Genomes and Genes
Affiliation: University of Southampton
- Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutationsWilliam J Tapper
Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
PLoS ONE 9:e86940. 2014..We therefore recommend non-default settings of the AFS in combination with stringent quality control when searching for causal mutation(s) that could have low levels of mutant reads due to post-zygotic mutation. ..
- A sequence-based integrated map of chromosome 22W J Tapper
Human Genetics Research Division, Southampton General Hospital, Southampton SO16 6YD, UK
Genome Res 11:1290-5. 2001..This sequence-based integrated map is represented in the genetic location database (LDB2000), which is available at http://cedar.genetics.soton.ac.uk/public_html/LDB2000.html...
- Recombination, interference and sequence: comparison of chromosomes 21 and 22W J Tapper
Human Genetic Research Division, University of Southampton, UK
Ann Hum Genet 66:75-86. 2002..These repeats are widely distributed on chromosome 22, perhaps offering greater opportunities for double recombinants to occur within smaller regions, whereas they are largely subtelomeric in distribution on chromosome 21...
- A metric linkage disequilibrium map of a human chromosomeW J Tapper
Human Genetics Division, School of Medicine, Southampton General Hospital, University of Southampton, Southampton, SO16 6YD, UK
Ann Hum Genet 67:487-94. 2003..Further analyses which investigate selection of informative SNPs and the effect of SNP allele frequency and marker density will refine this estimate...
- The influence of genetic variation in 30 selected genes on the clinical characteristics of early onset breast cancerWilliam Tapper
Human Genetics and Cancer Sciences Divisions, School of Medicine, Southampton General Hospital, University of Southampton, Southampton, SO16 6YD, UK
Breast Cancer Res 10:R108. 2008..Common variants that alter breast cancer risk are being discovered. Here, we determine how these variants influence breast cancer prognosis, risk and tumour characteristics...
- A comparison of methods to detect recombination hotspotsWilliam Tapper
Human Genetics Division, School of Medicine, Southampton General Hospital, University of Southampton, Southampton, UK
Hum Hered 66:157-69. 2008..We determine the correspondence between LDMAP and LDhat, and between LDMAP and LDhot by comparison with linkage maps and hotspots that have been verified by sperm typing...
- Extended tracts of homozygosity in outbred human populationsJane Gibson
Human Genetics Research Division, School of Medicine, University of Southampton, Southampton SO16 6YD, UK
Hum Mol Genet 15:789-95. 2006..Possible alternative mechanisms and the implications of long homozygous tracts in the genome are discussed...
- Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium mapsWeihua Zhang
Human Genetics Division, Duthie Building Mailpoint 808, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, United Kingdom
Proc Natl Acad Sci U S A 101:18075-80. 2004....
- CHROMSCAN: genome-wide association using a linkage disequilibrium mapAndrew Collins
Human Genetics Division, Southampton General Hospital, University of Southampton, School of Medicine, Duthie Building Mp808, Southampton SO 16 6YD, UK
J Hum Genet 53:121-6. 2008..Effective meta-analysis across multiple samples, increasingly important to combine evidence from genome-wide and other association data, is achieved through the weighted combination of location evidence provided by the programme...
- Genome-wide association of breast cancer: composite likelihood with imputed genotypesIoannis Politopoulos
Genetic Epidemiology and Bioinformatics Research Group, Human Genetics Research Division, University of Southampton, School of Medicine, Southampton General Hospital, Hants, UK
Eur J Hum Genet 19:194-9. 2011..Meta-analysis, which combines weighted evidence from composite likelihood in different samples, and refines putative disease locations, is facilitated through defining fixed regions on an underlying LD map...
- Effects of single SNPs, haplotypes, and whole-genome LD maps on accuracy of association mappingNikolas Maniatis
Human Genetics Division, University of Southampton, Southampton General Hospital, Southampton, UK
Genet Epidemiol 31:179-88. 2007..The results of the present study demonstrate the great potential of the genome HapMap LDU maps for high-resolution mapping of complex phenotypes...
- Determination of a gene and environment risk model for age-related macular degenerationJane Gibson
Genetic Epidemiology and Bioinformatics Group, University of Southampton, Human Genetics Division, Southampton General Hospital, Southampton, UK
Br J Ophthalmol 94:1382-7. 2010..In the current study we interrogated the genomic region in linkage disequilibrium (LD) with the SERPING1 gene, and modelled the contribution to disease of known genetic and environmental AMD risk factors...
- Positional cloning by linkage disequilibriumNikolas Maniatis
Human Genetics Division, University of Southampton, Southampton SO16 6YD, United Kingdom
Am J Hum Genet 74:846-55. 2004..These results provide a guide to efficient positional cloning by SNPs and a benchmark against which the power of positional cloning by haplotype-based alternatives may be measured...
