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Hai Y, Zhao W, Meng Q, Liu L, Wen Y. Bayesian linear mixed model with multiple random effects for family-based genetic studies. Front Genet 2023; 14:1267704. [PMID: 37928242 PMCID: PMC10620972 DOI: 10.3389/fgene.2023.1267704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Motivation: Family-based study design is one of the popular designs used in genetic research, and the whole-genome sequencing data obtained from family-based studies offer many unique features for risk prediction studies. They can not only provide a more comprehensive view of many complex diseases, but also utilize information in the design to further improve the prediction accuracy. While promising, existing analytical methods often ignore the information embedded in the study design and overlook the predictive effects of rare variants, leading to a prediction model with sub-optimal performance. Results: We proposed a Bayesian linear mixed model for the prediction analysis of sequencing data obtained from family-based studies. Our method can not only capture predictive effects from both common and rare variants, but also easily accommodate various disease model assumptions. It uses information embedded in the study design to form surrogates, where the predictive effects from unmeasured/unknown genetic and environmental risk factors can be modelled. Through extensive simulation studies and the analysis of sequencing data obtained from the Michigan State University Twin Registry study, we have demonstrated that the proposed method outperforms commonly adopted techniques. Availability: R package is available at https://github.com/yhai943/FBLMM.
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Affiliation(s)
- Yang Hai
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Wenxuan Zhao
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Qingyu Meng
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Long Liu
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yalu Wen
- Department of Statistics, University of Auckland, Auckland, New Zealand
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Woodbury-Smith M, Paterson AD, O'Connor I, Zarrei M, Yuen RKC, Howe JL, Thompson A, Parlier M, Fernandez B, Piven J, Scherer SW, Vieland V, Szatmari P. A genome-wide linkage study of autism spectrum disorder and the broad autism phenotype in extended pedigrees. J Neurodev Disord 2018; 10:20. [PMID: 29890955 PMCID: PMC5996536 DOI: 10.1186/s11689-018-9238-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Although several genetic variants for autism spectrum disorder (ASD) have now been identified, these largely occur sporadically or are de novo. Much less progress has been made in identifying inherited variants, even though the disorder itself is familial in the majority of cases. The objective of this study was to identify chromosomal regions that harbor inherited variants increasing the risk for ASD using an approach that examined both ASD and the broad autism phenotype (BAP) among a unique sample of extended pedigrees. METHODS ASD and BAP were assessed using standardized tools in 28 pedigrees from Canada and the USA, each with at least three ASD-diagnosed individuals from two nuclear families. Genome-wide linkage analysis was performed using the posterior probability of linkage (PPL) statistic, a quasi-Bayesian method that provides strength of evidence for or against linkage in an essentially model-free manner, with outcomes on the probability scale. RESULTS The results confirm appreciable interfamilial heterogeneity as well as a high level of intrafamilial heterogeneity. Both ASD and combined ASD/BAP specific loci are apparent. CONCLUSIONS Inclusion of subclinical phenotypes such as BAP should be more widely employed in genetic studies of ASD as a way of identifying inherited genetic variants for the disorder. Moreover, the results underscore the need for approaches to identifying genetic risk factors in extended pedigrees that are robust to high levels of inter/intrafamilial locus and allelic heterogeneity.
