P M Visscher

Summary

Affiliation: Queensland Institute of Medical Research
Country: Australia

Publications

  1. pmc Prediction of individual genetic risk to disease from genome-wide association studies
    Naomi R Wray
    Genetic Epidemiology, Queensland Institute of Medical Research, Queensland 4029, Brisbane, Australia
    Genome Res 17:1520-8. 2007
  2. doi request reprint Reconciling the analysis of IBD and IBS in complex trait studies
    Joseph E Powell
    Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
    Nat Rev Genet 11:800-5. 2010
  3. pmc Predicting unobserved phenotypes for complex traits from whole-genome SNP data
    Sang Hong Lee
    School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
    PLoS Genet 4:e1000231. 2008
  4. pmc Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations
    Yoshitaka Nagamine
    National Institute of Livestock and Grassland Science, Tsukuba 305 0901, Japan
    Genet Sel Evol 41:44. 2009
  5. pmc Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits
    Sang Hong Lee
    Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
    Genet Sel Evol 42:22. 2010
  6. pmc The Lothian Birth Cohort 1936: a study to examine influences on cognitive ageing from age 11 to age 70 and beyond
    Ian J Deary
    Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
    BMC Geriatr 7:28. 2007
  7. doi request reprint Whole genome approaches to quantitative genetics
    Peter M Visscher
    Queensland Institute of Medical Research, Brisbane, Australia
    Genetica 136:351-8. 2009
  8. pmc Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings
    Peter M Visscher
    Genetic Epidemiology Group, Queensland Institute of Medical Research, Brisbane, Australia
    PLoS Genet 2:e41. 2006
  9. ncbi request reprint The value of relatives with phenotypes but missing genotypes in association studies for quantitative traits
    Peter M Visscher
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Genet Epidemiol 30:30-6. 2006
  10. doi request reprint Statistical power to detect genetic Loci affecting environmental sensitivity
    Peter M Visscher
    Queensland Institute of Medical Research, Herston 4006, Australia
    Behav Genet 40:728-33. 2010

Collaborators

Detail Information

Publications100

  1. pmc Prediction of individual genetic risk to disease from genome-wide association studies
    Naomi R Wray
    Genetic Epidemiology, Queensland Institute of Medical Research, Queensland 4029, Brisbane, Australia
    Genome Res 17:1520-8. 2007
    ..Whether an individual with known genetic risk develops the disease depends on known and unknown environmental factors...
  2. doi request reprint Reconciling the analysis of IBD and IBS in complex trait studies
    Joseph E Powell
    Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
    Nat Rev Genet 11:800-5. 2010
    ..Recognizing this aim leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression...
  3. pmc Predicting unobserved phenotypes for complex traits from whole-genome SNP data
    Sang Hong Lee
    School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
    PLoS Genet 4:e1000231. 2008
    ..The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be applied in human medicine, forensics, or artificial selection programs...
  4. pmc Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations
    Yoshitaka Nagamine
    National Institute of Livestock and Grassland Science, Tsukuba 305 0901, Japan
    Genet Sel Evol 41:44. 2009
    ....
  5. pmc Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits
    Sang Hong Lee
    Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
    Genet Sel Evol 42:22. 2010
    ..Dominance and epistatic effects are typically confounded with additive genetic and non-genetic effects. This confounding may cause the estimated genetic variance components to be inaccurate and biased...
  6. pmc The Lothian Birth Cohort 1936: a study to examine influences on cognitive ageing from age 11 to age 70 and beyond
    Ian J Deary
    Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK
    BMC Geriatr 7:28. 2007
    ..A limitation of many studies is the lack of a sufficiently long period between cognitive assessments to examine determinants. Here, the aim is to examine influences on cognitive ageing between childhood and old age...
  7. doi request reprint Whole genome approaches to quantitative genetics
    Peter M Visscher
    Queensland Institute of Medical Research, Brisbane, Australia
    Genetica 136:351-8. 2009
    ..We review some of the theory underlying the variation in genetic identity, show applications to estimating genetic variance for height in humans and discuss other applications...
  8. pmc Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings
    Peter M Visscher
    Genetic Epidemiology Group, Queensland Institute of Medical Research, Brisbane, Australia
    PLoS Genet 2:e41. 2006
    ....
