Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits
Open accessAbstract
Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.
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IBD-based heritability of baseline skin pigmentation in ‡Khomani and Nama is 0.97 ± 0.15.
“We then used the familial relationships (Figure S1) and population-level endogamy to estimate heritability from IBD sharing among all individuals in the ‡Khomani and Nama; we obtain a similar estimate of hIBD2=0.97±0.15 (Methods, see also (Zaitlen et al., 2013)).”
From An Unexpectedly Complex Architecture for Skin Pigmentation in Africans (2017) · cites this paper as Zaitlen et al., 2013
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- Authors
- Zaitlen, N., Kraft, P., Patterson, N., Pasaniuc, B., Bhatia, G., Pollack, S., & Price, A. L.
- Affiliations
- University of California, San Francisco (US)
- Broad Institute (US)
- Corresponding author
- Zaitlen, Noah
- Price, Alkes L.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-05-30
- Volume
- 9
- Issue
- 5
- Pages
- e1003520
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3667752
- OpenAlex
- W1729875372
- Cited by
- 32
- References
- 44
- Citations by year
- 2025: 3 · 2024: 4 · 2023: 3 · 2022: 6 · 2021: 4 · 2020: 2 · 2019: 3 · 2018: 3 · 2017: 4
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R03HG006731, R01HG006399, R03HG005732)
- National Institute of Environmental Health Sciences (T32ES007142)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Physical Performance
- Keywords
- heritability, phenotypic correlation, shared environment, narrow-sense heritability, common SNPs, rare alleles, genetic architecture, phenotypic traits
- MeSH terms
- Genealogy and Heraldry, Genotype, Humans, Iceland, Models, Genetic, Phenotype, Genetic Variation, Polymorphism, Single Nucleotide, Siblings, Quantitative Trait Loci, Heredity
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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