BIGFAM - variance components analysis from relatives without genotype
Abstract Estimating variance components of phenotypes provides a fundamental basis for understanding complex traits. However, most existing methods require genotype data, which is costly to obtain and often unavailable, limiting their scalability. To address this limitation, we developed BIGFAM, a g...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60502-0 |
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| _version_ | 1849334449538334720 |
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| author | Jaeeun Jerry Lee Buhm Han |
| author_facet | Jaeeun Jerry Lee Buhm Han |
| author_sort | Jaeeun Jerry Lee |
| collection | DOAJ |
| description | Abstract Estimating variance components of phenotypes provides a fundamental basis for understanding complex traits. However, most existing methods require genotype data, which is costly to obtain and often unavailable, limiting their scalability. To address this limitation, we developed BIGFAM, a genotype-free framework that estimates variance components by genetic, shared environmental, and X chromosome effects using only phenotype data from relative pairs. We analyze variance components in Generation Scotland and UK Biobank datasets and demonstrate that BIGFAM’s estimates show high correlation with genotype-based methods ( $$r$$ r = 0.85 for heritability and 0.64 for X chromosome components). We identify strong nuclear-family-specific shared environmental effects in dietary-related phenotypes. These results establish a new approach for analyzing variance components across diverse populations without the need for genetic data. |
| format | Article |
| id | doaj-art-2e0db93c1448446896986fbdca68f338 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-2e0db93c1448446896986fbdca68f3382025-08-20T03:45:33ZengNature PortfolioNature Communications2041-17232025-07-0116111410.1038/s41467-025-60502-0BIGFAM - variance components analysis from relatives without genotypeJaeeun Jerry Lee0Buhm Han1Interdisciplinary Program in Bioengineering, Seoul National UniversityInterdisciplinary Program in Bioengineering, Seoul National UniversityAbstract Estimating variance components of phenotypes provides a fundamental basis for understanding complex traits. However, most existing methods require genotype data, which is costly to obtain and often unavailable, limiting their scalability. To address this limitation, we developed BIGFAM, a genotype-free framework that estimates variance components by genetic, shared environmental, and X chromosome effects using only phenotype data from relative pairs. We analyze variance components in Generation Scotland and UK Biobank datasets and demonstrate that BIGFAM’s estimates show high correlation with genotype-based methods ( $$r$$ r = 0.85 for heritability and 0.64 for X chromosome components). We identify strong nuclear-family-specific shared environmental effects in dietary-related phenotypes. These results establish a new approach for analyzing variance components across diverse populations without the need for genetic data.https://doi.org/10.1038/s41467-025-60502-0 |
| spellingShingle | Jaeeun Jerry Lee Buhm Han BIGFAM - variance components analysis from relatives without genotype Nature Communications |
| title | BIGFAM - variance components analysis from relatives without genotype |
| title_full | BIGFAM - variance components analysis from relatives without genotype |
| title_fullStr | BIGFAM - variance components analysis from relatives without genotype |
| title_full_unstemmed | BIGFAM - variance components analysis from relatives without genotype |
| title_short | BIGFAM - variance components analysis from relatives without genotype |
| title_sort | bigfam variance components analysis from relatives without genotype |
| url | https://doi.org/10.1038/s41467-025-60502-0 |
| work_keys_str_mv | AT jaeeunjerrylee bigfamvariancecomponentsanalysisfromrelativeswithoutgenotype AT buhmhan bigfamvariancecomponentsanalysisfromrelativeswithoutgenotype |