  9. ncbi request reprint The value of relatives with phenotypes but missing genotypes in association studies for quantitative traits
    Peter M Visscher
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Genet Epidemiol 30:30-6. 2006
    ..We show that a two-step procedure, in which missing genotypes are imputed and subsequently an association analysis is performed, is efficient and powerful...
  10. doi request reprint Statistical power to detect genetic Loci affecting environmental sensitivity
    Peter M Visscher
    Queensland Institute of Medical Research, Herston 4006, Australia
    Behav Genet 40:728-33. 2010
    ..3. For a locus that explains a given proportion of the variation in variance, twice the number of observations is needed for detection when compared to a locus that explains the same proportion of variation in phenotypes...
  11. pmc The limits of individual identification from sample allele frequencies: theory and statistical analysis
    Peter M Visscher
    Queensland Institute of Medical Research, Brisbane, Australia
    PLoS Genet 5:e1000628. 2009
    ..We show that these methods have similar statistical properties and have more desirable properties, in terms of type-I error rate and statistical power, than test statistics suggested in the literature...
  12. ncbi request reprint A note on the asymptotic distribution of likelihood ratio tests to test variance components
    Peter M Visscher
    Queensland Institute of Medical Research, Brisbane, Australia Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
    Twin Res Hum Genet 9:490-5. 2006
    ..The appropriate distribution of the likelihood ratio test statistic should be used in hypothesis testing and model selection...
  13. pmc Genome partitioning of genetic variation for height from 11,214 sibling pairs
    Peter M Visscher
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Am J Hum Genet 81:1104-10. 2007
    ....
  14. doi request reprint Genome-wide association studies of quantitative traits with related individuals: little (power) lost but much to be gained
    Peter M Visscher
    Genetic Epidemiology, Queensland Institute of Medical Research, Herston, Brisbane, Australia
    Eur J Hum Genet 16:387-90. 2008
    ..Therefore, the advantages of using relatives in GWAS for quantitative traits may well outweigh the small disadvantage in terms of statistical power...
  15. doi request reprint Heritability in the genomics era--concepts and misconceptions
    Peter M Visscher
    Queensland Institute of Medical Research, Royal Brisbane Hospital Post Office, Brisbane 4029, Queensland, Australia
    Nat Rev Genet 9:255-66. 2008
    ..Recent reports of substantial heritability for gene expression and new estimation methods using marker data highlight the relevance of heritability in the genomics era...
  16. ncbi request reprint Variation of estimates of SNP and haplotype diversity and linkage disequilibrium in samples from the same population due to experimental and evolutionary sample size
    P M Visscher
    Queensland Institute of Medical Research, Brisbane, Australia
    Ann Hum Genet 71:119-26. 2007
    ..The expected correlation coefficient of measures of linkage disequilibrium across samples from the same population has been quantified and found to be consistent with empirical estimates from the literature...
  17. ncbi request reprint Power of the classical twin design revisited: II detection of common environmental variance
    Peter M Visscher
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Twin Res Hum Genet 11:48-54. 2008
    ..We have developed a user-friendly web-based tool, TwinPower, to perform power calculations to detect either A or C for the classical twin design. This new tool can be found at http://genepi.qimr.edu.au/cgi-bin/twinpower.cgi...
  18. pmc Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood
    S H Lee
    The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
    Bioinformatics 28:2540-2. 2012
    ..We estimate a significant positive genetic correlation between risk of Type 2 diabetes and hypertension of ~0.31 (SE 0.14, P = 0.024)...
  19. pmc A genome-wide linkage scan for age at menarche in three populations of European descent
    Carl A Anderson
    Queensland Institute of Medical Research, Royal Brisbane Hospital, Queensland 4029, Australia
    J Clin Endocrinol Metab 93:3965-70. 2008
    ..Age at menarche (AAM) is an important trait both biologically and socially, a clearly defined event in female pubertal development, and has been associated with many clinically significant phenotypes...
