Peter Holmans

Summary

Affiliation: Cardiff University
Country: UK

Publications

  1. doi request reprint Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits
    Peter Holmans
    Biostatistics and Bioinformatics Unit, MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
    Adv Genet 72:141-79. 2010
  2. pmc Large-scale linkage analysis of 1302 affected relative pairs with rheumatoid arthritis
    Marian L Hamshere
    Biostatistics and Bioinformatics Unit and Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
    BMC Proc 1:S100. 2007
  3. pmc Combining linkage data sets for meta-analysis and mega-analysis: the GAW15 rheumatoid arthritis data set
    Ricardo Segurado
    Biostatistics and Bioinformatics Unit and Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
    BMC Proc 1:S104. 2007
  4. pmc The effect of linkage disequilibrium on linkage analysis of incomplete pedigrees
    Douglas F Levinson
    Department of Psychiatry, University of Pennsylvania School of Medicine, 353 Market Street, Philadelphia, PA, USA
    BMC Genet 6:S6. 2005
  5. pmc Covariate linkage analysis of GAW14 simulated data incorporating subclinical phenotype, sex, population, parent-of-origin, and interaction
    Marian L Hamshere
    Biostatistics and Bioinformatics Unit, Cardiff University, Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    BMC Genet 6:S45. 2005
  6. ncbi request reprint Genome screen for loci influencing age at onset and rate of decline in late onset Alzheimer's disease
    Peter Holmans
    Biostatistics and Bioinformatics Unit, Wales College of Medicine, Heath Park, Cardiff, United Kingdom
    Am J Med Genet B Neuropsychiatr Genet 135:24-32. 2005
  7. pmc Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder
    Peter Holmans
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Heath Park, CF23 6BQ Cardiff, UK
    Am J Hum Genet 85:13-24. 2009
  8. doi request reprint Identification of loci associated with schizophrenia by genome-wide association and follow-up
    Michael C O'Donovan
    Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
    Nat Genet 40:1053-5. 2008
  9. pmc Permutation-based approaches do not adequately allow for linkage disequilibrium in gene-wide multi-locus association analysis
    Valentina Moskvina
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
    Eur J Hum Genet 20:890-6. 2012
  10. pmc An examination of single nucleotide polymorphism selection prioritization strategies for tests of gene-gene interaction
    Valentina Moskvina
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
    Biol Psychiatry 70:198-203. 2011

Detail Information

Publications46

  1. doi request reprint Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits
    Peter Holmans
    Biostatistics and Bioinformatics Unit, MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
    Adv Genet 72:141-79. 2010
    ..Finally, a list of computer programs for performing pathway analysis on genome-wide association data is provided...
  2. pmc Large-scale linkage analysis of 1302 affected relative pairs with rheumatoid arthritis
    Marian L Hamshere
    Biostatistics and Bioinformatics Unit and Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
    BMC Proc 1:S100. 2007
    ....
  3. pmc Combining linkage data sets for meta-analysis and mega-analysis: the GAW15 rheumatoid arthritis data set
    Ricardo Segurado
    Biostatistics and Bioinformatics Unit and Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
    BMC Proc 1:S104. 2007
    ..The two approaches were compared, and give strong support to the HLA locus on chromosome 6 as a susceptibility locus. Other regions of interest include loci on chromosomes 11, 2, and 12...
  4. pmc The effect of linkage disequilibrium on linkage analysis of incomplete pedigrees
    Douglas F Levinson
    Department of Psychiatry, University of Pennsylvania School of Medicine, 353 Market Street, Philadelphia, PA, USA
    BMC Genet 6:S6. 2005
    ..Simulation studies on the observed pedigree structures and map can also be used to determine the effect of LD on a particular study...
  5. pmc Covariate linkage analysis of GAW14 simulated data incorporating subclinical phenotype, sex, population, parent-of-origin, and interaction
    Marian L Hamshere
    Biostatistics and Bioinformatics Unit, Cardiff University, Wales College of Medicine, Heath Park, Cardiff CF14 4XN, UK
    BMC Genet 6:S45. 2005
    ..Focusing on a randomly chosen replicate (42) we investigated the effect of the 12 subclinical phenotypes, sex, population, and parent-of-origin on the linkage signal from a model-free linkage analysis of Kofendrerd Personality Disorder...
