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Khan MI, Cs P. Case-Parent Trio Studies in Cleft Lip and Palate. Glob Med Genet 2021; 7:75-79. [PMID: 33392609 PMCID: PMC7772012 DOI: 10.1055/s-0040-1722097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is one of the most common congenital malformations in humans involving various genetic and environmental risk factors. The prevalence of CL/P varies according to geographical location, ethnicity, race, gender, and socioeconomic status, affecting approximately 1 in 800 live births worldwide. Genetic studies aim to understand the mechanisms contributory to a phenotype by measuring the association between genetic variants and also between genetic variants and phenotype population. Genome-wide association studies are standard tools used to discover genetic loci related to a trait of interest. Genetic association studies are generally divided into two main design types: population-based studies and family-based studies. The epidemiological population-based studies comprise unrelated individuals that directly compare the frequency of genetic variants between (usually independent) cases and controls. The alternative to population-based studies (case–control designs) includes various family-based study designs that comprise related individuals. An example of such a study is a case–parent trio design study, which is commonly employed in genetics to identify the variants underlying complex human disease where transmission of alleles from parents to offspring is studied. This article describes the fundamentals of case–parent trio study, trio design and its significances, statistical methods, and limitations of the trio studies.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth Cs
- Department of Orthodontics & Dentofacial Orthopedics, DAPM RV Dental College, Bangalore, Karnataka, India
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2
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Lee KY, Lee BD, Park JM, Lee YM, Moon E, Jeong HJ, Kim SY, Suh H, Chung YI, Kim SC. Investigation of Maternal Effects, Maternal-Fetal Interactions, and Parent-of-Origin Effects (Imprinting) for Candidate Genes Positioned on Chromosome 18q21, in Probands with Schizophrenia and their First-Degree Relatives. Psychiatry Investig 2019; 16:450-458. [PMID: 31247704 PMCID: PMC6603700 DOI: 10.30773/pi.2019.04.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/12/2019] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE A popular design for the investigation of such effects, including effects of parent-of-origin (imprinting), maternal genotype, and maternal-fetal genotype interactions, is to collect deoxyribonucleic acid (DNA) from affected offspring and their mothers and to compare with an appropriate control sample. We investigate the effects of estimation of maternal, imprinting and interaction effects using multimodal modeling using parents and their offspring with schizophrenia in Korean population. METHODS We have recruited 27 probands (with schizophrenia) with their parents and siblings whenever possible. We analyzed 20 SNPs of 7 neuronal genes in chromosome 18. We used EMIM analysis program for the estimation of maternal, imprinting and interaction effects using multimodal modeling. RESULTS Of analyzed 20 single nucleotide polymorphisms (SNPs), significant SNP (rs 2276186) was suggested in EMIM analysis for child genetics effects (p=0.0225438044) and child genetic effects allowing for maternal genetic effects (p=0.0209453210) with very stringent multiple comparison Bonferroni correction. CONCLUSION Our results are the pilot study for epigenetic study in mental disorder and help to understanding and use of EMIM statistical genetics analysis program with many limitations including small pedigree numbers.
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Affiliation(s)
- Kang Yoon Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Byung Dae Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Je Min Park
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Young Min Lee
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Eunsoo Moon
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea.,Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Hee Jeong Jeong
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Soo Yeon Kim
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Hwagyu Suh
- Department of Psychiatry, Pusan National University Hospital, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Young In Chung
- Department of Psychiatry, Pusan National University College of Medicine, Busan, Republic of Korea
| | - Seung Chul Kim
- Department of Obstetrics and Gynecology, Pusan National University Hospital, Busan, Republic of Korea
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3
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Cui Y, Yang H. Dissecting genomic imprinting and genetic conflict from a game theory prospective: Comment on: "Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition" by Qian Wang et al. Phys Life Rev 2017; 20:161-163. [PMID: 28159530 DOI: 10.1016/j.plrev.2017.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, United States.
