Subsampling Technique to Estimate Variance Component for UK-Biobank Traits
The estimation of heritability has been an important question in statistical genetics. Due to the clear mathematical properties, the modified Haseman–Elston regression has been found a bridge that connects and develops various parallel heritability estimation methods. With the increasing sample size...
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2021-03-01
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doaj-3fd8d257e1984e36a89ea55af69620612021-03-05T16:41:58ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-03-011210.3389/fgene.2021.612045612045Subsampling Technique to Estimate Variance Component for UK-Biobank TraitsTing Xu0Guo-An Qi1Jun Zhu2Hai-Ming Xu3Guo-Bo Chen4Guo-Bo Chen5Department of Mathematics, Zhejiang University, Hangzhou, ChinaDepartment of Agricultural and Biotechnology, Zhejiang University, Hangzhou, ChinaDepartment of Agricultural and Biotechnology, Zhejiang University, Hangzhou, ChinaDepartment of Agricultural and Biotechnology, Zhejiang University, Hangzhou, ChinaZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Clinical Research Institute, Hangzhou, ChinaKey Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, ChinaThe estimation of heritability has been an important question in statistical genetics. Due to the clear mathematical properties, the modified Haseman–Elston regression has been found a bridge that connects and develops various parallel heritability estimation methods. With the increasing sample size, estimating heritability for biobank-scale data poses a challenge for statistical computation, in particular that the calculation of the genetic relationship matrix is a huge challenge in statistical computation. Using the Haseman–Elston framework, in this study we explicitly analyzed the mathematical structure of the key term tr(KTK), the trace of high-order term of the genetic relationship matrix, a component involved in the estimation procedure. In this study, we proposed two estimators, which can estimate tr(KTK) with greatly reduced sampling variance compared to the existing method under the same computational complexity. We applied this method to 81 traits in UK Biobank data and compared the chromosome-wise partition heritability with the whole-genome heritability, also as an approach for testing polygenicity.https://www.frontiersin.org/articles/10.3389/fgene.2021.612045/fullpolygenicityUK Biobanksubsampling estimatoreffective number of markersHaseman-Elston regression |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ting Xu Guo-An Qi Jun Zhu Hai-Ming Xu Guo-Bo Chen Guo-Bo Chen |
spellingShingle |
Ting Xu Guo-An Qi Jun Zhu Hai-Ming Xu Guo-Bo Chen Guo-Bo Chen Subsampling Technique to Estimate Variance Component for UK-Biobank Traits Frontiers in Genetics polygenicity UK Biobank subsampling estimator effective number of markers Haseman-Elston regression |
author_facet |
Ting Xu Guo-An Qi Jun Zhu Hai-Ming Xu Guo-Bo Chen Guo-Bo Chen |
author_sort |
Ting Xu |
title |
Subsampling Technique to Estimate Variance Component for UK-Biobank Traits |
title_short |
Subsampling Technique to Estimate Variance Component for UK-Biobank Traits |
title_full |
Subsampling Technique to Estimate Variance Component for UK-Biobank Traits |
title_fullStr |
Subsampling Technique to Estimate Variance Component for UK-Biobank Traits |
title_full_unstemmed |
Subsampling Technique to Estimate Variance Component for UK-Biobank Traits |
title_sort |
subsampling technique to estimate variance component for uk-biobank traits |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-03-01 |
description |
The estimation of heritability has been an important question in statistical genetics. Due to the clear mathematical properties, the modified Haseman–Elston regression has been found a bridge that connects and develops various parallel heritability estimation methods. With the increasing sample size, estimating heritability for biobank-scale data poses a challenge for statistical computation, in particular that the calculation of the genetic relationship matrix is a huge challenge in statistical computation. Using the Haseman–Elston framework, in this study we explicitly analyzed the mathematical structure of the key term tr(KTK), the trace of high-order term of the genetic relationship matrix, a component involved in the estimation procedure. In this study, we proposed two estimators, which can estimate tr(KTK) with greatly reduced sampling variance compared to the existing method under the same computational complexity. We applied this method to 81 traits in UK Biobank data and compared the chromosome-wise partition heritability with the whole-genome heritability, also as an approach for testing polygenicity. |
topic |
polygenicity UK Biobank subsampling estimator effective number of markers Haseman-Elston regression |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.612045/full |
work_keys_str_mv |
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