  6. ncbi request reprint Genome screen for loci influencing age at onset and rate of decline in late onset Alzheimer's disease
    Peter Holmans
    Biostatistics and Bioinformatics Unit, Wales College of Medicine, Heath Park, Cardiff, United Kingdom
    Am J Med Genet B Neuropsychiatr Genet 135:24-32. 2005
    ..08) and chromosome 9 (max LOD = 3.34). The previously reported genome-wide linkage of AD to chromosome 10 was not influenced by any of the covariates studied...
  7. pmc Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder
    Peter Holmans
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Heath Park, CF23 6BQ Cardiff, UK
    Am J Hum Genet 85:13-24. 2009
    ..The method was also applied to a meta-analysis of bipolar disorder, and it implicated the modulation of transcription and cellular activity, including that which occurs via hormonal action, as an important player in pathogenesis...
  8. doi request reprint Identification of loci associated with schizophrenia by genome-wide association and follow-up
    Michael C O'Donovan
    Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
    Nat Genet 40:1053-5. 2008
    ..Meta-analysis provided strongest evidence for association around ZNF804A (P = 1.61 x 10(-7)) and this strengthened when the affected phenotype included bipolar disorder (P = 9.96 x 10(-9))...
  9. pmc Permutation-based approaches do not adequately allow for linkage disequilibrium in gene-wide multi-locus association analysis
    Valentina Moskvina
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
    Eur J Hum Genet 20:890-6. 2012
    ....
  10. pmc An examination of single nucleotide polymorphism selection prioritization strategies for tests of gene-gene interaction
    Valentina Moskvina
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
    Biol Psychiatry 70:198-203. 2011
    ..Aiming to minimize these statistical and computational burdens, we have explored approaches to prioritize SNPs for interaction analyses...
  11. pmc A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk
    Jade Chapman
    MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
    Hum Mol Genet 22:816-24. 2013
    ..Thus, in contrast to diseases such as schizophrenia, autism and attention deficit/hyperactivity disorder, CNVs do not appear to make a significant contribution to the development of AD...
  12. pmc Genome-wide analysis of copy number variants in attention deficit hyperactivity disorder: the role of rare variants and duplications at 15q13.3
    Nigel M Williams
    Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, and School of Medicine, Cardiff University, Cardiff, UK
    Am J Psychiatry 169:195-204. 2012
    ..Because of its multifactorial etiology, however, identifying the genes involved has been difficult. The authors followed up on recent findings suggesting that rare copy number variants (CNVs) may be important for ADHD etiology...
  13. doi request reprint Most genome-wide significant susceptibility loci for schizophrenia and bipolar disorder reported to date cross-traditional diagnostic boundaries
    Hywel J Williams
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Cardiff University, Cardiff, UK
    Hum Mol Genet 20:387-91. 2011
    ..7 × 10(-5)). Including earlier reported data for trans-disorder effects for ZNF804A and CACNA1C, six out of eight of the most robustly associated loci for either disorder show trans-disorder effects...
  14. ncbi request reprint Effects of differential genotyping error rate on the type I error probability of case-control studies
    Valentina Moskvina
    Bioinformatics and Biostatistics Unit, School of Medicine, Wales College of Medicine, Cardiff University, Cardiff, UK
    Hum Hered 61:55-64. 2006
    ....
  15. pmc A comparison of four clustering methods for brain expression microarray data
    Alexander L Richards
    Department of Psychological Medicine, School of Medicine, University Hospital Wales, Heath Park, Cardiff, Wales, UK
    BMC Bioinformatics 9:490. 2008
    ..The results are compared on speed, gene coverage and GO enrichment. The effects of combining the clusters produced by each method are also assessed...
  16. pmc Convergent evidence that oligodendrocyte lineage transcription factor 2 (OLIG2) and interacting genes influence susceptibility to schizophrenia
    Lyudmila Georgieva
    Department of Psychological Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
    Proc Natl Acad Sci U S A 103:12469-74. 2006
    ..Our data provide strong convergent evidence that variation in OLIG2 confers susceptibility to schizophrenia alone and as part of a network of genes implicated in oligodendrocyte function...