- Composite likelihood-based meta-analysis of breast cancer association studiesIoannis Politopoulos
Genetic Epidemiology and Bioinformatics Research Group, Human Genetics Research Division, University of Southampton, School of Medicine, Southampton General Hospital, Hampshire, UK
J Hum Genet 56:377-82. 2011..The PIK3AP1 gene region is highlighted in this analysis as a strong candidate for further study...
- The JAK2 46/1 haplotype predisposes to MPL-mutated myeloproliferative neoplasmsAmy V Jones
Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, United Kingdom
Blood 115:4517-23. 2010..No difference in sequence, splicing, or expression of JAK2 was found on 46/1 compared with other haplotypes, suggesting that any functional difference of JAK2 on 46/1, if it exists, must be relatively subtle...
- Cosmopolitan linkage disequilibrium mapsJane Gibson
Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
Hum Genomics 2:20-7. 2005..Although there must be finer scale differences between populations due to other processes (mutation, drift, selection), the results suggest that a whole-genome standard LD map would indeed be a useful resource for disease gene mapping...
- Association between the SERPING1 gene and age-related macular degeneration: a two-stage case-control studySarah Ennis
Genetic Epidemiology and Bioinformatics Group, University of Southampton, Human Genetics Division MP 808, Southampton General Hospital, Southampton, UK
Lancet 372:1828-34. 2008..Variants in complement 3 (C3) and an HLA locus containing both factor B and C2 genes have also been implicated. We aimed to identify further genetic risk factors for this disease...
- A genome wide meta-analysis study for identification of common variation associated with breast cancer prognosisSajjad Rafiq
Genetic Epidemiology and Bioinformatics Research Group, Human Genetics, Faculty of Medicine, University of Southampton, Southampton General Hospital, Hants, United Kingdom
PLoS ONE 9:e101488. 2014..We attempt to identify those SNPs which could impact overall survival irrespective of the age of onset...
- Support Vector Machine classifier for estrogen receptor positive and negative early-onset breast cancerRosanna Upstill-Goddard
Human Genetics and Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
PLoS ONE 8:e68606. 2013..Functional classification of the genes involved identifies enrichment of functions linked to the immune system, which is consistent with the current understanding of the biological role of estrogen receptors in breast cancer. ..
- Genome scanning by composite likelihoodNewton Morton
Human Genetics Division, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD, UK
Am J Hum Genet 80:19-28. 2007..An extension to meta-analysis is proposed. Other approaches to genome scanning and meta-analysis should, if possible, be similarly extended so that their operating characteristics can be compared...
- Mapping genes for common diseases: the case for genetic (LD) mapsAndrew Collins
Human Genetics, School of Medicine, University of Southampton, Southampton, UK
Hum Hered 58:2-9. 2004..The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence...
- Haplotypic analysis of the MMP-9 gene in relation to coronary artery diseaseAngharad R Morgan
Human Genetics Division, School of Medicine, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
J Mol Med (Berl) 81:321-6. 2003....
- Does haplotype diversity predict power for association mapping of disease susceptibility?Weihua Zhang
Human Genetics Division, University of Southampton, Southampton General Hospital, SO16 6YD Southampton, UK
Hum Genet 115:157-64. 2004..TagSNPs that are assigned to bins instead of haplotype blocks also lose power compared with random SNPs. This evidence favours a multi-stage design in which both models and density change adaptively...
- Identification of inherited genetic variations influencing prognosis in early-onset breast cancerSajjad Rafiq
Genetic Epidemiology and Bioinformatics Research Group, Human Genetics Research Division, University of Southampton School of Medicine, Southampton General Hospital, United Kingdom
Cancer Res 73:1883-91. 2013..7 years; Wilcoxon rank-sum test CC vs. CT, P = 4 × 10(-4) and CT vs. TT, P = 0.76). Four further loci may also be associated with prognosis...
- Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genesKatja Christodoulou
Genetic Epidemiology and Genomic Informatics Group, Human Genetics and Genomic Medicine, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK
Gut 62:977-84. 2013..Paediatric patients often manifest more extensive disease and a particularly severe disease course. It is likely that genetic predisposition plays a more substantial role in this group...
- Exome-based linkage disequilibrium maps of individual genes: functional clustering and relationship to diseaseJane Gibson
Genetic Epidemiology and Genomic Informatics Group, Human Genetics, University of Southampton, Southampton General Hospital, Southampton, UK
Hum Genet 132:233-43. 2013..Mutations in these genes may less likely lead to in utero lethality and be subject to less intense selection...
