Matthew Hurles

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Shotgun haplotyping: a novel method for surveying allelic sequence variation
    Sarah J Lindsay
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:e152. 2005
  2. pmc Characterising and predicting haploinsufficiency in the human genome
    Ni Huang
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    PLoS Genet 6:e1001154. 2010
  3. pmc The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age
    Jacqueline A L Macarthur
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 10:e1004195. 2014
  4. pmc Quantifying single nucleotide variant detection sensitivity in exome sequencing
    Alison M Meynert
    MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
    BMC Bioinformatics 14:195. 2013
  5. doi Older males beget more mutations
    Matthew Hurles
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 44:1174-6. 2012
  6. pmc Towards a comprehensive structural variation map of an individual human genome
    Andy W Pang
    Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Genome Biol 11:R52. 2010
  7. pmc Fast-evolving noncoding sequences in the human genome
    Christine P Bird
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Genome Biol 8:R118. 2007
  8. pmc 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 levels
    Ian Sudbery
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Genome Biol 10:R112. 2009
  9. pmc Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
    John 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
  10. pmc The functional impact of structural variation in humans
    Matthew E Hurles
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Trends Genet 24:238-45. 2008

Detail Information

Publications49

  1. pmc Shotgun haplotyping: a novel method for surveying allelic sequence variation
    Sarah J Lindsay
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:e152. 2005
    ....
  2. pmc Characterising and predicting haploinsufficiency in the human genome
    Ni Huang
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    PLoS Genet 6:e1001154. 2010
    ..These robust predictions of haploinsufficiency support clinical interpretation of novel loss-of-function variants and prioritization of variants and genes for follow-up studies...
  3. pmc The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age
    Jacqueline A L Macarthur
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 10:e1004195. 2014
    ....
  4. pmc Quantifying single nucleotide variant detection sensitivity in exome sequencing
    Alison M Meynert
    MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
    BMC Bioinformatics 14:195. 2013
    ..To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed...
  5. doi Older males beget more mutations
    Matthew Hurles
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 44:1174-6. 2012
    ..These studies represent the advent of a transformation in our understanding of mutation rates and processes, which may ultimately have public health implications...
  6. pmc Towards a comprehensive structural variation map of an individual human genome
    Andy 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...
  7. pmc Fast-evolving noncoding sequences in the human genome
    Christine 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...
  8. pmc 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 levels
    Ian Sudbery
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, UK
    Genome Biol 10:R112. 2009
    ....
  9. pmc Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
    John 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...
  10. pmc The functional impact of structural variation in humans
    Matthew E Hurles
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Trends Genet 24:238-45. 2008
    ....
  11. pmc How homologous recombination generates a mutable genome
    Matthew 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...
  12. pmc The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages
    Matthew 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...
  13. pmc Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots
    Matthew 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...
  14. pmc Gene duplication: the genomic trade in spare parts
    Matthew Hurles
    Wellcome Trust Sanger Institute near Cambridge in the United Kingdom
    PLoS Biol 2:E206. 2004
  15. pmc A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination
    Sarah 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...
  16. pmc A robust statistical method for case-control association testing with copy number variation
    Chris 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...
  17. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara 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...
  18. ncbi 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
  19. pmc Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history
    James A Traherne
    Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 2:e9. 2006
    ....
  20. pmc High-throughput haplotype determination over long distances by haplotype fusion PCR and ligation haplotyping
    Daniel 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...
  21. pmc Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping
    Daniel 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...
  22. pmc Mutation spectrum revealed by breakpoint sequencing of human germline CNVs
    Donald 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...
  23. pmc Global variation in copy number in the human genome
    Richard 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...
  24. pmc Assaying chromosomal inversions by single-molecule haplotyping
    Daniel 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...
  25. pmc Y chromosomal evidence for the origins of oceanic-speaking peoples
    Matthew 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...
  26. pmc The DNA sequence of the human X chromosome
    Mark 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...
  27. pmc Adaptive evolution of UGT2B17 copy-number variation
    Yali 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...
  28. pmc Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    Peter 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...
  29. pmc Origins and functional impact of copy number variation in the human genome
    Donald F Conrad
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
    Nature 464:704-12. 2010
    ....
  30. pmc Male demography in East Asia: a north-south contrast in human population expansion times
    Yali Xue
    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    Genetics 172:2431-9. 2006
    ....
  31. pmc Accurate and reliable high-throughput detection of copy number variation in the human genome
    Heike 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...
  32. pmc The variant call format and VCFtools
    Petr 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...
  33. pmc Germline rates of de novo meiotic deletions and duplications causing several genomic disorders
    Daniel J Turner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Nat Genet 40:90-5. 2008
    ....
  34. pmc Native American Y chromosomes in Polynesia: the genetic impact of the Polynesian slave trade
    Matthew E Hurles
    McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
    Am J Hum Genet 72:1282-7. 2003
    ....
  35. pmc Global haplotype diversity in the human insulin gene region
    John D H Stead
    Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
    Genome Res 13:2101-11. 2003
    ....
  36. pmc Dynamics of a human interparalog gene conversion hotspot
    Elena 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...
  37. pmc Evidence for widespread reticulate evolution within human duplicons
    Michael 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...
  38. ncbi A high-resolution survey of deletion polymorphism in the human genome
    Donald 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...
  39. pmc Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
    Daisuke Komura
    Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153 8904, Japan
    Genome Res 16:1575-84. 2006
    ....
  40. pmc Y chromosomal STRs haplotypes in two populations from Bolivia
    Juwon 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...
  41. pmc Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y
    Mark 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...
  42. pmc Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes
    Melanie J Pierson
    Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
    Mol Biol Evol 23:1966-75. 2006
    ....
  43. pmc Paired-end mapping reveals extensive structural variation in the human genome
    Jan 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...
  44. pmc The genetic legacy of the Mongols
    Tatiana 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...
  45. ncbi Copy number variation: new insights in genome diversity
    Jennifer 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...
  46. pmc The population genetics of structural variation
    Donald 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...
  47. ncbi A singular chromosome
    Matthew E Hurles
    Nat Genet 34:246-7. 2003
  48. pmc Challenges and standards in integrating surveys of structural variation
    Stephen 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...
  49. ncbi High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis
    Elena 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...