| | - Haitao Yang
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, United States
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4
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Balliu B, Tsonaka R, van der Woude D, Boehringer S, Houwing-Duistermaat JJ. Combining family and twin data in association studies to estimate the noninherited maternal antigens effect. Genet Epidemiol 2012; 36:811-9. [PMID: 22851506 DOI: 10.1002/gepi.21667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 06/06/2012] [Accepted: 06/20/2012] [Indexed: 11/08/2022]
Abstract
It is hypothesized that certain alleles can have a protective effect not only when inherited by the offspring but also as noninherited maternal antigens (NIMA). To estimate the NIMA effect, large samples of families are needed. When large samples are not available, we propose a combined approach to estimate the NIMA effect from ascertained nuclear families and twin pairs. We develop a likelihood-based approach allowing for several ascertainment schemes, to accommodate for the outcome-dependent sampling scheme, and a family-specific random term, to take into account the correlation between family members. We estimate the parameters using maximum likelihood based on the combined joint likelihood (CJL) approach. Simulations show that the CJL is more efficient for estimating the NIMA odds ratios as compared to a families-only approach. To illustrate our approach, we used data from a family and a twin study from the United Kingdom on rheumatoid arthritis, and confirmed the protective NIMA effect, with an odds ratio of 0.477 (95% CI 0.264-0.864).
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Affiliation(s)
- Brunilda Balliu
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
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5
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Howey R, Cordell HJ. PREMIM and EMIM: tools for estimation of maternal, imprinting and interaction effects using multinomial modelling. BMC Bioinformatics 2012; 13:149. [PMID: 22738121 PMCID: PMC3464602 DOI: 10.1186/1471-2105-13-149] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 06/09/2012] [Indexed: 01/28/2023] Open
Abstract
Background Here we present two new computer tools, PREMIM and EMIM, for the estimation of parental and child genetic effects, based on genotype data from a variety of different child-parent configurations. PREMIM allows the extraction of child-parent genotype data from standard-format pedigree data files, while EMIM uses the extracted genotype data to perform subsequent statistical analysis. The use of genotype data from the parents as well as from the child in question allows the estimation of complex genetic effects such as maternal genotype effects, maternal-foetal interactions and parent-of-origin (imprinting) effects. These effects are estimated by EMIM, incorporating chosen assumptions such as Hardy-Weinberg equilibrium or exchangeability of parental matings as required. Results In application to simulated data, we show that the inference provided by EMIM is essentially equivalent to that provided by alternative (competing) software packages such as MENDEL and LEM. However, PREMIM and EMIM (used in combination) considerably outperform MENDEL and LEM in terms of speed and ease of execution. Conclusions Together, EMIM and PREMIM provide easy-to-use command-line tools for the analysis of pedigree data, giving unbiased estimates of parental and child genotype relative risks.
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Affiliation(s)
- Richard Howey
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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6
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Childs EJ, Sobel EM, Palmer CGS, Sinsheimer JS. Detection of intergenerational genetic effects with application to HLA-B matching as a risk factor for schizophrenia. Hum Hered 2011; 72:161-72. [PMID: 22004985 DOI: 10.1159/000332051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/23/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND METHODS Association studies using unrelated individuals cannot detect intergenerational genetic effects contributing to disease. To detect these effects, we improve the extended maternal-fetal genotype (EMFG) incompatibility test to estimate any combination of maternal effects, offspring effects, and their interactions at polymorphic loci or multiple SNPs, using any size pedigrees. We explore the advantages of using extended pedigrees rather than nuclear families. We apply our methods to schizophrenia pedigrees to investigate whether the previously associated mother-daughter HLA-B matching is a genuine risk or the result of bias. RESULTS Simulations demonstrate that using the EMFG test with extended pedigrees increases power and precision, while partitioning extended pedigrees into nuclear families can underestimate intergenerational effects. Application to actual data demonstrates that mother-daughter HLA-B matching remains a schizophrenia risk factor. Furthermore, ascertainment and mate selection biases cannot by themselves explain the observed HLA-B matching and schizophrenia association. CONCLUSIONS Our results demonstrate the power of the EMFG test to examine intergenerational genetic effects, highlight the importance of pedigree rather than case/control or case-mother/control-mother designs, illustrate that pedigrees provide a means to examine alternative, non-causal mechanisms, and they strongly support the hypothesis that HLA-B matching is causally involved in the etiology of schizophrenia in females.