  17. pmc Support for the involvement of large copy number variants in the pathogenesis of schizophrenia
    George Kirov
    Department of Psychological Medicine, Cardiff University, Heath Park, Cardiff, UK
    Hum Mol Genet 18:1497-503. 2009
    ..2 and schizophrenia (P = 0.026). This study confirms the involvement of rare CNVs in the pathogenesis of schizophrenia and contributes to the growing list of specific CNVs that are implicated...
  18. pmc A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease
    Peter Holmans
    Department of Psychological Medicine and Neurology, Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre in Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
    Hum Mol Genet 22:1039-49. 2013
    ....
  19. pmc Evaluation of an approximation method for assessment of overall significance of multiple-dependent tests in a genomewide association study
    Valentina Moskvina
    MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
    Genet Epidemiol 35:861-6. 2011
    ..This is particularly relevant at a time of increasing public availability of significantly larger genetic data sets and should go a long way to assist in the rapid analysis of these data sets...
  20. pmc Strong evidence that KIAA0319 on chromosome 6p is a susceptibility gene for developmental dyslexia
    Natalie Cope
    Department of Psychological Medicine, Wales College of Medicine, Cardiff University, Cardiff, United Kingdom
    Am J Hum Genet 76:581-91. 2005
    ..006 in trios; 1-degree-of-freedom tests). Our data strongly implicate KIAA0319 as a susceptibility gene for dyslexia. The gene product is expressed in brain, but its specific function is currently unknown...
  21. pmc Genomewide significant linkage to recurrent, early-onset major depressive disorder on chromosome 15q
    Peter Holmans
    Biostatistics and Bioinformatics Unit, University of Wales College of Medicine, Cardiff, United Kingdom
    Am J Hum Genet 74:1154-67. 2004
    ..Chromosome 15q25.3-26.2 deserves further study as a candidate region for susceptibility to MDD...
  22. ncbi request reprint Streamlined analysis of pooled genotype data in SNP-based association studies
    Valentina Moskvina
    Bioinformatics and Biostatistics Unit, College of Medicine, Cardiff University, United Kingdom
    Genet Epidemiol 28:273-82. 2005
    ..By controlling the error rates in the absence of knowledge of the appropriate SNP-specific correction factors, each approach enhances the performance of DNA pooling, while considerably streamlining the method by reducing time and cost...
  23. pmc Analyses of single marker and pairwise effects of candidate loci for rheumatoid arthritis using logistic regression and random forests
    Beate Glaser
    Biostatistics and Bioinformatics Unit, and Department of Psychological Medicine, Cardiff University, School of Medicine, Heath Park, Cardiff, Wales, CF14 4XN, UK
    BMC Proc 1:S54. 2007
    ..Follow-up analysis, such as by LR, is required since RFs do not indicate high-risk genotype combinations...
  24. pmc Clinical and cognitive characteristics of children with attention-deficit hyperactivity disorder, with and without copy number variants
    Kate Langley
    Department of Psychological Medicine and Neurology, and MRC Centre for Neuropsychiatric Genetics, Cardiff University, Cardiff, UK
    Br J Psychiatry 199:398-403. 2011
    ..Submicroscopic, rare chromosomal copy number variants (CNVs) contribute to neurodevelopmental disorders but it is not known whether they define atypical clinical cases...
  25. pmc Rare chromosomal deletions and duplications in attention-deficit hyperactivity disorder: a genome-wide analysis
    Nigel M Williams
    MRC Centre in Neuropsychiatric Genetics and Genomics and Department of Psychological Medicine and Neurology, Cardiff University School of Medicine, Cardiff, UK
    Lancet 376:1401-8. 2010
    ..We aimed to establish whether burden of CNVs was increased in ADHD, and to investigate whether identified CNVs were enriched for loci previously identified in autism and schizophrenia...
  26. ncbi request reprint Genetics of recurrent early-onset major depression (GenRED): final genome scan report
    Peter Holmans
    Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 701A Welch Rd, Suite 3325, Palo Alto, CA 94304 5797, USA
    Am J Psychiatry 164:248-58. 2007
    ....