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Affiliation(s)
- Marc Woodbury-Smith
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary, Queen Victoria Road, Newcastle upon Tyne, NE1 4LP, UK. .,Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Irene O'Connor
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Mehdi Zarrei
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K C Yuen
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer L Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Morgan Parlier
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Bridget Fernandez
- Provincial Medical Genetics Program, Health Sciences Centre, St. John's, Newfoundland, Canada
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Veronica Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Peter Szatmari
- Centre for Addiction and Mental Health, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
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Morris N, Elston RC, Barnholtz-Sloan JS, Sun X. Novel approaches to the analysis of family data in genetic epidemiology. Front Genet 2015; 6:27. [PMID: 25705217 PMCID: PMC4319458 DOI: 10.3389/fgene.2015.00027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/19/2015] [Indexed: 01/08/2023] Open
Affiliation(s)
- Nathan Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University OH, USA ; Center for Clinical Investigation, Case Western Reserve University OH, USA
| | - Robert C Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University OH, USA ; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine OH, USA
| | - Jill S Barnholtz-Sloan
- Department of Epidemiology and Biostatistics, Case Western Reserve University OH, USA ; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine OH, USA
| | - Xiangqing Sun
- Department of Epidemiology and Biostatistics, Case Western Reserve University OH, USA
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Oikkonen J, Huang Y, Onkamo P, Ukkola-Vuoti L, Raijas P, Karma K, Vieland VJ, Järvelä I. A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions. Mol Psychiatry 2015; 20:275-82. [PMID: 24614497 PMCID: PMC4259854 DOI: 10.1038/mp.2014.8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/17/2013] [Accepted: 01/06/2014] [Indexed: 01/06/2023]
Abstract
Humans have developed the perception, production and processing of sounds into the art of music. A genetic contribution to these skills of musical aptitude has long been suggested. We performed a genome-wide scan in 76 pedigrees (767 individuals) characterized for the ability to discriminate pitch (SP), duration (ST) and sound patterns (KMT), which are primary capacities for music perception. Using the Bayesian linkage and association approach implemented in program package KELVIN, especially designed for complex pedigrees, several single nucleotide polymorphisms (SNPs) near genes affecting the functions of the auditory pathway and neurocognitive processes were identified. The strongest association was found at 3q21.3 (rs9854612) with combined SP, ST and KMT test scores (COMB). This region is located a few dozen kilobases upstream of the GATA binding protein 2 (GATA2) gene. GATA2 regulates the development of cochlear hair cells and the inferior colliculus (IC), which are important in tonotopic mapping. The highest probability of linkage was obtained for phenotype SP at 4p14, located next to the region harboring the protocadherin 7 gene, PCDH7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association. PCDH7 has been suggested to play a role in cochlear and amygdaloid complexes. Functional class analysis showed that inner ear and schizophrenia-related genes were enriched inside the linked regions. This study is the first to show the importance of auditory pathway genes in musical aptitude.
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Affiliation(s)
- J. Oikkonen
- Department of Medical Genetics, University of Helsinki, P.O. Box 63, 00014 University of Helsinki, Finland
- Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 University of Helsinki
| | - Y. Huang
- The Research Institute at Nationwide Children's Hospital & The Ohio State University, Columbus OH 43215, USA
| | - P. Onkamo
- Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 University of Helsinki
| | - L. Ukkola-Vuoti
- Department of Medical Genetics, University of Helsinki, P.O. Box 63, 00014 University of Helsinki, Finland
| | - P. Raijas
- DocMus Department, University of the Arts Helsinki, P.O. Box 86, 00251 Helsinki, Finland
| | - K. Karma
- DocMus Department, University of the Arts Helsinki, P.O. Box 86, 00251 Helsinki, Finland
| | - V. J. Vieland
- The Research Institute at Nationwide Children's Hospital & The Ohio State University, Columbus OH 43215, USA
| | - I. Järvelä
- Department of Medical Genetics, University of Helsinki, P.O. Box 63, 00014 University of Helsinki, Finland
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Vieland VJ, Walters KA, Azaro M, Brzustowicz LM, Lehner T. The value of regenotyping older linkage data sets with denser marker panels. Hum Hered 2014; 78:9-16. [PMID: 24969307 DOI: 10.1159/000360003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/27/2014] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES Linkage analysis can help determine regions of interest in whole-genome sequence studies. However, many linkage studies rely on older microsatellite (MSAT) panels. We set out to determine whether results would change if we regenotyped families using a dense map of SNPs. METHODS We selected 47 Hispanic-American families from the NIMH Repository and Genomics Resource (NRGR) schizophrenia data repository. We regenotyped all individuals with DNA available from the NRGR on the Affymetrix Lat Array. After optimizing SNP selection for inclusion on the linkage map, we compared information content (IC) and linkage results using MSAT, SNP and MSAT+SNP maps. RESULTS As expected, SNP provided a higher average IC (0.78, SD 0.03) than MSAT (0.51, SD 0.10) in a direct 'apples-to-apples' comparison using only individuals genotyped on both platforms; while MSAT+SNP provided only a slightly higher IC (0.82, SD 0.03). However, when utilizing all available individuals, including those who had genotypes available on only one platform, the IC was substantially increased using MSAT+SNP (0.76, SD 0.05) compared to SNP (0.61, SD 0.02). Linkage results changed appreciably between MSAT and MSAT+SNP in terms of magnitude, rank ordering and localization of peaks. CONCLUSIONS Regenotyping older family data can substantially alter the conclusions of linkage analyses.