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Affiliation(s)
- Erica J Childs
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
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7
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Ainsworth HF, Unwin J, Jamison DL, Cordell HJ. Investigation of maternal effects, maternal-fetal interactions and parent-of-origin effects (imprinting), using mothers and their offspring. Genet Epidemiol 2011; 35:19-45. [PMID: 21181895 PMCID: PMC3025173 DOI: 10.1002/gepi.20547] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many complex genetic effects, including epigenetic effects, may be expected to operate via mechanisms in the inter-uterine environment. A popular design for the investigation of such effects, including effects of parent-of-origin (imprinting), maternal genotype, and maternal-fetal genotype interactions, is to collect DNA from affected offspring and their mothers (case/mother duos) and to compare with an appropriate control sample. An alternative design uses data from cases and both parents (case/parent trios) but does not require controls. In this study, we describe a novel implementation of a multinomial modeling approach that allows the estimation of such genetic effects using either case/mother duos or case/parent trios. We investigate the performance of our approach using computer simulations and explore the sample sizes and data structures required to provide high power for detection of effects and accurate estimation of the relative risks conferred. Through the incorporation of additional assumptions (such as Hardy-Weinberg equilibrium, random mating and known allele frequencies) and/or the incorporation of additional types of control sample (such as unrelated controls, controls and their mothers, or both parents of controls), we show that the (relative risk) parameters of interest are identifiable and well estimated. Nevertheless, parameter interpretation can be complex, as we illustrate by demonstrating the mathematical equivalence between various different parameterizations. Our approach scales up easily to allow the analysis of large-scale genome-wide association data, provided both mothers and affected offspring have been genotyped at all variants of interest. Genet. Epidemiol. 35:19–45, 2011. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Holly F Ainsworth
- School of Mathematics and Statistics, Newcastle University, Newcastle upon Tyne, United Kingdom
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8
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Childs EJ, Palmer CGS, Lange K, Sinsheimer JS. Modeling maternal-offspring gene-gene interactions: the extended-MFG test. Genet Epidemiol 2010; 34:512-21. [PMID: 20552637 DOI: 10.1002/gepi.20508] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Maternal-fetal genotype (MFG) incompatibility is an interaction between the genes of a mother and offspring at a particular locus that adversely affects the developing fetus, thereby increasing susceptibility to disease. Statistical methods for examining MFG incompatibility as a disease risk factor have been developed for nuclear families. Because families collected as part of a study can be large and complex, containing multiple generations and marriage loops, we create the Extended-MFG (EMFG) Test, a model-based likelihood approach, to allow for arbitrary family structures. We modify the MFG test by replacing the nuclear-family based "mating type" approach with Ott's representation of a pedigree likelihood and calculating MFG incompatibility along with the Mendelian transmission probability. In order to allow for extension to arbitrary family structures, we make a slightly more stringent assumption of random mating with respect to the locus of interest. Simulations show that the EMFG test has appropriate type-I error rate, power, and precise parameter estimation when random mating holds. Our simulations and real data example illustrate that the chief advantages of the EMFG test over the earlier nuclear family version of the MFG test are improved accuracy of parameter estimation and power gains in the presence of missing genotypes.
