistical adjustment of genotyping error in a case-control study of childhood leukaemia.
Background: Genotyping has become more cost-effective and less invasive with the use of buccal cell sampling. However, low or fragmented DNA yields from buccal cells collected using FTA cards often requires additional whole genome amplification to produce sufficient DNA for genotyping. In our case-c...
| Published in: | BMC Medical Research Methodology Vol. 12; no. 1; pp. 141 - 142 |
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| Main Authors: | , , , , , , , |
| Format: | research Journal Article |
| Published: |
BioMed Central
2012
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104390141&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104390141 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 14712288 1CI1 jtl: BMC Medical Research Methodology issn: 14712288 maglogo: N pubinfo: dt: 2012 vid: 12 iid: 1 pid: 24147 pub: BioMed Central artinfo: ui: 104390141 NLM22970889 2011777582 10.1186/1471-2288-12-141 NLM22970889 PMC3514307 104390141 ppf: 141 ppct: 1 formats: tig: atl: Statistical adjustment of genotyping error in a case-control study of childhood leukaemia. aug: au: Cooper, Matthew N de Klerk, Nicholas H Greenop, Kathryn R Jamieson, Sarra E Anderson, Denise van Bockxmeer, Frank M Armstrong, Bruce K Milne, Elizabeth affil: Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, P,O, Box 855, West Perth, 6872, WA, Australia. mcooper@ichr.uwa.edu.au. sug: subj: DNA Leukemia Diagnosis Case Control Studies Child DNA Fingerprinting Methods Diagnostic Errors Female Genetics Genetic Techniques Human Leukemia Male Reagent Kits, Diagnostic Child: 6-12 years Female Male ab: Background: Genotyping has become more cost-effective and less invasive with the use of buccal cell sampling. However, low or fragmented DNA yields from buccal cells collected using FTA cards often requires additional whole genome amplification to produce sufficient DNA for genotyping. In our case-control study of childhood leukaemia, discordance was found between genotypes derived from blood and whole genome amplified FTA buccal DNA samples. We aimed to develop a user-friendly method to correct for this genotype misclassification, as existing methods were not suitable for use in our study.Methods: Discordance between the results of blood and buccal-derived DNA was assessed in childhood leukaemia cases who had both blood and FTA buccal samples. A method based on applying misclassification probabilities to measured data and combining results using multiple imputations, was devised to correct for error in the genotypes of control subjects, for whom only buccal samples were available, to minimize bias in the odds ratios in the case-control analysis.Results: Application of the correction method to synthetic datasets showed it was effective in producing correct odds ratios from data with known misclassification. Moreover, when applied to each of six bi-allelic loci, correction altered the odds ratios in the logically anticipated manner given the degree and direction of the misclassification revealed by the investigations in cases. The precision of the effect estimates decreased with decreasing size of the misclassification data set.Conclusions: Bias arising from differential genotype misclassification can be reduced by correcting results using this method whenever data on concordance of genotyping results with those from a different and probably better DNA source are available. pubtype: Academic Journal doctype: research Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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