Please use this identifier to cite or link to this item:
http://hdl.handle.net/2445/69341
Title: | Statistical inference for hardy-weinberg proportions in the presence of missing genotype information |
Author: | Graffelman, Jan Sánchez, Milagros Cook, Samantha Moreno Aguado, Víctor |
Keywords: | Genoma humà Estadística matemàtica Malalties hereditàries Human genome Mathematical statistics Genetic diseases |
Issue Date: | 31-Dec-2013 |
Publisher: | Public Library of Science (PLoS) |
Abstract: | In genetic association studies, tests for Hardy-Weinberg proportions are often employed as a quality control checking procedure. Missing genotypes are typically discarded prior to testing. In this paper we show that inference for Hardy-Weinberg proportions can be biased when missing values are discarded. We propose to use multiple imputation of missing values in order to improve inference for Hardy-Weinberg proportions. For imputation we employ a multinomial logit model that uses information from allele intensities and/or neighbouring markers. Analysis of an empirical data set of single nucleotide polymorphisms possibly related to colon cancer reveals that missing genotypes are not missing completely at random. Deviation from Hardy-Weinberg proportions is mostly due to a lack of heterozygotes. Inbreeding coefficients estimated by multiple imputation of the missings are typically lowered with respect to inbreeding coefficients estimated by discarding the missings. Accounting for missings by multiple imputation qualitatively changed the results of 10 to 17% of the statistical tests performed. Estimates of inbreeding coefficients obtained by multiple imputation showed high correlation with estimates obtained by single imputation using an external reference panel. Our conclusion is that imputation of missing data leads to improved statistical inference for Hardy-Weinberg proportions. |
Note: | Reproducció del document publicat a: http://dx.doi.org/10.1371/journal.pone.0083316 |
It is part of: | PLoS One, 2013, vol. 8, num. 12, p. e83316 |
URI: | http://hdl.handle.net/2445/69341 |
Related resource: | http://dx.doi.org/10.1371/journal.pone.0083316 |
ISSN: | 1932-6203 |
Appears in Collections: | Articles publicats en revistes (Ciències Clíniques) Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL)) |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
636500.pdf | 659.21 kB | Adobe PDF | View/Open |
This item is licensed under a Creative Commons License