Cited by 1,126Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestock

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A General Test of Association for Quantitative Traits in Nuclear Families

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Abecasis, G.R., Cardon, L.R., Cookson, W.O.C.·2000·The American Journal of Human Genetics

DOI 10.1086/302698PMC PMC1288332

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Abstract

High-resolution mapping is an important step in the identification of complex disease genes. In outbred populations, linkage disequilibrium is expected to operate over short distances and could provide a powerful fine-mapping tool. Here we build on recently developed methods for linkage-disequilibrium mapping of quantitative traits to construct a general approach that can accommodate nuclear families of any size, with or without parental information. Variance components are used to construct a test that utilizes information from all available offspring but that is not biased in the presence of linkage or familiality. A permutation test is described for situations in which maximum-likelihood estimates of the variance components are biased. Simulation studies are used to investigate power and error rates of this approach and to highlight situations in which violations of multivariate normality assumptions warrant the permutation test. The relationship between power and the level of linkage disequilibrium for this test suggests that the method is well suited to the analysis of dense maps. The relationship between power and family structure is investigated, and these results are applicable to study design in complex disease, especially for late-onset conditions for which parents are usually not available. When parental genotypes are available, power does not depend greatly on the number of offspring in each family. Power decreases when parental genotypes are not available, but the loss in power is negligible when four or more offspring per family are genotyped. Finally, it is shown that, when siblings are available, the total number of genotypes required in order to achieve comparable power is smaller if parents are not genotyped.