- Fine-scale linkage disequilibrium mapping of age-related macular degeneration in the complement factor H gene regionSarah Ennis
Genetic Epidemiology and Bioinformatics Group, Human Genetics Division MP 808, Southampton General Hospital, Southampton, UK
Br J Ophthalmol 91:966-70. 2007..To present results from a nested association study of the complement factor H (CFH) gene region using a novel methodology that uses a high-resolution genetic linkage disequilibrium map to estimate a point location for a causal mutation...
- Toward positional cloning with SNPsNewton E Morton
Human Genetics, Southampton General Hospital, UK
Curr Opin Mol Ther 4:259-64. 2002....
- Linkage disequilibrium maps and location databasesWilliam Tapper
Human Genetics Division, Southampton General Hospital, UK
Methods Mol Biol 376:23-45. 2007..This chapter provides an overview of the data requirements and methodology used to construct LDU maps, their applications outside association mapping, and their integration into location databases...
- Properties of linkage disequilibrium (LD) mapsWeilhua Zhang
Human Genetics Division, University of Southampton, Southampton SO16 6YD, United Kingdom
Proc Natl Acad Sci U S A 99:17004-7. 2002..No alternative representation of linkage disequilibrium (some of which are loosely called maps) has these properties, suggesting that LD maps are optimal for positional cloning of genes determining disease susceptibility...
- Individual disease risk and multimetric analysis of Crohn diseaseJane Gibson
Human Genetics Division, School of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom
Proc Natl Acad Sci U S A 105:15843-7. 2008..Until such a test is exploited by competing statisticians, their Herculean efforts will be inconclusive, and the costly advances from increased sample size will be suboptimal and disappointing...
- Linkage disequilibrium in human populationsChristine Lonjou
Human Genetics Division, University of Southampton, Duthie Building MP 808, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, United Kingdom
Proc Natl Acad Sci U S A 100:6069-74. 2003....
- The influence of common polymorphisms on breast cancerDiana Eccles
Human Genetics Division, School of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, SO16 6YD, UK
Cancer Treat Res 155:15-32. 2010..Inherited genetic variants may well be one of the other factors that need to be taken into account in assessing prognosis and planning treatment...
- Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genomeWinston Lau
Human Genetics Division, Duthie Building Mailpoint 808, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
Bioinformatics 23:517-9. 2007..Availability: The LD maps, LDMAP-cluster and documentation are available from: http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/LDMAP. Supplementary information: Supplementary data are available at Bioinformatics online...
- Independent effects of the -219 G>T and epsilon 2/ epsilon 3/ epsilon 4 polymorphisms in the apolipoprotein E gene on coronary artery disease: the Southampton Atherosclerosis StudyShu Ye
Human Genetics Division, University of Southampton School of Medicine, Southampton SO16 6YD, UK
Eur J Hum Genet 11:437-43. 2003....
- Allelic association: linkage disequilibrium structure and gene mappingAndrew Collins
Human Genetics Division, Southampton General Hospital, University of Southampton, Duthie Building 808, Tremona Road, Southampton, SO16 6YD, UK
Mol Biotechnol 41:83-9. 2009..This review introduces this exciting and complex field by encompassing this range of topics...
- Genome variation: a review of Web resourcesAndrew Collins
Human Genetics Research Division, University of Southampton, Southampton, UK
Methods Mol Biol 713:129-39. 2011....
- TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individualsAndrew Chase
Wessex Regional Genetics Laboratory, Salisbury, Wiltshire, UK
Haematologica 95:20-6. 2010..Here we describe the first example of a human polymorphic in-frame fusion of two unrelated genes associated with a copy number variant...
- Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populationsReuben J Pengelly
Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building MP 808, Tremona Road, Southampton, SO16 6YD, UK
BMC Genomics 16:666. 2015..Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution...
- A multimetric approach to analysis of genome-wide association by single markers and composite likelihoodJane Gibson
Human Genetics Division, School of Medicine, University of Southampton, Southampton SO16 6YD, United Kingdom
Proc Natl Acad Sci U S A 105:2592-7. 2008....
- Fine mapping of the X-linked recessive congenital idiopathic nystagmus locus at Xq24-q26.3James Edward Self
Clinical Neurosciences Division, University of Southampton, Southampton, UK
Mol Vis 12:1211-6. 2006..To refine the interval for X-linked congenital idiopathic nystagmus at Xq24-q26.3 and to evaluate a novel candidate gene (Muscleblind-like 3 gene [MBNL3])...
- Mapping a gene for rheumatoid arthritis on chromosome 18q21William Tapper
Human Genetics Division, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, Hampshire SO16 6YD, UK
BMC Proc 1:S18. 2007....
- The distinguishing sequence characteristics of mouse imprinted genesXiayi Ke
Human Genetics, Duthie Building 808, University of Southampton, Tremona Road, Southampton SO16 6YD, UK
Mamm Genome 13:639-45. 2002..The differences between the sequence characteristics of imprinted and control genes have also enabled us to develop a discriminant function that can be used in a genome-wide screen to identify candidate imprinted genes...