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Affiliation(s)
- Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
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Piven J, Vieland VJ, Parlier M, Thompson A, O'Conner I, Woodbury-Smith M, Huang Y, Walters KA, Fernandez B, Szatmari P. A molecular genetic study of autism and related phenotypes in extended pedigrees. J Neurodev Disord 2013; 5:30. [PMID: 24093601 PMCID: PMC3851306 DOI: 10.1186/1866-1955-5-30] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/23/2013] [Indexed: 12/19/2022] Open
Abstract
Background Efforts to uncover the risk genotypes associated with the familial nature of autism spectrum disorder (ASD) have had limited success. The study of extended pedigrees, incorporating additional ASD-related phenotypes into linkage analysis, offers an alternative approach to the search for inherited ASD susceptibility variants that complements traditional methods used to study the genetics of ASD. Methods We examined evidence for linkage in 19 extended pedigrees ascertained through ASD cases spread across at least two (and in most cases three) nuclear families. Both compound phenotypes (i.e., ASD and, in non-ASD individuals, the broad autism phenotype) and more narrowly defined components of these phenotypes, e.g., social and repetitive behavior, pragmatic language, and anxiety, were examined. The overarching goal was to maximize the aggregate information available on the maximum number of individuals and to disaggregate syndromic phenotypes in order to examine the genetic underpinnings of more narrowly defined aspects of ASD behavior. Results Results reveal substantial between-family locus heterogeneity and support the importance of previously reported ASD loci in inherited, familial, forms of ASD. Additional loci, not seen in the ASD analyses, show evidence for linkage to the broad autism phenotype (BAP). BAP peaks are well supported by multiple subphenotypes (including anxiety, pragmatic language, and social behavior) showing linkage to regions overlapping with the compound BAP phenotype. Whereas 'repetitive behavior’, showing the strongest evidence for linkage (Posterior Probability of Linkage = 62% at 6p25.2-24.3, and 69% at 19p13.3), appears to be linked to novel regions not detected with other compound or narrow phenotypes examined in this study. Conclusions These results provide support for the presence of key features underlying the complexity of the genetic architecture of ASD: substantial between-family locus heterogeneity, that the BAP appears to correspond to sets of subclinical features segregating with ASD within pedigrees, and that different features of the ASD phenotype segregate independently of one another. These findings support the additional study of larger, even more individually informative pedigrees, together with measurement of multiple, behavioral- and biomarker-based phenotypes, in both affected and non-affected individuals, to elucidate the complex genetics of familial ASD.
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Affiliation(s)
- Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, CB# 3367, Chapel Hill, NC 27599, USA
| | - Veronica J Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA.,Department of Pediatrics and Department of Statistics, The Ohio State University, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Morgan Parlier
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, School of Medicine, CB# 3367, Chapel Hill, NC 27599, USA
| | - Ann Thompson
- McMaster Department of Psychiatry and Behavioural Neurosciences, 1200 Main Street west, L9H 3Z5, Hamilton, ON, Canada
| | - Irene O'Conner
- McMaster Department of Psychiatry and Behavioural Neurosciences, 1200 Main Street west, L9H 3Z5, Hamilton, ON, Canada
| | - Mark Woodbury-Smith
- McMaster Department of Psychiatry and Behavioural Neurosciences, 1200 Main Street west, L9H 3Z5, Hamilton, ON, Canada
| | - Yungui Huang
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Kimberly A Walters
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Bridget Fernandez
- Provincial Medical Genetics Program, Health Sciences Center, 300 Prince Philip Drive, A1B 3V6, St. John's, Newfoundland, Canada
| | - Peter Szatmari
- McMaster Department of Psychiatry and Behavioural Neurosciences, 1200 Main Street west, L9H 3Z5, Hamilton, ON, Canada.,Centre for Addiction and Mental Health, University of Toronto, 80 Workman Way, Toronto, ON, Canada
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