  27. pmc Association of late-onset Alzheimer's disease with genetic variation in multiple members of the GAPD gene family
    Yonghong Li
    Celera Diagnostics, Alameda, CA 94502, USA
    Proc Natl Acad Sci U S A 101:15688-93. 2004
    ..Our observations raise the possibility that GAPD genes are AD risk factors, a hypothesis that is consistent with the role of GAPD in neuronal apoptosis...
  28. ncbi request reprint Association of ABCA1 with late-onset Alzheimer's disease is not observed in a case-control study
    Yonghong Li
    Celera Diagnostics, Alameda, CA, USA
    Neurosci Lett 366:268-71. 2004
    ..Further, we did not observe significant and replicated association of other ABCA1 SNPs we examined with the disease, thus these ABCA1 variants do not appear to influence the risk of LOAD in this study...
  29. ncbi request reprint Investigating the role of p11 (S100A10) sequence variation in susceptibility to major depression
    Ranjana Verma
    Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Am J Med Genet B Neuropsychiatr Genet 144:1079-82. 2007
    ..2%, P = 0.15). None of the tag SNPs showed any evidence of association. Our results do not support a major role for either common or rare p11 SNPs with MDD. Several limitations of the study are discussed...
  30. ncbi request reprint Alpha-T-catenin is expressed in human brain and interacts with the Wnt signaling pathway but is not responsible for linkage to chromosome 10 in Alzheimer's disease
    Victoria Busby
    Department of Neuroscience, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
    Neuromolecular Med 5:133-46. 2004
    ..None of these SNPs was associated with disease. Although an excellent candidate, we conclude that CTNNA3 is unlikely to account for the AD susceptibility locus on chromosome 10...
  31. ncbi request reprint Variation in the urokinase-plasminogen activator gene does not explain the chromosome 10 linkage signal for late onset AD
    Amanda J Myers
    Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri, USA
    Am J Med Genet B Neuropsychiatr Genet 124:29-37. 2004
    ..Eight polymorphisms spanning the entire gene were examined using case control (CC) and family-based association methods. No association was observed by any method making it unlikely that variation in PLAU explains our linkage data...
  32. ncbi request reprint Genetics of recurrent early-onset depression (GenRED): design and preliminary clinical characteristics of a repository sample for genetic linkage studies
    Douglas F Levinson
    Department of Psychiatry and Center for Neurobiology and Behavior, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104 3309, USA
    Am J Med Genet B Neuropsychiatr Genet 119:118-30. 2003
    ..This suggests comparability of our cases to those in earlier large family studies. This dataset should prove useful for genetic studies of a highly familial form of major depressive disorder...
  33. ncbi request reprint Genetic association of the APP binding protein 2 gene (APBB2) with late onset Alzheimer disease
    Yonghong Li
    Celera Diagnostics, Alameda, California 94502, USA
    Hum Mutat 25:270-7. 2005
    ..43 [95% CI: 1.61-3.67]; OR(het)=2.15 [95% CI: 1.46-3.17]; P=0.00006) in the combined sample set. Our data raise the possibility that genetic variations in APBB2 may affect LOAD susceptibility...
  34. ncbi request reprint Full genome screen for Alzheimer disease: stage II analysis
    Amanda Myers
    Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Am J Med Genet 114:235-44. 2002
    ..Of the seven markers we tested in family-based and case control samples, the only nominally positive association we found was with the 167 bp allele of marker D10S1217 (chi-square=7.11, P=0.045, df=1)...
  35. ncbi request reprint Association studies between risk for late-onset Alzheimer's disease and variants in insulin degrading enzyme
    Petra Nowotny
    Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA
    Am J Med Genet B Neuropsychiatr Genet 136:62-8. 2005
    ..Although our results are not universally negative, we were unable to replicate the results of previous studies and conclude that common variants or haplotypes of these variants in IDE are not major risk factors for LOAD...