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Affiliation(s)
- Erica J Childs
- Department of Biostatistics, University of California, Los Angeles, California, USA
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9
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Evidence for maternal-fetal genotype incompatibility as a risk factor for schizophrenia. J Biomed Biotechnol 2010; 2010:576318. [PMID: 20379378 PMCID: PMC2850511 DOI: 10.1155/2010/576318] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 02/09/2010] [Accepted: 02/20/2010] [Indexed: 12/22/2022] Open
Abstract
Prenatal/obstetric complications are implicated in schizophrenia susceptibility. Some complications may arise from maternal-fetal genotype incompatibility, a term used to describe maternal-fetal genotype combinations that produce an adverse prenatal environment. A review of maternal-fetal genotype incompatibility studies suggests that schizophrenia susceptibility is increased by maternal-fetal genotype combinations at the RHD and HLA-B loci. Maternal-fetal genotype combinations at these loci are hypothesized to have an effect on the maternal immune system during pregnancy which can affect fetal neurodevelopment and increase schizophrenia susceptibility. This article reviews maternal-fetal genotype incompatibility studies and schizophrenia and discusses the hypothesized biological role of these ‘‘incompatibility genes”. It concludes that research is needed to further elucidate the role of RHD and HLA-B maternal-fetal genotype incompatibility in schizophrenia and to identify other genes that produce an adverse prenatal environment through a maternal-fetal genotype incompatibility mechanism. Efforts to develop more sophisticated study designs and data analysis techniques for modeling maternal-fetal genotype incompatibility effects are warranted.
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10
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Jamieson SE, Cordell H, Petersen E, McLeod R, Gilbert RE, Blackwell JM. Host genetic and epigenetic factors in toxoplasmosis. Mem Inst Oswaldo Cruz 2010; 104:162-9. [PMID: 19430638 DOI: 10.1590/s0074-02762009000200006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 02/17/2009] [Indexed: 12/29/2022] Open
Abstract
Analysing human genetic variation provides a powerful tool in understanding risk factors for disease. Toxoplasma gondii acquired by the mother can be transmitted to the fetus. Infants with the most severe clinical signs in brain and eye are those infected early in pregnancy when fetal immunity is least well developed. Genetic analysis could provide unique insight into events in utero that are otherwise difficult to determine. We tested the hypothesis that propensity for T. gondii to cause eye disease is associated with genes previously implicated in congenital or juvenile onset ocular disease. Using mother-child pairs from Europe (EMSCOT) and child/parent trios from North America (NCCCTS), we demonstrated that ocular and brain disease in congenital toxoplasmosis associate with polymorphisms in ABCA4 encoding ATP-binding cassette transporter, subfamily A, member 4 previously associated with juvenile onset retinal dystrophies including Stargardt's disease. Polymorphisms at COL2A1 encoding type II collagen, previously associated with Stickler syndrome, associated only with ocular disease in congenital toxoplasmosis. Experimental studies showed that both ABCA4 and COL2A1 show isoform-specific epigenetic modifications consistent with imprinting, which provided an explanation for the patterns of inheritance observed. These genetic and epigenetic risk factors provide unique insight into molecular pathways in the pathogenesis of disease.
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Affiliation(s)
- Sarra E Jamieson
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, PO Box 855, West Perth, Western Australia 6872, Australia
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11
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Crespi B. Genomic imprinting in the development and evolution of psychotic spectrum conditions. Biol Rev Camb Philos Soc 2008; 83:441-93. [PMID: 18783362 DOI: 10.1111/j.1469-185x.2008.00050.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting.
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Affiliation(s)
- Bernard Crespi
- Department of Biosciences, Simon Fraser University, Burnaby BCV5A1S6, Canada.
