Conditions for the validity of SNP-based heritability estimation

James J. Lee, Carson C. Chow

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


The heritability of a trait (h2) is the proportion of its population variance caused by genetic differences, and estimates of this parameter are important for interpreting the results of genome-wide association studies (GWAS). In recent years, researchers have adopted a novel method for estimating a lower bound on heritability directly from GWAS data that uses realized genetic similarities between nominally unrelated individuals. The quantity estimated by this method is purported to be the contribution to heritability that could in principle be recovered from association studies employing the given panel of SNPs (hSNP2). Thus far, the validity of this approach has mostly been tested empirically. Here, we provide a mathematical explication and show that the method should remain a robust means of obtaining hSNP2 under circumstances wider than those under which it has so far been derived.

Original languageEnglish (US)
Pages (from-to)1011-1022
Number of pages12
JournalHuman Genetics
Issue number8
StatePublished - Aug 2014

Bibliographical note

Funding Information:
Acknowledgments We thank Doug speed and Xiang Zhou for answering our queries. this work was supported by the Intramural Program of the nIH, the national Institute of Diabetes and Digestive and Kidney Diseases (nIDDK). assistance with phenotype harmonization and genotype cleaning, as well as with general study coordination, was provided by the Gene environment association studies, Geneva Coordinating Center (U01 HG004446). assistance with data cleaning was provided by the national Center for Biotechnology Information.


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