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Method
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“, 2016) but replace the observed genotype information in that test with robust within-family genotypic information derived from the QTDT framework (Abecasis et al., 2000). In the following sections, we first introduce how we construct our test statistics using the KDC framework and how we make these statistics robust…”
BackgroundMethodInfluential
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Diao, G., & Lin, D. Y. (2020) · BMC Genetics · doi:10.1186/s12863-020-00902-x · Cited by 6
Left Ventricular Radial Function Associated With Genetic Variation in the cGMP-Dependent Protein Kinase
Kuznetsova, T., Citterio, L., Zagato, L., Carpini, S. D., Thijs, L., Casamassima, N., D’hooge, J., Bianchi, G., Manunta, P., & Staessen, J. A. (2013) · Hypertension · doi:10.1161/hypertensionaha.113.01630 · Cited by 6
An Extension of the Regression of Offspring on Mid‐Parent to Test for Association and Estimate Locus‐Specific Heritability: The Revised ROMP Method
Roy‐Gagnon, M., Mathias, R. A., Fallin, M. D., Jee, S. H., Broman, K. W., & Wilson, A. F. (2007) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2007.00401.x · Cited by 6
“Intra-familial tests of association and linkage have also been developed in likelihood-based, variance components contexts (Abecasis et al. 2000; Fulker et al. 1999).”
BackgroundMethodInfluential
A family-based association test to detect gene–gene interactions in the presence of linkage
Lobel, L. D., Thijs, L., Kuznetsova, T., Staessen, J. A., & Steen, K. V. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.45 · Cited by 6
Genetic determinants of circulating levels of tumor necrosis factor receptor II and their association with TNF-RII gene polymorphisms
Vistoropsky, Y., Ermakov, S. V., Toliat, M. R., Trofimov, S., Altmüller, J., Malkin, I., Nürnberg, P., & Livshits, G. (2010) · Cytokine · doi:10.1016/j.cyto.2010.04.013 · Cited by 6
Accurate and flexible power calculations on the spot: Applications to genomic research
Allison, D. B., Birkner, T., Moondan, A., Page, G. P., Patki, A., Tiwari, H. K., & Zhang, S. (2011) · Statistics and Its Interface · doi:10.4310/sii.2011.v4.n3.a9 · Cited by 6
HLA alleles and fissured tongue
Kalifatidis, A., Albanidou-Farmaki, E., Daniilidis, M., Markopoulos, A. K., Karyotis, N., & Antoniades, D. (2010) · International Journal of Immunogenetics · doi:10.1111/j.1744-313x.2010.00944.x · Cited by 6
“Relative risks (RR) were calculated where a particular genotype showed a 7, 509–511 509 significantly increased or decreased incidence of fissured tongue subjects compared with unrelated controls (Abecasis et al., 2000).”
Background
Detecting X‐linked common and rare variant effects in family‐based sequencing studies
Turkmen, A., & Lin, S. (2020) · Genetic Epidemiology · doi:10.1002/gepi.22352 · Cited by 6
“Linear mixed effect models are powerful tools used to account for multiple sources of heterogeneity including family relatedness Abecasis, Cardon, and Cookson (2000).”
Method
Quantitative Trait Locus Mapping in Rice
Gouda, G., Sabarinathan, S., Gupta, M. K., Donde, R., Dash, G. K., Ponnana, M., Rajesh, N., Rathore, S. K., Pati, P., Vadde, R., et al. (2021) · Springer eBooks · doi:10.1007/978-981-16-3997-5_3 · Cited by 6
Genomic regions associated with ventro-cranial chronic pleuritis in pig
Sørensen, K. K., Gregersen, V. R., Christensen, O. F., Velander, I. H., & Bendixen, C. (2011) · Journal of Animal Breeding and Genetics · doi:10.1111/j.1439-0388.2010.00914.x · Cited by 6
K45R variant of squalene synthase increases total cholesterol levels in two study samples from a French Canadian population
Do, R., Paré, G., Montpetit, A., Hudson, T. J., Gaudet, D., & Engert, J. C. (2008) · Human Mutation · doi:10.1002/humu.20702 · Cited by 6
“Association tests were performed in the family-based sample using the QTDT program [Abecasis et al., 2000].”
Method
Power, Validity, Bias and Robustness of Family‐based Association Analysis Methods in the Presence of Linkage for Late Onset Diseases
Nsengimana, J., & Barrett, J. H. (2008) · Annals of Human Genetics · doi:10.1111/j.1469-1809.2008.00475.x · Cited by 6
“It has since been extended to other family and trait types by different authors (e. g. Allison, 1997; Spielman & Ewens, 1998; Clayton, 1999; Abecasis et al. 2000).”
Background
Anthropometric and bone-related biochemical factors are associated with different haplotypes of ANKH locus
Korostishevsky, M., Vistoropsky, Y., Malkin, I., Kobyliansky, E. D., & Livshits, G. (2008) · Annals of Human Biology · doi:10.1080/03014460802304588 · Cited by 6
“…et al. (2001), which was implemented in the FBAT program; (2) the extreme offspring design t-test (EOT) proposed by Malkin et al. (2002b), which was implemented in the MAN-7 package; and (3) the orthogonal test (OT) proposed by Abecasis et al. (2002), which was implemented in the QTDT program.”
Method
Renal function in relation to three candidate genes in a Chinese population
Wang, J.-G., Liu, L., Zagato, L., Xie, J., Fagard, R. H., Jin, K., Wang, J., Li, Y., Bianchi, G., Staessen, J. A., et al. (2004) · Journal of Molecular Medicine · doi:10.1007/s00109-004-0574-8 · Cited by 6
“Sensitivity analyses in parents and offspring and QTDT analyses which allowed for population stratification and admixture [24] were confirmatory.”
Pedigree Selection and Tests of Linkage in a Hutterite Asthma Pedigree
Greenwood, C. M. T., Bureau, A., Loredo‐Osti, J. C., Roslin, N. M., CRUMLEY, M. J., Brewer, C. G., Fujiwara, T., Goldstein, D. R., & Morgan, K. W. (2001) · Genetic Epidemiology · doi:10.1002/gepi.2001.21.s1.s244 · Cited by 6
Combined Linkage and Association Analysis in Pedigrees
Siegmund, K. D., Vora, H., & Gauderman, W. J. (2001) · Genetic Epidemiology · doi:10.1002/gepi.2001.21.s1.s358 · Cited by 6
Genetic and environmental influences on human responses to odors
Knaapila, A. (2008) · Työväentutkimus Vuosikirja · doi:10.13140/rg.2.1.3779.0560 · Cited by 6
Practical barriers to identifying complex trait loci.
Cardon, L. R. (2003) · American Psychological Association eBooks · doi:10.1037/10480-004 · Cited by 6
