Estimating narrow-sense heritability using family data from admixed populations
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 r...
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ftuniaarhuspubl:oai:pure.atira.dk:publications/d088c88a-44d8-4455-9cc8-959dfff18a56 2023-10-01T03:56:21+02:00 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 2020 https://pure.au.dk/portal/da/publications/estimating-narrowsense-heritability-using-family-data-from-admixed-populations(d088c88a-44d8-4455-9cc8-959dfff18a56).html https://doi.org/10.1038/s41437-020-0311-2 http://www.scopus.com/inward/record.url?scp=85083242758&partnerID=8YFLogxK eng eng info:eu-repo/semantics/restrictedAccess 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 , vol. 124 , no. 6 , pp. 751-762 . https://doi.org/10.1038/s41437-020-0311-2 LINKAGE ANALYSIS MODEL SNP-BASED HERITABILITY TRAITS TRIAL article 2020 ftuniaarhuspubl https://doi.org/10.1038/s41437-020-0311-2 2023-09-06T22:58:47Z 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. Article in Journal/Newspaper Greenland greenlander* greenlandic Aarhus University: Research Greenland Heredity 124 6 751 762 |
institution |
Open Polar |
collection |
Aarhus University: Research |
op_collection_id |
ftuniaarhuspubl |
language |
English |
topic |
LINKAGE ANALYSIS MODEL SNP-BASED HERITABILITY TRAITS TRIAL |
spellingShingle |
LINKAGE ANALYSIS MODEL SNP-BASED HERITABILITY TRAITS TRIAL 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 |
topic_facet |
LINKAGE ANALYSIS MODEL SNP-BASED HERITABILITY TRAITS TRIAL |
description |
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. |
format |
Article in Journal/Newspaper |
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 |
author_facet |
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 |
author_sort |
Athanasiadis, Georgios |
title |
Estimating narrow-sense heritability using family data from admixed populations |
title_short |
Estimating narrow-sense heritability using family data from admixed populations |
title_full |
Estimating narrow-sense heritability using family data from admixed populations |
title_fullStr |
Estimating narrow-sense heritability using family data from admixed populations |
title_full_unstemmed |
Estimating narrow-sense heritability using family data from admixed populations |
title_sort |
estimating narrow-sense heritability using family data from admixed populations |
publishDate |
2020 |
url |
https://pure.au.dk/portal/da/publications/estimating-narrowsense-heritability-using-family-data-from-admixed-populations(d088c88a-44d8-4455-9cc8-959dfff18a56).html https://doi.org/10.1038/s41437-020-0311-2 http://www.scopus.com/inward/record.url?scp=85083242758&partnerID=8YFLogxK |
geographic |
Greenland |
geographic_facet |
Greenland |
genre |
Greenland greenlander* greenlandic |
genre_facet |
Greenland greenlander* greenlandic |
op_source |
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 , vol. 124 , no. 6 , pp. 751-762 . https://doi.org/10.1038/s41437-020-0311-2 |
op_rights |
info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1038/s41437-020-0311-2 |
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Heredity |
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124 |
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6 |
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