Linear mixed model for heritability estimation that explicitly addresses environmental variation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 113, Issue 27, 2016, Pages 7377-7382

  Heckerman, David ^a   Gurdasani, Deepti ^b,c   Kadie, Carl ^a   Pomilla, Cristina ^b,c   Carstensen, Tommy ^b,c   Martin, Hilary ^b   Ekoru, Kenneth ^b,c   Nsubuga, Rebecca N ^d   Ssenyomo, Gerald ^d   Kamali, Anatoli ^d   Kaleebu, Pontiano ^d   Widmer, Christian ^a   Sandhu, Manjinder S ^b,c  

^a MICROSOFT RESEARCH   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d AIDS   (Uganda)

Author keywords

Environment; Gaussian radial basis function; Heritability estimation; Linear mixed model; Model misspecification

Indexed keywords

ALANINE AMINOTRANSFERASE; ALBUMIN; ALKALINE PHOSPHATASE; ASPARTIC ACID; BILIRUBIN; GLUCOSE; HEMOGLOBIN; HEMOGLOBIN A1C; HIGH DENSITY LIPOPROTEIN CHOLESTEROL; LOW DENSITY LIPOPROTEIN; TRIACYLGLYCEROL;

ADOLESCENT; ALANINE AMINOTRANSFERASE BLOOD LEVEL; ALBUMIN BLOOD LEVEL; ALKALINE PHOSPHATASE BLOOD LEVEL; ANTHROPOMETRY; ARTICLE; BILIRUBIN BLOOD LEVEL; BLOOD GROUP; BLOOD PRESSURE; CHOLESTEROL BLOOD LEVEL; COHORT ANALYSIS; CONTROLLED STUDY; ENVIRONMENT; FEMALE; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; GLYCEMIC CONTROL; HEMOGLOBIN BLOOD LEVEL; HERITABILITY; HUMAN; LINEAR MIXED MODEL; LIPOPROTEIN BLOOD LEVEL; LIVER FUNCTION TEST; MAJOR CLINICAL STUDY; MALE; PHENOTYPE; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL; SIMULATION; STATISTICAL MODEL; UGANDA; BIOLOGICAL MODEL; INHERITANCE;

ENVIRONMENT; HUMANS; INHERITANCE PATTERNS; LINEAR MODELS; MODELS, GENETIC; PHENOTYPE;

EID: 84977263932     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1510497113     Document Type: Article

References (24)

1. Fisher RA (1918) The correlation between relatives on the supposition of Mendelian inheritance. Trans R Soc Edinb 52:399-433.
2. Wright S (1920) The relative importance of heredity and environment in determining the piebald pattern of guinea-pigs. Proc Natl Acad Sci USA 6(6):320-332.
3. Falconer DS, Mackay TFC (1996) Introduction to Quantitative Genetics (Longman, Harlow, UK).
4. LynchM,WalshB(1998)Genetics and Analysis of Quantitative Traits (Sinauer, Sunderland, MA).
5. National Genome Human Research Institute (2015) National Genome Human Research Institute. Available at https://www.genome.gov/.
6. Zaitlen N, Kraft P (2012) Heritability in the genome-wide association era. Hum Genet 131(10):1655-1664.
7. Valdar W, et al. (2006) Genetic and environmental effects on complex traits in mice. Genetics 174(2):959-984.
8. Yang J, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42(7):565-569.
9. Hayes BJ, Visscher PM, Goddard ME (2009) Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res 91(1):47-60.
10. Bernhard S, Smola AJ (2001) Learning with Kernels (MIT Press, Cambridge, MA).
11. Rasmussen CE, Williams CKI (2006) Gaussian Processes for Machine Learning (MIT Press, Cambridge, MA).
12. Cordell HJ (2002) Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11(20):2463-2468.
13. Balding DJ, Nichols RA (1995) A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96(1-2):3-12.
14. Riha J, et al. (2014) Urbanicity and lifestyle risk factors for cardiometabolic diseases in rural Uganda: A cross-sectional study. PLoS Med 11(7):e1001683.
15. Eichler EE, et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11(6):446-450.
16. Zaitlen N, et al. (2013) Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. PLoS Genet 9(5):e1003520.
17. Stern MP, et al. (1996) Evidence for linkage of regions on chromosomes 6 and 11 to plasma glucose concentrations in Mexican Americans. Genome Res 6(8):724-734.
18. Christakis NA, Fowler JH (2007) The spread of obesity in a large social network over 32 years. N Engl J Med 357(4):370-379.
19. Asiki G, et al.; GPC team (2013) The general population cohort in rural southwestern Uganda: A platform for communicable and non-communicable disease studies. Int J Epidemiol 42(1):129-141.
20. Manichaikul A, et al. (2010) Robust relationship inference in genome-wide association studies. Bioinformatics 26(22):2867-2873.
21. Abecasis GR, Cherny SS, Cookson WO, Cardon LR (2002) Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30(1):97-101.
22. O'Connell J, et al. (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet 10(4):e1004234.
23. Price AL, et al. (2011) Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet 7(2):e1001317.
24. Tseng CL, et al. (2005) Seasonal patterns in monthly hemoglobin A1c values. Am J Epidemiol 161(6):565-574.