Self-citation
Mapping quantitative effects of oligogenes by allelic association
ZHANG, W., Collins, A. R., Abecasis, G. R., Cardon, L. R., & Morton, N. E. (2002) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2002.00111.x · Cited by 6
Self-citation
Familial resemblances in human whole blood transcriptome
Tremblay, B. L., Guénard, F., Lamarche, B., Përusse, L., & Vohl, M. (2018) · BMC Genomics · doi:10.1186/s12864-018-4698-6 · Cited by 5
“[35] We used full general models in which the variance in gene expression levels of each probe and DNA methylation levels of each CpG site were partitioned into polygenic effects (Vg), common environmental effects shared by family members (Vc), and non-shared environmental effects unique to each individual (Ve).”
Method
Left ventricular diastolic function associated with common genetic variation in ATP12Ain a general population
Knez, J., Salvi, E., Tikhonoff, V., Stolarz‐Skrzypek, K., Ryabikov, A. N., Thijs, L., Braga, D., Kloch‐Badełek, M., Malyutina, S. K., Casiglia, E., et al. (2014) · BMC Medical Genetics · doi:10.1186/s12881-014-0121-6 · Cited by 5
“[20] in the QTDT software (version 2.”
Gene-environment interaction tests for family studies with quantitative phenotypes: A review and extension to longitudinal measures
Moreno-Macías, H., Romieu, I., London, S. J., & Laird, N. M. (2010) · Human Genomics · doi:10.1186/1479-7364-4-5-302 · Cited by 5
“Assuming one outcome per individual, in the two-step modelling approach, the null hypothesis H0 : b3 1⁄4 0, was tested using (21), (22) and the QBAT-I statistic:”
MethodInfluential
Statistical equivalent of the classical TDT for quantitative traits and multivariate phenotypes
Haldar, T., & Ghosh, S. (2015) · Journal of Genetics · doi:10.1007/s12041-015-0563-4 · Cited by 5
Replication of the association of common rs9939609 variant of FTO with increased BMI in an Australian adult twin population but no evidence for gene by environment (G x E) interaction
Cornes, B. K., Lind, P. A., Medland, S. E., Montgomery, G. W., Nyholt, D. R., & Martin, N. G. (2009) · Faculty of Health; Institute of Health and Biomedical Innovation · Cited by 5
PopPAnTe: population and pedigree association testing for quantitative data
Visconti, A., Al-Shafai, M. N., Al‐Muftah, W., Zaghlool, S. B., Mangino, M., Suhre, K., & Falchi, M. (2017) · BMC Genomics · doi:10.1186/s12864-017-3527-7 · Cited by 5
“PopPAnTe implements an exact linear mixed model equivalent to that implemented in the QTDT software [4].”
BackgroundMethod
Investigating structural impact of a valine to isoleucine substitution on anti-Müllerian hormone in silico and genetic association of the variant and AMH expression with egg production in chickens
Dang, L., Liu, R., Zhao, W., Zhou, W., Min, Y., & Wang, Z. (2020) · Journal of Integrative Agriculture · doi:10.1016/s2095-3119(20)63176-8 · Cited by 5
A comparative study of three methods for detecting association of quantitative traits in samples of related subjects
Pierre, A. S., Vitezica, Z. G., & Martinez, M. M. (2009) · BMC Proceedings · doi:10.1186/1753-6561-3-s7-s122 · Cited by 5
“Background For pedigree-based association analysis, several methods have been developed that utilize information about transmission of alleles, such as the orthogonal test for within-family variation (quantitative transmission-disequilibrium test, or QTDT) [1,2].”
Implementation of a Combined Association-Linkage Model for Quantitative Traits in Linear Mixed Model Procedures of Statistical Packages
Beem, A. L., & Boomsma, D. I. (2006) · Twin Research and Human Genetics · doi:10.1375/183242706777591272 · Cited by 5
Association Analysis of Population-Based Quantitative Trait Data: An Assessment of ANOVA
Ghosh, S., & De, G. (2007) · Human Heredity · doi:10.1159/000101426 · Cited by 5
Polymorphisms of the tumor necrosis factor-alpha receptor 2 gene are associated with obesity phenotypes among 405 Caucasian nuclear families
Zhao, L.-J., Xiong, D.-H., Pan, F., Liu, X.-G., Recker, R. R., & Deng, H. (2008) · Human Genetics · doi:10.1007/s00439-008-0536-2 · Cited by 5
“When signiWcant association is observed, the approximate phenotypic variation, due to the detected marker, is calculated as 2p(1 ¡ p)a2, where p is the allele frequency of the marker, and a is the estimate of additive eVect, i.e., E( w) = a (Abecasis et al. 2000a).”
One-stage design is empirically more powerful than two-stage design for family-based genome-wide association studies
Rohlfs, R. V., Taylor, C. A., Mirea, L., Bull, S. B., Corey, M. L., & Anderson, A. D. (2007) · BMC Proceedings · doi:10.1186/1753-6561-1-s1-s137 · Cited by 5
Association Studies of QTL for Multi-Allele Markers by Mixed Models
Fan, R., & Jung, J. (2002) · Human Heredity · doi:10.1159/000068839 · Cited by 5
Quantifying the Relationship Between Gene Expressions and Trait Values in General Pedigrees
Lü, Y., Liu, P., Liu, Y.-J., Xu, F., & Deng, H. (2004) · Genetics · doi:10.1534/genetics.104.031666 · Cited by 5
“Simulations showed that permutation tests warrant correct type I errors under violations of multivariate normality assumption (Abecasis et al. 2000).”
Method
Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study
Chiang, M.-C., Marina Barysheva, A., McMahon, K. L., de Zubicaray, G. I., Johnson, K., Martin, N. G., Toga, A. W., Wright, M. J., & Thompson, P. M. (2011) · IEEE International Symposium on Biomedical Imaging (ISBI) · doi:10.1109/isbi.2011.5872533 · Cited by 5
“The mean FA for each ROI was associated respectively with each genotyped SNP across the whole genome (n = 529,497), using the Quantitative Transmission Disequilibrium Test (QTDT) program [10].”
Method
Linkage and association studies of QTL for nuclear families by mixed models
Fan, R. (2003) · Biostatistics · doi:10.1093/biostatistics/4.1.75 · Cited by 5
Left ventricular structure in relation to the human SAH gene in the European Project on Genes in Hypertension
for the European Project on Genes in Hypertension (EPOGH) Investigators, Jin, Y., Kuznetsova, T., Tikhonoff, V., Thijs, L., Hasenkamp, S., Bäumer, V., Stolarz‐Skrzypek, K., Ryabikov, A. N., Richart, T., et al. (2009) · Hypertension Research · doi:10.1038/hr.2008.30 · Cited by 5

