Daniel J Turner

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. 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
  2. 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
  3. 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
  4. doi request reprint 96-plex molecular barcoding for the Illumina Genome Analyzer
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 733:279-98. 2011
  5. 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
  6. pmc A large genome center's improvements to the Illumina sequencing system
    Michael A Quail
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nat Methods 5:1005-10. 2008
  7. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
  8. pmc A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
    Lars Barquist
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 41:4549-64. 2013
  9. doi request reprint Amplification-free library preparation for paired-end Illumina sequencing
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 733:257-66. 2011
  10. doi request reprint Target-enrichment strategies for next-generation sequencing
    Lira Mamanova
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 7:111-8. 2010

Detail Information

Publications28

  1. 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...
  2. 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...
  3. 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...
  4. doi request reprint 96-plex molecular barcoding for the Illumina Genome Analyzer
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 733:279-98. 2011
    ....
  5. 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...
  6. pmc A large genome center's improvements to the Illumina sequencing system
    Michael A Quail
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nat Methods 5:1005-10. 2008
    ....
  7. pmc Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:291-5. 2009
    ..We illustrate this by generating and analyzing DNA sequences from extremely (G+C)-poor (Plasmodium falciparum), (G+C)-neutral (Escherichia coli) and (G+C)-rich (Bordetella pertussis) genomes...
  8. pmc A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
    Lars Barquist
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 41:4549-64. 2013
    ..We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks...
  9. doi request reprint Amplification-free library preparation for paired-end Illumina sequencing
    Iwanka Kozarewa
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 733:257-66. 2011
    ..To overcome these difficulties, we developed an amplification-free library preparation. By the use of custom adapters, unamplified, ligated samples can hybridize directly to the oligonucleotides on the flowcell surface...
  10. doi request reprint Target-enrichment strategies for next-generation sequencing
    Lira Mamanova
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 7:111-8. 2010
    ..We also provide detailed protocols for each technology so that end users can find the best compromise between sensitivity, specificity and uniformity for their particular project...
  11. pmc Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
    Magnus Manske
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 487:375-9. 2012
    ..An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome...
  12. doi request reprint Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq)
    Lira Mamanova
    The Wellcome Trust Sanger Institute, Cambridge, UK
    Nat Protoc 6:1736-47. 2011
    ..This approach removes PCR biases and duplicates, generates strand-specific paired-end data and is highly reproducible. The procedure can be performed quickly, taking 2 d to generate clusters from mRNA...
  13. pmc A simple method for directional transcriptome sequencing using Illumina technology
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 37:e148. 2009
    ..Hence, this simple method should prove a useful tool in aiding genome annotation and gene expression studies in both prokaryotes and eukaryotes...
  14. pmc Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data
    Min Hu
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    Hum Genet 131:665-74. 2012
    ....
  15. pmc FRT-seq: amplification-free, strand-specific transcriptome sequencing
    Lira Mamanova
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 7:130-2. 2010
    ..The method is compatible with paired- or single-end sequencing...
  16. pmc Improved protocols for the illumina genome analyzer sequencing system
    Michael A Quail
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
    Curr Protoc Hum Genet . 2009
    ....
  17. pmc Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
    Samuel O Oyola
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    BMC Genomics 13:1. 2012
    ..We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences...
  18. pmc Mobilization of giant piggyBac transposons in the mouse genome
    Meng Amy Li
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
    Nucleic Acids Res 39:e148. 2011
    ..Furthermore, these 100-kb transposons can also be excised from the genome without leaving a footprint. The development of piggyBac as a large cargo vector will facilitate a wider range of genetic and genomic applications...
  19. pmc Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
    Gemma C Langridge
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
    Genome Res 19:2308-16. 2009
    ..Typhi in the gall bladder. This screen validated our hypothesis that we can simultaneously assay every gene in the genome to identify niche-specific essential genes...
  20. pmc The GENCODE exome: sequencing the complete human exome
    Alison J Coffey
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Eur J Hum Genet 19:827-31. 2011
    ..9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing...
  21. doi request reprint Improved Protocols for Illumina Sequencing
    Iraad F Bronner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
    Curr Protoc Hum Genet 80:18.2.1-42. 2014
    ....
  22. pmc High altitude adaptation in Daghestani populations from the Caucasus
    Luca Pagani
    The Wellcome Trust Sanger Institute, Hinxton, UK
    Hum Genet 131:423-33. 2012
    ..These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation...
  23. pmc Insights into hominid evolution from the gorilla genome sequence
    Aylwyn Scally
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Nature 483:169-75. 2012
    ..The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution...
  24. 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...
  25. pmc Next-generation sequencing of vertebrate experimental organisms
    Daniel J Turner
    Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Mamm Genome 20:327-38. 2009
    ..We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics...
  26. 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
    ....
  27. 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...
  28. ncbi request reprint Harnessing asymmetrical substrate recognition by thermostable EndoV to achieve balanced linear amplification in multiplexed SNP typing
    Daniel J Turner
    Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
    Biochem Cell Biol 84:232-42. 2006
    ..3-fold in their original representation. Because only a single primer is necessary, primer artefacts and nonspecific amplification products are minimized...