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Schmitz B, De Maria R, Gatsios D, Chrysanthakopoulou T, Landolina M, Gasparini M, Campolo J, Parolini M, Sanzo A, Galimberti P, Bianchi M, Lenders M, Brand E, Parodi O, Lunati M, Brand SM. Identification of Genetic Markers for Treatment Success in Heart Failure Patients. ACTA ACUST UNITED AC 2014; 7:760-70. [DOI: 10.1161/circgenetics.113.000384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background—
Cardiac resynchronization therapy (CRT) can improve ventricular size, shape, and mass and reduce mitral regurgitation by reverse remodeling of the failing ventricle. About 30% of patients do not respond to this therapy for unknown reasons. In this study, we aimed at the identification and classification of CRT responder by the use of genetic variants and clinical parameters.
Methods and Results—
Of 1421 CRT patients, 207 subjects were consecutively selected, and CRT responder and nonresponder were matched for their baseline parameters before CRT. Treatment success of CRT was defined as a decrease in left ventricular end-systolic volume >15% at follow-up echocardiography compared with left ventricular end-systolic volume at baseline. All other changes classified the patient as CRT nonresponder. A genetic association study was performed, which identified 4 genetic variants to be associated with the CRT responder phenotype at the allelic (
P
<0.035) and genotypic (
P
<0.031) level: rs3766031 (
ATPIB1
), rs5443 (
GNB3
), rs5522 (
NR3C2
), and rs7325635 (
TNFSF11
). Machine learning algorithms were used for the classification of CRT patients into responder and nonresponder status, including combinations of the identified genetic variants and clinical parameters.
Conclusions—
We demonstrated that rule induction algorithms can successfully be applied for the classification of heart failure patients in CRT responder and nonresponder status using clinical and genetic parameters. Our analysis included information on alleles and genotypes of 4 genetic loci, rs3766031 (
ATPIB1
), rs5443 (
GNB3
), rs5522 (
NR3C2
), and rs7325635 (
TNFSF11
), pathophysiologically associated with remodeling of the failing ventricle.
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Affiliation(s)
- Boris Schmitz
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Renata De Maria
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Dimitris Gatsios
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Theodora Chrysanthakopoulou
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Maurizio Landolina
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Maurizio Gasparini
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Jonica Campolo
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Marina Parolini
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Antonio Sanzo
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Paola Galimberti
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Michele Bianchi
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Malte Lenders
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Eva Brand
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Oberdan Parodi
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Maurizio Lunati
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
| | - Stefan-Martin Brand
- From the Institute of Sports Medicine, Molecular Genetics of Cardiovascular Disease (B.S., S.-M.B.) and Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology (B.S., M. Lenders, E.B.), University Hospital Münster, Münster, Germany; Cardiothoracic and Vascular Department, CNR Institute of Clinical Physiology, Niguarda Ca’ Granda Hospital, Milan, Italy (R.D.M., J.C., M.P., O.P.); University of Ioannina, Department of Biomedical Research, Ioannina University Campus (D.G.); Neuron
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Frikke-Schmidt R, Tybjærg-Hansen A, Dyson G, Haase CL, Benn M, Nordestgaard BG, Sing CF. Subgroups at high risk for ischaemic heart disease:identification and validation in 67 000 individuals from the general population. Int J Epidemiol 2014; 44:117-28. [PMID: 25361584 DOI: 10.1093/ije/dyu215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The aetiology of ischaemic heart disease (IHD) is complex and is influenced by a spectrum of environmental factors and susceptibility genes. Traditional statistical modelling considers such factors to act independently in an additive manner. The Patient Rule-Induction Method (PRIM) is a multi-model building strategy for evaluating risk attributable to context-dependent gene and environmental effects. METHODS PRIM was applied to 9073 participants from the prospective Copenhagen City Heart Study (CCHS). Gender-specific cumulative incidences were estimated for subgroups defined by categories of age, smoking, hypertension, diabetes, body mass index, total cholesterol, high-density lipoprotein cholesterol and triglycerides and by 94 single nucleotide variants (SNVs).Cumulative incidences for subgroups were validated using an independently ascertained sample of 58 240 participants from the Copenhagen General Population Study (CGPS). RESULTS In the CCHS the overall cumulative incidences were 0.17 in women and 0.21 in men. PRIM identified six and four mutually exclusive subgroups in women and men, respectively, with cumulative incidences of IHD ranging from 0.02 to 0.34. Cumulative incidences of IHD generated by PRIM in the CCHS were validated in four of the six subgroups of women and two of the four subgroups of men in the CGPS. CONCLUSIONS PRIM identified high-risk subgroups characterized by specific contexts of selected values of traditional risk factors and genetic variants. These subgroups were validated in an independently ascertained cohort study. Thus, a multi-model strategy may identify groups of individuals with substantially higher risk of IHD than the overall risk for the general population.