Authors: Abecasis, G. R., Cardon, L. R., & Cookson, W. O. C.
Affiliations: Centre for Human Genetics (GB)
Corresponding author: Abecasis, G.R.
ORCID: Abecasis, G.R.
Venue: The American Journal of Human Genetics
Publisher: Elsevier BV
Published: 2000-01
Volume: 66
Issue: 1
Pages: 279-292
ISSN: 0002-9297 (ISSN-L)
DOI: 10.1086/302698
PMC: PMC1288332
OpenAlex: W2078625752
Cited by: 1,126
References: 30
Citations by year: 2026: 2 · 2025: 3 · 2024: 7 · 2023: 7 · 2022: 6 · 2021: 13 · 2020: 15 · 2019: 13 · 2018: 18 · 2017: 23 · 2016: 22 · 2015: 26 · 2014: 27 · 2013: 38 · 2012: 51
FWCI: 27.12
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 4948 d)
Locations: The American Journal of Human Genetics (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Wellcome Trust
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords: association mapping, quantitative traits, nuclear family, variance components, permutation tests, fine mapping, power analysis, family structure, parental genotypes, multivariate normality, research design
MeSH terms: Genetics, Population, Humans, Models, Genetic, Nuclear Family, Linkage Disequilibrium, Quantitative Trait, Heritable

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A General Test of Association for Quantitative Traits in Nuclear Families

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