Biological techniques articles within Nature Reviews Genetics

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  • Review Article |

    Biases in synonymous codon usage are pervasive across taxa, genomes and genes, and understanding their causes has implications for molecular evolution and biotechnology. This article assesses the competing models for codon bias, in light of genome-scale and high-throughput data.

    • Joshua B. Plotkin
    •  & Grzegorz Kudla

  • Opinion |

    Identity by descent (IBD) — the probability that two alleles descended from a common ancestor — is used in fundamental applications such as gene mapping and estimating heritability. The authors offer a solution to the confusion between IBD and identity by state (IBS) that is caused by the common practice of using dense SNPs to estimate IBD.

    • Joseph E. Powell
    • , Peter M. Visscher
    •  & Michael E. Goddard

  • Review Article |

    Understanding the intrinsic sequence specificity of proteins — particularly of transcription factors — that interact with DNA is an important component of studies of gene regulation. Several recently developed methods have greatly increased the throughput of protein–DNA interaction studies, and the sophistication of computational modelling is improving.

    • Gary D. Stormo
    •  & Yue Zhao

  • Opinion |

    Batch effects can lead to incorrect biological conclusions but are not widely considered. The authors show that batch effects are relevant to a range of high-throughput 'omics' data sets and are crucial to address. They also explain how batch effects can be mitigated.

    • Jeffrey T. Leek
    • , Robert B. Scharpf
    •  & Rafael A. Irizarry

  • Science and Society |

    The generation of transgenic non-human primates provides a potential means to understand the genetic differences that distinguish humans from our nearest evolutionary relatives. However, the same features that make non-human primates good models for such research also raise serious ethical concerns.

    • Marilyn E. Coors
    • , Jacqueline J. Glover
    •  & James M. Sikela

  • Review Article |

    Zinc finger nucleases (ZFNs) are versatile tools for making precise modifications to genomes, and their use is now established in a range of model systems. ZFNs are also showing potential in human gene therapy, and several clinical trials are underway.

    • Fyodor D. Urnov
    • , Edward J. Rebar
    •  & Philip D. Gregory

  • Review Article |

    Are humans evolving? Applying evolutionary biology tools to large-scale medical and epidemiological data sets shows that traits in many human populations are experiencing natural selection and have the genetic potential to respond to it.

    • Stephen C. Stearns
    • , Sean G. Byars
    •  & Douglas Ewbank

  • From The Editors |

    Why context is important for understanding gene regulation. And view our FREE audio slideshow.

  • Review Article |

    A huge range of genome-scale data sets — including genomic, epigenomic and transcriptomic information — are now available, and it is widely acknowledged that combining several data sets can provide important biological insights. However, there are practical, conceptual and computational challenges to data integration.

    • R. David Hawkins
    • , Gary C. Hon
    •  & Bing Ren

  • Review Article |

    Genotype imputation is an important tool for genome-wide association studies as it increases power, aids in fine-mapping of associations and facilitates meta-analyses. This Review provides a guide to and comparison of imputation methods and discusses association testing using imputed data.

    • Jonathan Marchini
    •  & Bryan Howie

  • Viewpoint |

    Four human disease geneticists express their views about the changing landscape of human disease studies and the impact of technological progress on establishing links between a pathogenic genomic variant and a disease phenotype.

    • Stylianos E. Antonarakis
    • , Aravinda Chakravarti
    •  & John Hardy

  • Review Article |

    Despite the yield of genome-wide association studies, the variants identified explain little of the heritability of most complex diseases. This unexplained heritability could be partly due to gene–environment (G×E) interactions. This Review provides a guide to designs and analytical approaches for studying specific G×E interactions.

    • Duncan Thomas

  • Review Article |

    Mapping DNA methylation is vital for understanding the importance of this epigenetic mark in health and disease. Recent years have seen rapid progress in the development of techniques for genome-scale methylation profiling; this Review introduces and evaluates the available methods.

    • Peter W. Laird

  • Review Article |

    Genome-wide association studies are not widespread in Africa, partly because of the challenges of dealing with population structure and high genomic diversity. New approaches in statistical imputation and whole-genome sequencing are now set to exploit these features for fine mapping causal variants.

    • Yik-Ying Teo
    • , Kerrin S. Small
    •  & Dominic P. Kwiatkowski

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