  20. ncbi request reprint Calculation of IBD probabilities with dense SNP or sequence data
    Jonathan M Keith
    School of Mathematical Sciences, Queensland University of Technology, Brisbane, Qld 4001, Australia
    Genet Epidemiol 32:513-9. 2008
    ..We also confirm a previous finding that ignoring linkage disequilibrium in founder haplotypes can cause errors in the calculation of IBD probabilities...
  21. pmc Common SNPs explain a large proportion of the heritability for human height
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 42:565-9. 2010
    ....
  22. pmc Theoretical and empirical power of regression and maximum-likelihood methods to map quantitative trait loci in general pedigrees
    Xijiang Yu
    School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    Am J Hum Genet 75:17-26. 2004
    ..We show that this regression method is not necessarily more powerful nor computationally more efficient than a maximum-likelihood variance-component approach. We advocate the use of empirical power to compare trait-mapping methods...
  23. doi request reprint Prioritization of positional candidate genes using multiple web-based software tools
    Tobias A Thornblad
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Twin Res Hum Genet 10:861-70. 2007
    ..Our results suggest that the best approach to classify a minimum set of candidate genes is to take those genes that are prioritized by multiple prioritization tools...
  24. ncbi request reprint Power of the classical twin design revisited
    Peter M Visscher
    School of Biological Sciences, University of Edinburgh, Scotland, United Kingdom
    Twin Res 7:505-12. 2004
    ..All theoretical results were validated using simulation. The derived expressions can be used to calculate power of the classical twin design in a simple and rapid manner...
  25. ncbi request reprint Estimation of variance components for age at menarche in twin families
    Carl A Anderson
    Genetic Epidemiology Group, Queensland Institute of Medical Research, Brisbane 4029, Australia
    Behav Genet 37:668-77. 2007
    ..50 and 0.54, and common environmental effects to be 0.31 and 0.29, respectively. We conclude that variation in AAM can be explained by additive genetic and common environmental components...
  26. pmc Quantitative trait locus analysis of longitudinal quantitative trait data in complex pedigrees
    Stuart Macgregor
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 171:1365-76. 2005
    ..The CF-based techniques should allow efficient multivariate analyses of many data sets in human and natural population genetics...
  27. pmc Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays
    Stuart Macgregor
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Nucleic Acids Res 36:e35. 2008
    ..The large cost savings with Illumina HumanHap300-based pooling imply that future studies need only be limited by the availability of samples and not cost...
  28. pmc Data and theory point to mainly additive genetic variance for complex traits
    William G Hill
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 4:e1000008. 2008
    ..We conclude that interactions at the level of genes are not likely to generate much interaction at the level of variance...
  29. ncbi request reprint The use of linear mixed models to estimate variance components from data on twin pairs by maximum likelihood
    Peter M Visscher
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Scotland, United Kingdom
    Twin Res 7:670-4. 2004
    ..The linear mixed model framework is particularly useful for analyzing multiple traits in extended (twin) families with a large number of random effects...
  30. doi request reprint Investigation of the relationship between smoking and appendicitis in Australian twins
    Chris Oldmeadow
    Department of Mathematical Sciences, Queensland University of Technology, Mathematical Sciences, O Block, Gardens Point Campus, Brisbane, Australia
    Ann Epidemiol 18:631-6. 2008
    ..Previous studies have shown an increased risk for cigarette smokers but no accounts for the timing of exposure to smoking relative to appendectomy were made...
  31. doi request reprint Prediction of individual genetic risk of complex disease
    Naomi R Wray
    Genetic Epidemiology and Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
    Curr Opin Genet Dev 18:257-63. 2008
    ..We conclude that with larger GWAS sample sizes or by combining studies, accurate prediction of genetic risk will be possible, even if the causal mutations or the mechanisms by which they affect susceptibility are unknown...
  32. pmc Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry
    Brian P McEvoy
    Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia
    Am J Hum Genet 87:297-305. 2010
    ....
  33. pmc Association mapping in outbred populations: power and efficiency when genotyping parents and phenotyping progeny
    Stephen F Chenoweth
    Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
    Genetics 181:755-65. 2009
    ..A web-based application implementing our expressions has been developed to aid in the design of indirect association studies...