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12
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Palmer CG, Mallery E, Turunen JA, Hsieh HJ, Peltonen L, Lonnqvist J, Woodward JA, Sinsheimer JS. Effect of Rhesus D incompatibility on schizophrenia depends on offspring sex. Schizophr Res 2008; 104:135-45. [PMID: 18692992 PMCID: PMC2572267 DOI: 10.1016/j.schres.2008.06.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 06/20/2008] [Accepted: 06/29/2008] [Indexed: 01/15/2023]
Abstract
Rhesus D incompatibility increases risk for schizophrenia, with some evidence that risk is limited to male offspring. The purpose of this study is to determine whether risk for schizophrenia due to Rhesus D incompatibility differs by offspring sex using a nuclear family-based candidate gene approach and a meta-analysis approach. The genetic study is based on a sample of 277 nuclear families with RHD genotype data on at least one parent and at least one child diagnosed with schizophrenia or related disorder. Meta-analysis inclusion criteria were (1) well-defined sample of schizophrenia patients with majority born before 1970, (2) Rhesus D incompatibility phenotype or genotype data available on mother and offspring, and by offspring sex. Two of ten studies, plus the current genetic study sample, fulfilled these criteria, for a total of 358 affected males and 226 affected females. The genetic study found that schizophrenia risk for incompatible males was significantly greater than for compatible offspring (p=0.03), while risk for incompatible and compatible females was not significantly different (p=.32). Relative risks for incompatible males and females were not significantly different from each other. Meta-analysis using a larger number of affected males and females supports their difference. Taken together, these results provide further support that risk of schizophrenia due to Rhesus D incompatibility is limited to incompatible males, although a weak female incompatibility effect cannot be excluded. Sex differences during fetal neurodevelopment should be investigated to fully elucidate the etiology of schizophrenia.
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Affiliation(s)
- Christina G.S. Palmer
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, CA, 90095, USA, Department of Human Genetics, University of California, Los Angeles, CA, 90095, USA,Corresponding author. UCLA Semel Institute, 760 Westwood Plaza, Rm 47-422, Los Angeles, CA 90095, USA. Tel.: +1 310 794 4796; fax: +1 310 206 4446. E-mail address: (C.G.S. Palmer)
| | - Erin Mallery
- Department of Biostatistics, University of California, Los Angeles, CA, 90095, USA
| | - Joni A. Turunen
- Institute for Molecular Medicine Finland FIMM and National Public Health Institute, 00251 Helsinki, Finland
| | - Hsin-Ju Hsieh
- Genentech Corporation, San Francisco, CA, 94080, USA
| | - Leena Peltonen
- Institute for Molecular Medicine Finland FIMM and National Public Health Institute, 00251 Helsinki, Finland, Department of Medical Genetics, University of Helsinki, 00251 Helsinki, Finland, Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02142, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jouko Lonnqvist
- Department of Mental Health and Alcohol Research, National Public Health Institute, 00251 Helsinki, Finland, Department of Psychiatry, University of Helsinki, 00251 Helsinki, Finland
| | - J. Arthur Woodward
- School of Social Sciences, Humanities and Arts, University of California, Merced, CA, 95344, USA
| | - Janet S. Sinsheimer
- Department of Human Genetics, University of California, Los Angeles, CA, 90095, USA, Department of Biostatistics, University of California, Los Angeles, CA, 90095, USA, Department of Biomathematics, University of California, Los Angeles, CA, 90095 USA
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Buyske S. Maternal genotype effects can alias case genotype effects in case-control studies. Eur J Hum Genet 2008; 16:783-5. [PMID: 18398431 DOI: 10.1038/ejhg.2008.74] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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14
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Hsieh HJ, Palmer CGS, Harney S, Chen HW, Bauman L, Brown MA, Sinsheimer JS. Using the maternal-fetal genotype incompatibility test to assess non-inherited maternal HLA-DRB1 antigen coding alleles as rheumatoid arthritis risk factors. BMC Proc 2007; 1 Suppl 1:S124. [PMID: 18466466 PMCID: PMC2367472 DOI: 10.1186/1753-6561-1-s1-s124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Non-inherited maternal antigens encoded by specific HLA-DRB1 alleles (NIMA) have been implicated as a rheumatoid arthritis (RA) risk factor. Using genotype data from North American Rheumatoid Arthritis Consortium study participants and the maternal-fetal genotype incompatibility (MFG) test, we find evidence for offspring allelic effects but no evidence for NIMA as a RA risk factor. We discuss possible reasons why our result conflicts with several previous studies (including one of our own) that used RA patients from northern Europe.
