The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
A Better Coefficient of Determination for Genetic Profile Analysis
Abstract
Genome‐wide association studies have facilitated the construction of risk predictors for disease from multiple Single Nucleotide Polymorphism markers. The ability of such “genetic profiles” to predict outcome is usually quantified in an independent data set. Coefficients of determination (R2) have been a useful measure to quantify the goodness‐of‐fit of the genetic profile. Various pseudo‐R2 measures for binary responses have been proposed. However, there is no standard or consensus measure because the concept of residual variance is not easily defined on the observed probability scale. Unlike other nongenetic predictors such as environmental exposure, there is prior information on genetic predictors because for most traits there are estimates of the proportion of variation in risk in the population due to all genetic factors, the heritability. It is this useful ability to benchmark that makes the choice of a measure of goodness‐of‐fit in genetic profiling different from that of nongenetic predictors. In this study, we use a liability threshold model to establish the relationship between the observed probability scale and underlying liability scale in measuring R2 for binary responses. We show that currently used R2 measures are difficult to interpret, biased by ascertainment, and not comparable to heritability. We suggest a novel and globally standard measure of R2 that is interpretable on the liability scale. Furthermore, even when using ascertained case‐control studies that are typical in human disease studies, we can obtain an R2 measure on the liability scale that can be compared directly to heritability.
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Cites
Introduction to Quantitative Genetics.
Edwards, A. W. F., & Falconer, D. S. (1982) · Biometrics · doi:10.2307/2529912 · Cited by 21,447
A note on a general definition of the coefficient of determination
NAGELKERKE, N. J. D. (1991) · Biometrika · doi:10.1093/biomet/78.3.691 · Cited by 5,927
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder
The International Schizophrenia Consortium (2009) · Nature · doi:10.1038/nature08185 · Cited by 4,821
A statistical model for the analysis of ordinal level dependent variables
McKelvey, R. D., & Zavoina, W. (1975) · The Journal of Mathematical Sociology · doi:10.1080/0022250x.1975.9989847 · Cited by 2,599
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
the NIDDK IBD Genetics Consortium, Barrett, J. C., the Belgian-French IBD Consortium, the Wellcome Trust Case Control Consortium, Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., et al. (2008) · Nature Genetics · doi:10.1038/ng.175 · Cited by 2,593
The measurement of urban travel demand
McFadden, D. (1974) · Journal of Public Economics · doi:10.1016/0047-2727(74)90003-6 · Cited by 2,546
Plackett, R. L., & Cox, D. R. (1971) · Journal of the Royal Statistical Society. Series A (General) · doi:10.2307/2344247 · Cited by 2,264
The Type 1 Diabetes Genetics Consortium, Barrett, J. C., Clayton, D. G., Concannon, P., Akolkar, B., Cooper, J. D., Erlich, H. A., Julier, C., Morahan, G., Nerup, J., et al. (2009) · Nature Genetics · doi:10.1038/ng.381 · Cited by 1,746
Introduction to Quantitative Genetics
Xu, S. (2022) · Quantitative Genetics · doi:10.1007/978-3-030-83940-6_1 · Cited by 1,559
The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation
Study, T. I. H. C. (2010) · Science · doi:10.1126/science.1195271 · Cited by 1,171
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Biological insights from 108 schizophrenia-associated genetic loci
Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577
Chicco, D., Warrens, M. J., & Jurman, G. (2021) · PeerJ Computer Science · doi:10.7717/peerj-cs.623 · Cited by 5,380
Mapping genomic loci implicates genes and synaptic biology in schizophrenia
Trubetskoy, V., Pardiñas, A. F., Qi, T., Panagiotaropoulou, G., Awasthi, S., Bigdeli, T. B., Bryois, J., Chen, C.-Y., Dennison, C. A., Hall, L. S., et al. (2022) · Nature · doi:10.1038/s41586-022-04434-5 · Cited by 2,964
Self-citationGenetic relationship between five psychiatric disorders estimated from genome-wide SNPs
Cross-Disorder Group of the Psychiatric Genomics Consortium (2013) · Nature Genetics · doi:10.1038/ng.2711 · Cited by 2,263
GERAD1 Consortium, Pardiñas, A. F., CRESTAR Consortium, Holmans, P., Pocklington, A. J., Escott-Price, V., Ripke, S., Carrera, N., Legge, S. E., Bishop, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0059-2 · Cited by 1,552
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Metadata
- Authors
- Lee, S. H., Goddard, M. E., Wray, N. R., & Visscher, P. M.
- Venue
- Genetic Epidemiology
- Publisher
- Wiley
- Published
- 2012-04
- Volume
- 36
- Issue
- 3
- Pages
- 214-224
- ISSN
- 0741-0395 (ISSN-L)
- 1098-2272
- OpenAlex
- W1608887304
- Cited by
- 349
- References
- 54
- FWCI
- 4.07
- Type
- journal article
- Language
- en
- Open access
- closed
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- Lee, S. H., Goddard, M. E., Wray, N. R., & Visscher, P. M. (2012). A Better Coefficient of Determination for Genetic Profile Analysis. Genetic Epidemiology. https://doi.org/10.1002/gepi.21614
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