  36. ncbi request reprint Genetics of recurrent early-onset major depression (GenRED): significant linkage on chromosome 15q25-q26 after fine mapping with single nucleotide polymorphism markers
    Douglas F Levinson
    Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 701A Welch Rd, Suite 3325, Palo Alto, CA 94304 5797, USA
    Am J Psychiatry 164:259-64. 2007
    ....
  37. ncbi request reprint Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants
    Andrew Grupe
    Celera Diagnostics, 1401 Harbor Bay Parkway, Alameda, CA 94502, USA
    Hum Mol Genet 16:865-73. 2007
    ..This is a missense mutation in the galanin-like peptide precursor gene (P = 0.00005, OR = 1.2, false positive rate = 0.87)...
  38. pmc A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease
    Andrew Grupe
    Celera Diagnostics, Alameda, CA, USA
    Am J Hum Genet 78:78-88. 2006
    ..0165). These results indicate that variants in the RPS3A homologue are associated with LOAD and implicate this gene, adjacent genes, or other functional variants (e.g., noncoding RNAs) in the pathogenesis of this disorder...
  39. ncbi request reprint Bipolar affective puerperal psychosis: genome-wide significant evidence for linkage to chromosome 16
    Ian Jones
    Department of Psychological Medicine, Henry Wellcome Building, Wales School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN UK
    Am J Psychiatry 164:1099-104. 2007
    ..The authors conducted a search by systematic whole genome linkage scan for loci influencing vulnerability to bipolar affective puerperal psychosis...
  40. ncbi request reprint Detecting gene-gene interactions using affected sib pair analysis with covariates
    Peter Holmans
    MRC Biostatistics Unit, Cambridge, UK
    Hum Hered 53:92-102. 2002
    ..If disease-associated genotypes are available, it may be worth re-analysing the whole genome...
  41. ncbi request reprint Evidence that common variation in NEDD9 is associated with susceptibility to late-onset Alzheimer's and Parkinson's disease
    Yonghong Li
    Celera, 1401 Harbor Bay Parkway, Alameda, CA 94502, USA
    Hum Mol Genet 17:759-67. 2008
    ..These data implicate NEDD9 as a novel susceptibility gene for LOAD and possibly PD...
  42. pmc Linkage disequilibrium mapping of a chromosome 15q25-26 major depression linkage region and sequencing of NTRK3
    Ranjana Verma
    Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Biol Psychiatry 63:1185-9. 2008
    ..Here we present initial linkage-disequilibrium (LD) fine mapping of this signal and sequence analysis of NTRK3 (neurotrophic receptor kinase-3), a biologically plausible candidate gene...
  43. ncbi request reprint Ubiquilin 1 polymorphisms are not associated with late-onset Alzheimer's disease
    Scott Smemo
    Department of Psychiatry, Washington University School of Medicine, 660 S Euclid Street, St Louis, MO 63110, USA
    Ann Neurol 59:21-6. 2006
    ..We did not find any evidence that this single nucleotide polymorphism, or any of six others tested in UBQLN1, increases risk for LOAD...
  44. ncbi request reprint Genomewide linkage scan in schizoaffective disorder: significant evidence for linkage at 1q42 close to DISC1, and suggestive evidence at 22q11 and 19p13
    Marian L Hamshere
    Department of Psychological Medicine, School of Medicine, Cardiff University, Wales
    Arch Gen Psychiatry 62:1081-8. 2005
    ..However, twin data suggest that, in addition to genes with specificity for these phenotypes, there exist genes that simultaneously influence susceptibility to schizophrenia, bipolar disorder, and schizoaffective disorder...
  45. ncbi request reprint Multiple testing in the genomics era: findings from Genetic Analysis Workshop 15, Group 15
    Lisa J Martin
    Department of Pediatrics, Cincinnati Children s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Genet Epidemiol 31:S124-31. 2007
    ..We show that while each approach may have certain advantages, adequate error control is largely dependent upon the question under consideration and often requires the use of multiple analytic strategies...
  46. ncbi request reprint A survey of genetic human cortical gene expression
    Amanda J Myers
    Laboratory of Neurogenetics, National Institute on Aging, Porter Neuroscience Building, National Institutes of Health Main Campus, Bethesda, Maryland 20892, USA
    Nat Genet 39:1494-9. 2007
    ....