Research Topics
Species | Matthew HurlesSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Detail Information
Publications
Towards a comprehensive structural variation map of an individual human genomeAndy W Pang
Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
Genome Biol 11:R52. 2010..It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions...- Fast-evolving noncoding sequences in the human genomeChristine P Bird
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Genome Biol 8:R118. 2007..These conserved noncoding (CNC) sequences may well harbor critical regulatory variants that have driven recent human evolution... - Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levelsIan Sudbery
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
Genome Biol 10:R112. 2009.... - Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridizationJohn C Marioni
Computational Biology Group, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
Genome Biol 8:R228. 2007..However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined... - The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineagesMatthew E Hurles
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
Am J Hum Genet 76:894-901. 2005..As a result of their equally balanced admixed ancestry, the Malagasy may represent an ideal population in which to identify loci underlying complex traits of both anthropological and medical interest... - How homologous recombination generates a mutable genomeMatthew Hurles
Wellcome Trust Sanger Institute, Genome Campus, Cambridge, CB10 1SA, UK
Hum Genomics 2:179-86. 2005..Comparisons of whole-genome sequences reveal the expansion of gene family clusters to be an important mode of genome evolution. The negative aspect of this genomic dynamism is the contribution of these rearrangements to genetic diseases... 
Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspotsMatthew E Hurles
Molecular Genetics Laboratory, McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
Genome Biol 5:R55. 2004..We have investigated, by comparative sequencing, the evolution of two hotspots of non-allelic homologous recombination on the Y chromosome that lie within paralogous sequences known to sponsor deletions resulting in male infertility...- Gene duplication: the genomic trade in spare partsMatthew Hurles
Wellcome Trust Sanger Institute near Cambridge in the United Kingdom
PLoS Biol 2:E206. 2004 - The functional impact of structural variation in humansMatthew E Hurles
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Trends Genet 24:238-45. 2008.... - A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombinationSarah J Lindsay
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
Am J Hum Genet 79:890-902. 2006..We propose that a large-scale project to map sequence variation within segmental duplications would reveal a wealth of novel chromosomal-rearrangement hotspots... - A robust statistical method for case-control association testing with copy number variationChris Barnes
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Genet 40:1245-52. 2008..We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools... - Relative impact of nucleotide and copy number variation on gene expression phenotypesBarbara E Stranger
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Science 315:848-53. 2007..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans... 
Are 100,000 "SNPs" useless?Matthew Hurles
Molecular Genetics Laboratory, McDonald Institute for, Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK
Science 298:1509; author reply 1509. 2002- Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human historyJames A Traherne
Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom
PLoS Genet 2:e9. 2006.... - Assaying chromosomal inversions by single-molecule haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Nat Methods 3:439-45. 2006..The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer... - Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
Nucleic Acids Res 36:e82. 2008..4 kb apart on chromosome 7, and which influence an individual's susceptibility to systemic lupus erythematosus... - Y chromosomal evidence for the origins of oceanic-speaking peoplesMatthew E Hurles
McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom
Genetics 160:289-303. 2002..Furthermore, it is demonstrated that a geographical rather than linguistic classification of Oceanic populations best accounts for their extant Y chromosomal diversity... - The DNA sequence of the human X chromosomeMark T Ross
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 434:325-37. 2005..Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence... - High-throughput haplotype determination over long distances by haplotype fusion PCR and ligation haplotypingDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Protoc 4:1771-83. 2009..Products are resolved by capillary electrophoresis. Once optimized, the procedure can be performed quickly, taking a day and a half to generate phased haplotypes from genomic DNA... - Mutation spectrum revealed by breakpoint sequencing of human germline CNVsDonald F Conrad
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Nat Genet 42:385-91. 2010..Despite a rich literature on DNA repair processes, reconstruction of the molecular events generating each of these mutations is not yet possible... - Global variation in copy number in the human genomeRichard Redon
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies... - Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencingPeter J Campbell
