Estimating narrow-sense heritability using family data from admixed populations

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Standard

Estimating narrow-sense heritability using family data from admixed populations. / Athanasiadis, Georgios; Speed, Doug; Andersen, Mette K; Appel, Emil V R; Grarup, Niels; Brandslund, Ivan; Jørgensen, Marit Eika; Larsen, Christina Viskum Lytken; Bjerregaard, Peter; Hansen, Torben; Albrechtsen, Anders.

In: Heredity, Vol. 124, No. 6, 2020, p. 751-762.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Athanasiadis, G, Speed, D, Andersen, MK, Appel, EVR, Grarup, N, Brandslund, I, Jørgensen, ME, Larsen, CVL, Bjerregaard, P, Hansen, T & Albrechtsen, A 2020, 'Estimating narrow-sense heritability using family data from admixed populations', Heredity, vol. 124, no. 6, pp. 751-762. https://doi.org/10.1038/s41437-020-0311-2

APA

Athanasiadis, G., Speed, D., Andersen, M. K., Appel, E. V. R., Grarup, N., Brandslund, I., Jørgensen, M. E., Larsen, C. V. L., Bjerregaard, P., Hansen, T., & Albrechtsen, A. (2020). Estimating narrow-sense heritability using family data from admixed populations. Heredity, 124(6), 751-762. https://doi.org/10.1038/s41437-020-0311-2

CBE

Athanasiadis G, Speed D, Andersen MK, Appel EVR, Grarup N, Brandslund I, Jørgensen ME, Larsen CVL, Bjerregaard P, Hansen T, Albrechtsen A. 2020. Estimating narrow-sense heritability using family data from admixed populations. Heredity. 124(6):751-762. https://doi.org/10.1038/s41437-020-0311-2

MLA

Vancouver

Athanasiadis G, Speed D, Andersen MK, Appel EVR, Grarup N, Brandslund I et al. Estimating narrow-sense heritability using family data from admixed populations. Heredity. 2020;124(6):751-762. https://doi.org/10.1038/s41437-020-0311-2

Author

Athanasiadis, Georgios ; Speed, Doug ; Andersen, Mette K ; Appel, Emil V R ; Grarup, Niels ; Brandslund, Ivan ; Jørgensen, Marit Eika ; Larsen, Christina Viskum Lytken ; Bjerregaard, Peter ; Hansen, Torben ; Albrechtsen, Anders. / Estimating narrow-sense heritability using family data from admixed populations. In: Heredity. 2020 ; Vol. 124, No. 6. pp. 751-762.

Bibtex

@article{d088c88a44d844559cc8959dfff18a56,
title = "Estimating narrow-sense heritability using family data from admixed populations",
abstract = "Estimating total narrow-sense heritability in admixed populations remains an open question. In this work, we used extensive simulations to evaluate existing linear mixed-model frameworks for estimating total narrow-sense heritability in two population-based cohorts from Greenland, and compared the results with data from unadmixed individuals from Denmark. When our analysis focused on Greenlandic sib pairs, and under the assumption that shared environment among siblings has a negligible effect, the model with two relationship matrices, one capturing identity by descent and one capturing identity by state, returned heritability estimates close to the true simulated value, while using each of the two matrices alone led to downward biases. When phenotypes correlated with ancestry, heritability estimates were inflated. Based on these observations, we propose a PCA-based adjustment that recovers the true simulated heritability. We use this knowledge to estimate the heritability of ten quantitative traits from the two Greenlandic cohorts, and report differences such as lower heritability for height in Greenlanders compared with Europeans. In conclusion, narrow-sense heritability in admixed populations is best estimated when using a mixture of genetic relationship matrices on individuals with at least one first-degree relative included in the sample.",
keywords = "LINKAGE ANALYSIS, MODEL, SNP-BASED HERITABILITY, TRAITS, TRIAL",
author = "Georgios Athanasiadis and Doug Speed and Andersen, {Mette K} and Appel, {Emil V R} and Niels Grarup and Ivan Brandslund and J{\o}rgensen, {Marit Eika} and Larsen, {Christina Viskum Lytken} and Peter Bjerregaard and Torben Hansen and Anders Albrechtsen",
year = "2020",
doi = "10.1038/s41437-020-0311-2",
language = "English",
volume = "124",
pages = "751--762",
journal = "Heredity",
issn = "0018-067X",
publisher = "Nature Publishing Group",
number = "6",

}

RIS

TY - JOUR

T1 - Estimating narrow-sense heritability using family data from admixed populations

AU - Athanasiadis, Georgios

AU - Speed, Doug

AU - Andersen, Mette K

AU - Appel, Emil V R

AU - Grarup, Niels

AU - Brandslund, Ivan

AU - Jørgensen, Marit Eika

AU - Larsen, Christina Viskum Lytken

AU - Bjerregaard, Peter

AU - Hansen, Torben

AU - Albrechtsen, Anders

PY - 2020

Y1 - 2020

N2 - Estimating total narrow-sense heritability in admixed populations remains an open question. In this work, we used extensive simulations to evaluate existing linear mixed-model frameworks for estimating total narrow-sense heritability in two population-based cohorts from Greenland, and compared the results with data from unadmixed individuals from Denmark. When our analysis focused on Greenlandic sib pairs, and under the assumption that shared environment among siblings has a negligible effect, the model with two relationship matrices, one capturing identity by descent and one capturing identity by state, returned heritability estimates close to the true simulated value, while using each of the two matrices alone led to downward biases. When phenotypes correlated with ancestry, heritability estimates were inflated. Based on these observations, we propose a PCA-based adjustment that recovers the true simulated heritability. We use this knowledge to estimate the heritability of ten quantitative traits from the two Greenlandic cohorts, and report differences such as lower heritability for height in Greenlanders compared with Europeans. In conclusion, narrow-sense heritability in admixed populations is best estimated when using a mixture of genetic relationship matrices on individuals with at least one first-degree relative included in the sample.

AB - Estimating total narrow-sense heritability in admixed populations remains an open question. In this work, we used extensive simulations to evaluate existing linear mixed-model frameworks for estimating total narrow-sense heritability in two population-based cohorts from Greenland, and compared the results with data from unadmixed individuals from Denmark. When our analysis focused on Greenlandic sib pairs, and under the assumption that shared environment among siblings has a negligible effect, the model with two relationship matrices, one capturing identity by descent and one capturing identity by state, returned heritability estimates close to the true simulated value, while using each of the two matrices alone led to downward biases. When phenotypes correlated with ancestry, heritability estimates were inflated. Based on these observations, we propose a PCA-based adjustment that recovers the true simulated heritability. We use this knowledge to estimate the heritability of ten quantitative traits from the two Greenlandic cohorts, and report differences such as lower heritability for height in Greenlanders compared with Europeans. In conclusion, narrow-sense heritability in admixed populations is best estimated when using a mixture of genetic relationship matrices on individuals with at least one first-degree relative included in the sample.

KW - LINKAGE ANALYSIS

KW - MODEL

KW - SNP-BASED HERITABILITY

KW - TRAITS

KW - TRIAL

UR - http://www.scopus.com/inward/record.url?scp=85083242758&partnerID=8YFLogxK

U2 - 10.1038/s41437-020-0311-2

DO - 10.1038/s41437-020-0311-2

M3 - Journal article

C2 - 32273574

VL - 124

SP - 751

EP - 762

JO - Heredity

JF - Heredity

SN - 0018-067X

IS - 6

ER -