  34. doi request reprint Genetics of human height
    Brian P McEvoy
    Queensland Institute of Medical Research, Royal Brisbane Hospital Post Office, Brisbane, Queensland 4029, Australia
    Econ Hum Biol 7:294-306. 2009
    ..Despite a successful start to height gene mapping, there remain considerable theoretical, technological, and statistical hurdles to be overcome in order to unravel its full genetic basis...
  35. doi request reprint Within-family outliers: segregating alleles or environmental effects? A linkage analysis of height from 5815 sibling pairs
    Beben Benyamin
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Eur J Hum Genet 16:516-24. 2008
    ..We suggest that the effect of within-family outliers deserves further investigation via theoretical and simulation studies...
  36. doi request reprint Family-based genome-wide association studies
    Beben Benyamin
    Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029, Australia
    Pharmacogenomics 10:181-90. 2009
    ....
  37. pmc A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies
    Sang Hong Lee
    Queensland Institute of Medical Research, Herston, Queensland, Australia
    Genet Epidemiol 34:854-62. 2010
    ..This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations...
  38. pmc Geographical structure and differential natural selection among North European populations
    Brian P McEvoy
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Genome Res 19:804-14. 2009
    ....
  39. ncbi request reprint Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines
    Allan F McRae
    Genetic Epidemiology Group, Queensland Institute of Medical Research, Herston, QLD 4029, Australia
    Hum Mol Genet 16:364-73. 2007
    ..Analysis of the variability of probe binding intensities within a probe set indicated that results are robust to the possible presence of polymorphisms in the target sequences...
  40. pmc A versatile gene-based test for genome-wide association studies
    Jimmy Z Liu
    Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia
    Am J Hum Genet 87:139-45. 2010
    ..We have implemented the approach in both an easy-to-use web interface, which only requires the uploading of markers with their association p-values, and a separate downloadable application...
  41. pmc Power and SNP tagging in whole mitochondrial genome association studies
    Allan F McRae
    Queensland Institute of Medical Research, Brisbane 4006, Australia
    Genome Res 18:911-7. 2008
    ..The strong concordance in allele frequencies and linkage disequilibrium between the European sequences and the Australian sample indicates that the results presented here are transferable across populations of European descent...
  42. doi request reprint Association study of common mitochondrial variants and cognitive ability
    Enda M Byrne
    Queensland Statistical Genetics, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD, 4029, Australia
    Behav Genet 39:504-12. 2009
    ..These genes warrant further investigation in both functional and association studies with larger cohorts...
  43. pmc Sporadic cases are the norm for complex disease
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Eur J Hum Genet 18:1039-43. 2010
    ....
  44. doi request reprint Vitamin D receptor gene polymorphisms have negligible effect on human height
    Stuart Macgregor
    Genetic Epidemiology, Queensland Institute of Medical Research, Australia
    Twin Res Hum Genet 11:488-94. 2008
    ..Our results did not support any role for two other regions (rs10735810, rs7139166) of VDR in explaining variation in height...
  45. doi request reprint Comparing apples and oranges: equating the power of case-control and quantitative trait association studies
    Jian Yang
    Queensland Institute of Medical Research, Brisbane, Australia
    Genet Epidemiol 34:254-7. 2010
    ..With equal sample size, when v=K, the power of CC association study is much less than that of QT association study because of the information lost by transforming a quantitative continuous trait to a binary trait...
  46. pmc Narrowing the boundaries of the genetic architecture of schizophrenia
    Naomi R Wray
    Genetic Epidemiology and Queensland Statistical Genetics, Queensland Institute of Medical Research, 330 Herston Road, Brisbane 4029, Australia
    Schizophr Bull 36:14-23. 2010
    ..The first generation of studies have generated hypotheses that should be testable in the near future and will further narrow the boundaries on genetic architectures that are consistent with empirical data...
  47. doi request reprint The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies
    Enda M Byrne
    Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Eur J Hum Genet 16:1396-403. 2008
    ..No evidence was found for structure within ancestral groups. These results have implications for future association studies in the Australian population, and other populations of heterogeneous ancestry...
