AUTHOR=Xu Ting , Qi Guo-An , Zhu Jun , Xu Hai-Ming , Chen Guo-Bo 

TITLE=Subsampling Technique to Estimate Variance Component for UK-Biobank Traits

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.612045

DOI=10.3389/fgene.2021.612045

ISSN=1664-8021

ABSTRACT=<p>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 <italic>tr</italic>(<bold><italic>K</italic></bold><sup><italic>T</italic></sup><bold><italic>K</italic></bold>), 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 <italic>tr</italic>(<bold><italic>K</italic></bold><sup><italic>T</italic></sup><bold><italic>K</italic></bold>) 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.</p>