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Affiliation(s)
- Hsin-Ju Hsieh
- Genentech, Inc, 1 DNA Way, South San Francisco, California 94080, USA.
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15
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de Andrade M, Allen AS. Summary of contributions to GAW15 Group 13: candidate gene association studies. Genet Epidemiol 2007; 31 Suppl 1:S110-7. [DOI: 10.1002/gepi.20287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Hsieh HJ, Palmer CGS, Sinsheimer JS. Allowing for missing data at highly polymorphic genes when testing for maternal, offspring and maternal-fetal genotype incompatibility effects. Hum Hered 2006; 62:165-74. [PMID: 17065817 DOI: 10.1159/000096444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 08/07/2006] [Indexed: 12/20/2022] Open
Abstract
Genes can be associated with disease through an individual's inherited genotype, the maternal genotype or the interaction between these two. When the gene is highly polymorphic, it is more difficult to identify the gene's functional role than for less polymorphic loci, because different alleles at the locus may be associated with the disease through separate and joint effects from maternal and offspring genotypes. Family-based studies are used to test genetic associations because of their robustness to population stratification. However, parental genotype data are often missing, and omitting incompletely genotyped families is inefficient. Methods have been proposed to accommodate incomplete families in family-based association studies. They are not easily generalized to allow simultaneous examination of offspring allelic, maternal allelic and maternal-fetal genotype (MFG) incompatibility effects. Since many MFG incompatibility effects occur through matching between maternal and offspring's genotypes, we present an identity-by-state (IBS) framework to incorporate incomplete families in the MFG test when modeling genetic effects produced by a polymorphic gene. Using simulations, we examine the MFG test's performance with incomplete parental genotype data and an IBS framework. The MFG test using the IBS framework is immune to population stratification and efficiently uses information from incomplete families.
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Affiliation(s)
- Hsin-Ju Hsieh
- Biostatistics, University of California, Los Angeles, CA, USA
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17
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Palmer CGS, Hsieh HJ, Reed EF, Lonnqvist J, Peltonen L, Woodward JA, Sinsheimer JS. HLA-B maternal-fetal genotype matching increases risk of schizophrenia. Am J Hum Genet 2006; 79:710-5. [PMID: 16960807 PMCID: PMC1592576 DOI: 10.1086/507829] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Accepted: 07/16/2006] [Indexed: 12/20/2022] Open
Abstract
Schizophrenia and human leukocyte antigen (HLA) matching between couples or between mothers and offspring have independently been associated with prenatal/obstetric complications, including preeclampsia and low birth weight. Here, we report the results of a family-based candidate-gene study that brings together these two disparate lines of research by assessing maternal-fetal genotype matching at HLA-A, -B, and -DRB1 as a risk factor of schizophrenia. We used a conditional-likelihood modeling approach with a sample of 274 families that had at least one offspring with schizophrenia or a related spectrum disorder. A statistically significant HLA-B maternal-fetal genotype-matching effect on schizophrenia was demonstrated for female offspring (P=.01; parameter estimate 1.7 [95% confidence interval 1.22-2.49]). Because the matching effect could be associated with pregnancy complications rather than with schizophrenia per se, these findings are consistent with the neurodevelopmental hypothesis of schizophrenia and with accumulating evidence that the prenatal period is involved in the origins of this disease. Our approach demonstrates how genetic markers can be used to characterize the biology of prenatal risk factors of schizophrenia.
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Affiliation(s)
- Christina G S Palmer
- Department of Psychiatry and Biobehavioral Sciences, University of California-Los Angeles, Los Angeles, CA 90095, USA.
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