Accounting for heteroscedasticity and censoring in chromosome partitioning analyses

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dc.contributor.author Kemppainen, Petri
dc.contributor.author Husby, Arild
dc.date.accessioned 2019-02-28T10:05:01Z
dc.date.available 2019-02-28T10:05:01Z
dc.date.issued 2018-12
dc.identifier.citation Kemppainen , P & Husby , A 2018 , ' Accounting for heteroscedasticity and censoring in chromosome partitioning analyses ' , Evolution Letters , vol. 2 , no. 6 , pp. 599-609 . https://doi.org/10.1002/evl3.88
dc.identifier.other PURE: 122780632
dc.identifier.other PURE UUID: 01fded7c-91c1-4c2a-9924-caa64035eacf
dc.identifier.other WOS: 000452990000006
dc.identifier.other ORCID: /0000-0003-1911-8351/work/54791796
dc.identifier.uri http://hdl.handle.net/10138/299699
dc.description.abstract A fundamental assumption in quantitative genetics is that traits are controlled by many loci of small effect. Using genomic data, this assumption can be tested using chromosome partitioning analyses, where the proportion of genetic variance for a trait explained by each chromosome (h(c)(2)), is regressed on its size. However, as h(c)(2)-estimates are necessarily positive (censoring) and the variance increases with chromosome size (heteroscedasticity), two fundamental assumptions of ordinary least squares (OLS) regression are violated. Using simulated and empirical data we demonstrate that these violations lead to incorrect inference of genetic architecture. The degree of bias depends mainly on the number of chromosomes and their size distribution and is therefore specific to the species; using published data across many different species we estimate that not accounting for this effect overall resulted in 28% false positives. We introduce a new and computationally efficient resampling method that corrects for inflation caused by heteroscedasticity and censoring and that works under a large range of dataset sizes and genetic architectures in empirical datasets. Our new method substantially improves the robustness of inferences from chromosome partitioning analyses. en
dc.format.extent 11
dc.language.iso eng
dc.relation.ispartof Evolution Letters
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject Chromosome partitioning
dc.subject heritability
dc.subject infinitesimal model
dc.subject genomic relatedness
dc.subject GCTA
dc.subject SNP heritability
dc.subject GENOME-WIDE ASSOCIATION
dc.subject GENETIC ARCHITECTURE
dc.subject MISSING HERITABILITY
dc.subject QUANTITATIVE TRAITS
dc.subject COMMON SNPS
dc.subject CHALLENGES
dc.subject SCHIZOPHRENIA
dc.subject PROPORTION
dc.subject DISSECTION
dc.subject SIZE
dc.subject 219 Environmental biotechnology
dc.title Accounting for heteroscedasticity and censoring in chromosome partitioning analyses en
dc.type Article
dc.contributor.organization External Funding
dc.contributor.organization Ecological Genetics Research Unit
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1002/evl3.88
dc.relation.issn 2056-3744
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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