  48. pmc Common variants in TMPRSS6 are associated with iron status and erythrocyte volume
    Beben Benyamin
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Nat Genet 41:1173-5. 2009
    ..1 x 10(-10)). We also find suggestive evidence of association with blood hemoglobin levels (combined P = 5.3 x 10(-7)). These findings demonstrate the involvement of TMPRSS6 in control of iron homeostasis and in normal erythropoiesis...
  49. pmc Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels
    Beben Benyamin
    Queensland Institute of Medical Research, Brisbane 4029, Australia
    Am J Hum Genet 84:60-5. 2009
    ....
  50. pmc The genetic interpretation of area under the ROC curve in genomic profiling
    Naomi R Wray
    Genetic Epidemiology and Queensland Statistical Genetics, Queensland Institute of Medical Research, Brisbane, Australia
    PLoS Genet 6:e1000864. 2010
    ..We provide a strategy to estimate proportion of genetic variance explained on the liability scale from estimates of AUC, disease prevalence, and heritability (or sibling recurrence risk) available as an online calculator...
  51. ncbi request reprint Genome-wide linkage analysis of multiple measures of neuroticism of 2 large cohorts from Australia and the Netherlands
    Naomi R Wray
    Department of Genetic Epidemiology, Queensland Institute of Medical Research, 300 Herston Rd, Brisbane, Australia 4029
    Arch Gen Psychiatry 65:649-58. 2008
    ..Studying this personality dimension can give insights into the etiology of these important psychiatric disorders...
  52. ncbi request reprint Simple method to analyze SNP-based association studies using DNA pools
    Peter M Visscher
    Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, United Kingdom
    Genet Epidemiol 24:291-6. 2003
    ..The impact of experimental errors on the power of association studies is shown...
  53. pmc Robust estimation of experimentwise P values applied to a genome scan of multiple asthma traits identifies a new region of significant linkage on chromosome 20q13
    Manuel A R Ferreira
    Queensland Institute of Medical Research, Brisbane, Australia
    Am J Hum Genet 77:1075-85. 2005
    ....
  54. pmc Modeling linkage disequilibrium in natural populations: the example of the Soay sheep population of St. Kilda, Scotland
    Allan F McRae
    Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Genetics 171:251-8. 2005
    ....
  55. ncbi request reprint Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues
    Grant W Montgomery
    Queensland Institute of Medical Research, Brisbane, Australia
    Twin Res Hum Genet 8:346-52. 2005
    ..Our results demonstrate highly accurate and reproducible genotyping for the Affymetrix GeneChip Human Mapping Set in lymphocyte and buccal DNA samples...
  56. ncbi request reprint False disease region identification from identity-by-descent haplotype sharing in the presence of phenocopies
    Stuart Macgregor
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh, United Kingdom
    Twin Res Hum Genet 9:9-16. 2006
    ....
  57. pmc A simple linear regression method for quantitative trait loci linkage analysis with censored observations
    Carl A Anderson
    Institute of Evolutionary Biology, University of Edinburgh, Scotland
    Genetics 173:1735-45. 2006
    ..On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software...
  58. pmc Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates
    Stuart Macgregor
    Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
    Nucleic Acids Res 34:e55. 2006
    ..With 20 arrays (10 for cases, 10 for controls), over half of the information could be extracted from this sample...
  59. ncbi request reprint A simple method to localise pleiotropic susceptibility loci using univariate linkage analyses of correlated traits
    Manuel A R Ferreira
    Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane, Australia
    Eur J Hum Genet 14:953-62. 2006
    ..We illustrate the utility of our approach with a genome scan of three asthma traits measured in families with a twin proband...
  60. ncbi request reprint Precision and bias of a normal finite mixture distribution model to analyze twin data when zygosity is unknown: simulations and application to IQ phenotypes on a large sample of twin pairs
    Beben Benyamin
    Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
    Behav Genet 36:935-46. 2006
    ..For the mixture distribution model, violation of the bivariate normality assumption will produce biased estimates...
  61. ncbi request reprint Residual linkage: why do linkage peaks not disappear after an association study?
    Scott Gordon
    Queensland Institute of Medical Research, 300 Herston Road, Herston, 4029 Brisbane, Australia
    Hum Genet 121:77-82. 2007
    ..Our findings are general and apply to linkage mapping of any phenotype and to any pedigree structure...