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nat Genet 40:722-9. 2008..The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy... - Adaptive evolution of UGT2B17 copy-number variationYali Xue
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Am J Hum Genet 83:337-46. 2008..In contrast, diversity was low in East Asia where a single haplotype predominated, suggesting positive selection for the deletion in this part of the world... - Origins and functional impact of copy number variation in the human genomeDonald F Conrad
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
Nature 464:704-12. 2010.... - Shotgun haplotyping: a novel method for surveying allelic sequence variationSarah J Lindsay
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nucleic Acids Res 33:e152. 2005.... - Accurate and reliable high-throughput detection of copy number variation in the human genomeHeike Fiegler
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
Genome Res 16:1566-74. 2006..Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method... - Male demography in East Asia: a north-south contrast in human population expansion timesYali Xue
Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Genetics 172:2431-9. 2006.... - The variant call format and VCFtoolsPetr Danecek
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Bioinformatics 27:2156-8. 2011..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. AVAILABILITY: http://vcftools.sourceforge.net.. - Native American Y chromosomes in Polynesia: the genetic impact of the Polynesian slave tradeMatthew E Hurles
McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
Am J Hum Genet 72:1282-7. 2003.... - Germline rates of de novo meiotic deletions and duplications causing several genomic disordersDaniel J Turner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
Nat Genet 40:90-5. 2008.... - Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomesMelanie J Pierson
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
Mol Biol Evol 23:1966-75. 2006.... - The genetic legacy of the MongolsTatiana Zerjal
Department of Biochemistry, University of Oxford, Oxford, United Kingdom
Am J Hum Genet 72:717-21. 2003..The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior... - Global haplotype diversity in the human insulin gene regionJohn D H Stead
Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
Genome Res 13:2101-11. 2003.... - Y chromosomal STRs haplotypes in two populations from BoliviaJuwon Lee
Department of Human Genetics and Public Health, School of Medicine, University of Tokushima, Tokushima, Japan
Leg Med (Tokyo) 9:43-7. 2007..Moreover, this study includes data about two Bolivian populations which were not previously reported, this will help in building a world-wide database for future use in forensic and legal studies... - Dynamics of a human interparalog gene conversion hotspotElena Bosch
Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
Genome Res 14:835-44. 2004..Analysis of great ape homologs shows that conversion in this hotspot has a deep evolutionary history... - Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin YMark A Jobling
Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
Hum Mol Genet 16:307-16. 2007..The persistence and expansion of deletion lineages, together with direct phenotypic evidence, suggests that absence of these genes has no major deleterious effects... - Evidence for widespread reticulate evolution within human dupliconsMichael S Jackson
Institute of Human Genetics, University of Newcastle upon Tyne, International Centre for Life, Newcastle upon Tyne, United Kingdom
Am J Hum Genet 77:824-40. 2005..This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution... - Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arraysDaisuke Komura
Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
Genome Res 16:1575-84. 2006.... - Paired-end mapping reveals extensive structural variation in the human genomeJan O Korbel
Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA
Science 318:420-6. 2007..The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans... - A high-resolution survey of deletion polymorphism in the human genomeDonald F Conrad
Department of Human Genetics, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Genet 38:75-81. 2006..Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data... - A singular chromosomeMatthew E Hurles
Nat Genet 34:246-7. 2003 - Copy number variation: new insights in genome diversityJennifer L Freeman
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
Genome Res 16:949-61. 2006..Current efforts are directed toward a more comprehensive cataloging and characterization of CNVs that will provide the basis for determining how genomic diversity impacts biological function, evolution, and common human diseases... - Challenges and standards in integrating surveys of structural variationStephen W Scherer
The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14 701, Ontario M5G 1L7, Canada
Nat Genet 39:S7-15. 2007..From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research... - High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysisElena Bosch
Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
Hum Genet 112:353-63. 2003..However, the extreme sex bias in the admixture makes the later event more likely as the source... - The population genetics of structural variationDonald F Conrad
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Nat Genet 39:S30-6. 2007..We summarize recent dramatic advances, describe the diverse mutational origins of chromosomal rearrangements and argue that their complexity necessitates a re-evaluation of existing population genetic methods...