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Affiliation(s)
- Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Greg Dyson
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christiane L Haase
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Benn
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charles F Sing
- Department of Clinical Biochemistry, Rigshospitalet, The Copenhagen General Population Study, Herlev Hospital, The Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen, Denmark, Department of Oncology, Wayne State University, Detroit, USA, Department of Clinical Biochemistry, Gentofte Hospital, Department of Clinical Biochemistry, Herlev Hospital, Copenhagen, Denmark, Department of Human Genetics, University of Michigan, Ann Arbor, USA and Copenhagen University Hospital and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Govindaraju DR, Pencina KM, Raj DS, Massaro JM, Carnes BA, D'Agostino RB. A systems analysis of age-related changes in some cardiac aging traits. Biogerontology 2013; 15:139-52. [PMID: 24337960 DOI: 10.1007/s10522-013-9486-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/05/2013] [Indexed: 01/04/2023]
Abstract
Aging process or senescence affects the expression of a wide range of phenotypic traits throughout the life span of organisms. These traits often show modular, synergistic, and even antagonistic relationships, and are also influenced by genomic, developmental, physiological and environmental factors. The cardiovascular system (CVS) in humans represents a major modular system in which the relationships among physiological, anatomical and morphological traits undergo continuous remodeling throughout the life span of an individual. Here we extend the concept of developmental plasticity in order to study the relationships among 14 traits measured on 3,412 individuals from the Framingham Heart Study cohort, relative to age and gender, using exploratory structural equation modeling-a form of systems analysis. Our results reveal differing patterns of association among cardiac traits in younger and older persons in both sexes, indicating that physiological and developmental factors may be channeled differentially in relation to age and gender during the remodeling process. We suggest that systems approaches are necessary in order to understand the coordinated functional relationships among traits of the CVS over the life course of individuals.
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Affiliation(s)
- D R Govindaraju
- Division of Gerontology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA,
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4
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McIntosh AM, Bennett C, Dickson D, Anestis SF, Watts DP, Webster TH, Fontenot MB, Bradley BJ. The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes). PLoS One 2012; 7:e47760. [PMID: 23112842 PMCID: PMC3480407 DOI: 10.1371/journal.pone.0047760] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/20/2012] [Indexed: 12/21/2022] Open
Abstract
Background The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer’s disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus. Methodology and Principal Findings To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele. Conclusions We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.
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Affiliation(s)
- Annick M. McIntosh
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Calvin Bennett
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Dara Dickson
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Stephanie F. Anestis
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - David P. Watts
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Timothy H. Webster
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - M. Babette Fontenot
- Division of Behavioral Sciences, New Iberia Research Center, University of Louisiana at Lafayette, Lafayette, Louisiana, United States of America
| | - Brenda J. Bradley
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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Sebastiani P, Solovieff N, Sun JX. Naïve Bayesian Classifier and Genetic Risk Score for Genetic Risk Prediction of a Categorical Trait: Not so Different after all! Front Genet 2012; 3:26. [PMID: 22393331 PMCID: PMC3289795 DOI: 10.3389/fgene.2012.00026] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 02/12/2012] [Indexed: 12/21/2022] Open
Abstract
One of the most popular modeling approaches to genetic risk prediction is to use a summary of risk alleles in the form of an unweighted or a weighted genetic risk score, with weights that relate to the odds for the phenotype in carriers of the individual alleles. Recent contributions have proposed the use of Bayesian classification rules using Naïve Bayes classifiers. We examine the relation between the two approaches for genetic risk prediction and show that the methods are mathematically related. In addition, we study the properties of the two approaches and describe how they can be generalized to include various models of inheritance.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health Boston, MA, USA
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6
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Bañares VG, Bardach A, Peterson G, Tavella MJ, Schreier LE. APOE −491 T allele may reduce the risk of atherosclerotic lesions among middle-aged women. Mol Cell Biochem 2011; 362:123-31. [DOI: 10.1007/s11010-011-1134-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/22/2011] [Indexed: 01/10/2023]
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7
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Frikke-Schmidt R. Genetic variation in ABCA1 and risk of cardiovascular disease. Atherosclerosis 2011; 218:281-2. [PMID: 21601208 DOI: 10.1016/j.atherosclerosis.2011.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 11/25/2022]
Affiliation(s)
- Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen, Denmark.
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