  62. pmc HLA and genomewide allele sharing in dizygotic twins
    Grant W Montgomery
    Molecular and Genetic Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, QLD 4029, Australia
    Am J Hum Genet 79:1052-8. 2006
    ..Our results imply that gene-mapping studies based on affected sibling pairs that include DZ pairs will not suffer from false-positive results due to loci involved in embryo survival...
  63. ncbi request reprint Genetic and phenotypic stability of measures of neuroticism over 22 years
    Naomi R Wray
    Genetic Epidermology, Queensland Institute of Medical Research, Brisbane, Australia
    Twin Res Hum Genet 10:695-702. 2007
    ..33 for a single measure to .43 for mean score because of the reduction in the estimate of the environmental variance, and this will increase power in genetic linkage or association studies of neuroticism...
  64. ncbi request reprint Bias, precision and heritability of self-reported and clinically measured height in Australian twins
    Stuart Macgregor
    Genetic Epidemiology, Queensland Institute of Medical Research, Herston Road, Brisbane, Australia
    Hum Genet 120:571-80. 2006
    ..Moderate reduction in error (through the use of accurate clinical or multiple self-report measures) increased the effective sample size by 22%; elimination of measurement error led to increases in effective sample size of 41%...
  65. pmc GCTA: a tool for genome-wide complex trait analysis
    Jian Yang
    Queensland Statistical Genetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
    Am J Hum Genet 88:76-82. 2011
    ..The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets...
  66. pmc Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis
    Jodie N Painter
    Molecular Epidemiology, Queensland Institute of Medical Research, Herston, Queensland, Australia
    Nat Genet 43:51-4. 2011
    ..4 × 10⁻⁹ (OR = 1.20, 95% CI 1.13-1.27) for 'all' endometriosis in our combined datasets of 5,586 cases and 9,331 controls. rs12700667 is located in an intergenic region upstream of the plausible candidate genes NFE2L3 and HOXA10...
  67. ncbi request reprint European and Polynesian admixture in the Norfolk Island population
    B P McEvoy
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Heredity (Edinb) 105:229-34. 2010
    ..Accurate knowledge of ancestry will be important in future attempts to use the Island population in admixture mapping approaches to find the genes that underlie differences in the risk to some diseases between Europeans and Polynesians...
  68. ncbi request reprint Classification based upon gene expression data: bias and precision of error rates
    Ian A Wood
    School of Mathematical Sciences, Queensland University of Technology, Gardens Point, Brisbane, QLD, Australia
    Bioinformatics 23:1363-70. 2007
    ....
  69. ncbi request reprint A new regulatory variant in the interleukin-6 receptor gene associates with asthma risk
    J A Revez
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Genes Immun 14:441-6. 2013
    ..04-fold (P=0.0419). Genetic risk scores based on IL6R regulatory variants may prove useful in explaining variation in clinical response to tocilizumab, an anti-IL-6R monoclonal antibody...
  70. ncbi request reprint Joint multi-population analysis for genetic linkage of bipolar disorder or "wellness" to chromosome 4p
    P M Visscher
    Institute of Cell, Animal and Population Biology, University of Edinburgh, United Kingdom
    Am J Med Genet B Neuropsychiatr Genet 133:18-24. 2005
    ..Studies reporting linkage to the same region require careful scrutiny and preferably joint or meta analysis on the same basis in order to ensure that the results are truly comparable...
  71. pmc Legacy of mutiny on the Bounty: founder effect and admixture on Norfolk Island
    Stuart Macgregor
    Queensland Institute of Medical Research, Brisbane, QLD, Australia
    Eur J Hum Genet 18:67-72. 2010
    ..In conclusion, both founder effect and extreme admixture have substantially influenced the genetic architecture of a variety of CVD-related traits in this population...
  72. pmc Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion
    A A E Vinkhuyzen
    Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Transl Psychiatry 2:e102. 2012
    ....
  73. doi request reprint Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses
    P M Visscher
    Queensland Institute of Medical Research, Herston, Queensland, Australia
    Mol Psychiatry 17:474-85. 2012
    ..We conclude that larger experimental sample sizes are essential to further our understanding of the biology underlying psychiatric disorders...