- MaGIC: a program to generate targeted marker sets for genome-wide association studiesClaire L Simpson
Institute of Psychiatry, Kings College London, London, UK
Biotechniques 37:996-9. 2004..The program and source code is freely available at http://cogent.iop.kcl.ac.uk/MaGIC.cogx...
- The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination patternFrancisco M De La Vega
Applied Biosystems, Foster City, California 94404, USA
Genome Res 15:454-62. 2005..Our results have practical implications for the rational design and selection of SNPs for disease association studies...
- The impact of SNP density on fine-scale patterns of linkage disequilibriumXiayi Ke
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Hum Mol Genet 13:577-88. 2004..The results suggest that very dense marker sets will be required to yield stable views of fine-scale LD in the human genome...
- The power and statistical behaviour of allele-sharing statistics when applied to models with two disease lociYin Y Shugart
Epidemiology Department, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
J Genet 81:99-103. 2002..On the other hand, when the thresholds are determined empirically under the null hypothesis, S(all) in GENEHUNTER and statistic E have similar power...
- Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studiesSusan Service
Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095, USA
Nat Genet 38:556-60. 2006..Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping...
- A first-generation metric linkage disequilibrium map of bovine chromosome 6Mehar S Khatkar
Centre for Advanced Technologies in Animal Genetics and Reproduction REPROGEN, University of Sydney and CRC for Innovative Dairy Products, Camden NSW 2570, Australia
Genetics 174:79-85. 2006..The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies...
- The BRCA1 Ashkenazi founder mutations occur on common haplotypes and are not highly correlated with anonymous single nucleotide polymorphisms likely to be used in genome-wide case-control association studiesLutecia H Mateus Pereira
Laboratory of Population Genetics, National Cancer Institute, Bethesda, MD 20892, USA
BMC Genet 8:68. 2007..We evaluated LD using pairwise and haplotype-based methods, and assessed correlation of SNPs with the founder mutations using Pearson's correlation coefficient...
- Repair of oxidative DNA damage: assessing its contribution to cancer preventionAndrew Collins
Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 0RD, UK
Mutagenesis 17:489-93. 2002..what is the extent of intra-individual variation; is repair modulated by environmental factors or induced by damage; are there differences in repair capacity between men and women; what is the association of DNA repair with ageing?..
- Does occupational exposure to mineral fibres cause DNA or chromosome damage?Maria Dusinska
Institute of Preventive and Clinical Medicine, Research Base of the Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovak Republic
Mutat Res 553:103-10. 2004..The conclusion from this study is that, overall, rockwool exposure has no deleterious effect on genetic stability in humans...
- Complex segregation analysis of nasopharyngeal carcinoma in Guangdong, China: evidence for a multifactorial mode of inheritance (complex segregation analysis of NPC in China)Wei Hua Jia
Department of Experimental Research, Cancer Center, Sun Yat Sen University, Guangzhou 510060, China
Eur J Hum Genet 13:248-52. 2005..The current results do not provide evidence for a major gene and the observed data are best explained by a multifactorial mode of inheritance for NPC...
- The origin of trisomy 13Heather E Hall
Center for Reproductive Biology and School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 4660, USA
Am J Med Genet A 143:2242-8. 2007..As with other trisomies, failure to recombine is an important contributor to nondisjunction of chromosome 13...
- A comparative location database (CompLDB): map integration within and between speciesWebber Liao
Reprogen, Faculty of Veterinary Science, University of Sydney, B19, New South Wales 2006, Australia
Mamm Genome 18:287-99. 2007..angis.org.au/ldb/...
- Non-disjunction of chromosome 13Merete Bugge
Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
Hum Mol Genet 16:2004-10. 2007..This study supports the evidence for subtle chromosome-specific influences on the mechanisms that determine non-disjunction of human chromosomes, consistent with the diversity of findings for other trisomies...
- 32nd annual meeting of European Environmental Mutagen Society. DNA damage and repair fundamental aspects and contribution to human disordersBarbara Tudek
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02 106 Warsaw, Poland
DNA Repair (Amst) 2:765-81. 2003
- PCR designer for restriction analysis of various types of sequence mutationXiayi Ke
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Bioinformatics 18:1688-9. 2002..The program, supported by a WWW web interface, is intended to be used online...
- Polymorphisms in a disintegrin and metalloprotease 33 (ADAM33) predict impaired early-life lung functionAngela Simpson
North West Lung Centre, Wythenshawe Hospital, Manchester M23 9LT, UK
Am J Respir Crit Care Med 172:55-60. 2005..Asthma commonly originates in early life in association with impaired lung function, which tracks to adulthood...