  74. doi request reprint Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents
    E M Byrne
    Queensland Statistical Genetics, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4029, Australia
    Diabetologia 52:2359-68. 2009
    ....
  75. ncbi request reprint Prediction of the confidence interval of quantitative trait Loci location
    Peter M Visscher
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
    Behav Genet 34:477-82. 2004
    ..It is shown that this shape explains why confidence intervals from the Log of Odds (LOD) drop-off method and bootstrap results frequently differ for real data sets...
  76. pmc Linkage disequilibrium in the domesticated pig
    Jeremie Nsengimana
    Universite Catholique de Louvain, Faculte d Ingenierie Biologique, agronomique et environnementale, Unité de Génétique, 1348 Louvain la Neuve, Belgium
    Genetics 166:1395-404. 2004
    ..These results suggest that mapping methods based on LD may be valuable even with only moderately dense marker spacing in pigs...
  77. ncbi request reprint On the mapping of quantitative trait loci at marker and non-marker locations
    Grant A Walling
    Roslin Institute Edinburgh, Roslin, Midlothian EH25 9PS, UK
    Genet Res 79:97-106. 2002
    ..This study discusses the impact the findings could have on the calculation of thresholds and confidence intervals produced by bootstrap methods...
  78. pmc Longitudinal variance-components analysis of the Framingham Heart Study data
    Stuart Macgregor
    Biostatistics and Bioinformatics Unit, University of Wales College of Medicine, Heath Hospital, Cardiff, United Kingdom
    BMC Genet 4:S22. 2003
    ..The traits of interest were BMI, HDLC, total cholesterol, and height. The longitudinal method allowed the characterization of the change in QTL effects with aging. A QTL affecting BMI was shown to act mainly at early ages...
  79. ncbi request reprint Is schizophrenia linked to chromosome 1q?
    Stuart Macgregor
    Institute of Cell, Animal and Population Biology, Ashworth Laboratory, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
    Science 298:2277; author reply 2277. 2002
  80. ncbi request reprint Power of QTL detection using association tests with family controls
    Jules Hernández-Sánchez
    Roslin Institute Edinburgh, Roslin, Midlothian EH25 9PS, Scotland, UK
    Eur J Hum Genet 11:819-27. 2003
    ..Deterministic power calculations are a powerful tool for researchers to plan and evaluate experiments and obviate the need for elaborate simulation studies...
  81. pmc Quantitative trait loci variation for growth and obesity between and within lines of pigs (Sus scrofa)
    Yoshitaka Nagamine
    Division of Genetics and Biometry, Roslin Institute Edinburgh, Midlothian EH25 9PS, United Kingdom
    Genetics 164:629-35. 2003
    ....
  82. pmc SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis
    Stephanie Le Hellard
    Medical Genetics Section, Molecular Medicine Centre, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
    Nucleic Acids Res 30:e74. 2002
    ..Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies...
  83. pmc Novel multilocus measure of linkage disequilibrium to estimate past effective population size
    Ben J Hayes
    Victorian Institute of Animal Science, Department of Natural Resources and Environment, Attwood, Victoria, 3049, Australia
    Genome Res 13:635-43. 2003
    ..Results indicated an exponentially increasing N in humans and a declining N in dairy cattle. CSH is a valuable statistic for inferring population histories from haplotype data, and has implications for mapping of disease loci...
  84. pmc Conventional multipoint nonparametric linkage analysis is not necessarily inherently biased
    Peter M Visscher
    Am J Hum Genet 75:718-20; author reply 723-7. 2004
  85. doi request reprint Linkage analysis in a large family from Pakistan with depression and a high incidence of consanguineous marriages
    Muhammad Ayub
    St Luke s Hospital, Middlesborough, UK
    Hum Hered 66:190-8. 2008
    ..The effect of inbreeding on linkage analysis in an extended pedigree is discussed...
  86. doi request reprint Estimation of the time of divergence between Japanese Mishima Island cattle and other cattle populations using microsatellite DNA markers
    Yoshitaka Nagamine
    National Institute of Livestock and Grassland Science, Tsukuba 305 0901, Japan
    J Hered 99:202-7. 2008
    ..51-0.60. However, historical reports dated over 100 years do not support changes in fertility, so that there is no evidence for inbreeding depression...
  87. ncbi request reprint Identification of twin pairs from large population-based samples
    Dinand Webbink
    CPB Netherlands Bureau for Economic Policy Analysis, The Hague, The Netherlands
    Twin Res Hum Genet 9:496-500. 2006
    ....
  88. pmc Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries)
    Dario Beraldi
    Institute of Evolutionary Biology, University of Edinburgh, UK
    Genetics 173:1521-37. 2006
    ..These findings represent an advance in the dissection of the genetic diversity in the wild and provide the foundation for QTL analyses in the study population...
  89. pmc Estimation of recombination rate and detection of recombination hotspots from dense single-nucleotide polymorphism trio data
    Peter M Visscher
    Genetics 173:2415-7. 2006
  90. pmc Recent human effective population size estimated from linkage disequilibrium
    Albert Tenesa
    Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh, UK
    Genome Res 17:520-6. 2007
    ..The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago...
  91. ncbi request reprint Mapping quantitative trait Loci underlying fitness-related traits in a free-living sheep population
    Dario Beraldi
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
    Evolution 61:1403-16. 2007
    ..We discuss the prospects for refining estimates of QTL position and effect size in the study population, and for QTL searches in free-living pedigrees in general...
  92. ncbi request reprint QTL Express: mapping quantitative trait loci in simple and complex pedigrees
    George Seaton
    Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    Bioinformatics 18:339-40. 2002
    ..User input of three files containing a marker map, trait data and marker genotypes allows mapping of single or multiple QTL by the regression approach, with the option to perform permutation or bootstrap tests...
  93. ncbi request reprint Replicated linkage for eye color on 15q using comparative ratings of sibling pairs
    Danielle Posthuma
    Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
    Behav Genet 36:12-7. 2006
    ..A. Teasdale, R. D, and Box, N. F. (2001). Gene 277:49-62]. Our results demonstrate that comparative measures on relatives can be used in genetic linkage analysis...
  94. ncbi request reprint Large, consistent estimates of the heritability of cognitive ability in two entire populations of 11-year-old twins from Scottish mental surveys of 1932 and 1947
    Beben Benyamin
    School of Biological Sciences, University of Edinburgh, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
    Behav Genet 35:525-34. 2005
    ..More generally for studies in genetics, the methodological innovation developed here implies that large (national) data collections can provide sufficient information on twin pairs to estimate genetic parameters, even without zygosity...
  95. pmc Combined genome scans for body stature in 6,602 European twins: evidence for common Caucasian loci
    Markus Perola
    Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
    PLoS Genet 3:e97. 2007
    ..To facilitate the genetic studies of stature we have also set up a website that lists all stature genome scans published and their most significant loci (http://www.genomeutwin.org/stature_gene_map.htm)...
  96. ncbi request reprint Genome-wide linkage disequilibrium from 100,000 SNPs in the East Finland founder population
    Pekka Uimari
    Jurilab Ltd, Microkatu 1, 70210 Kuopio, Finland
    Twin Res Hum Genet 8:185-97. 2005
    ..However, the recombination rate does not explain all the variation found in LD. We also report a number of long chromosomal regions where exceptionally high or low LD were detected...
  97. ncbi request reprint Does sharing the same class in school improve cognitive abilities of twins?
    Dinand Webbink
    CPB Netherlands Bureau for Economic Policy Analysis, The Hague, The Netherlands
    Twin Res Hum Genet 10:573-80. 2007
    ..In the analysis of the effect of a separation of at least 3 years we find that separation increases language performance between Grade 6 and 8 for opposite-sex pairs...
  98. ncbi request reprint Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)
    Dario Beraldi
    Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
    Int J Parasitol 37:121-9. 2007
    ....
  99. ncbi request reprint Power of direct vs. indirect haplotyping in association studies
    Stuart Thomas
    Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh, UK
    Genet Epidemiol 26:116-24. 2004
    ..In the context of multipurpose, prospective cohort studies (e.g., the UK Biobank study), there may be a general value in establishing a series of directly haplotyped individuals to serve as controls for a number of alternative studies...