Computational genome biology - Associate Faculty group

Chris Ponting's Associate Faculty group analyses next-generation sequencing data to better understand basic biological and disease processes.

To further explore the biological pathways involved in health and disease, the group is addressing three challenges in disease genomics. First, we are taking advantage of the vast amounts of genome-wide genotype and resequencing data that are relevant to human disease, in particular neurological disorders. Second, we are coupling these data to phenotypic, genomic and molecular functional annotations in order to extend our existing approaches to prioritising causative genes and alleles. Finally, we are taking full advantage of the power of evolutionary approaches to infer the molecular functions of disease-associated genes.

[Wellcome Library, London]

Background

It has been over 10 years since the first human genome assembly was announced. Since then we have gained hugely in our understanding of our place in the tree of life, our genome's paucity of coding sequence and the enormous complexity of its transcriptional outputs. Nonetheless, many great challenges remain in relating genomic sequence and functional variation to phenotypic differences.

Research

The group is currently undertaking the following analysis types:

  • evolutionary and functional investigation of long intergenic noncoding RNAs;
  • comparative analyses of various bird and fish genomes;
  • exon resequencing of a cohort of Parkinson's patients (with Richard Durbin's group);
  • high-level sequence analysis, unearthing unexpected distant homologies;
  • the functional impact of transposable element insertions.

Resources

Collaborations

In addition to working with researchers at the Sanger Institute, we also work closely with The Oxford Parkinson's Disease Centre (OPDC). This is a unique interdisciplinary research centre focussed on understanding the earliest pathological pathways in Parkinson's disease, founded by the £5m Monument Discovery award from Parkinson's UK.
The Oxford Parkinson's Disease Centre (OPDC)

Selected Publications

  • 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.

    Rands CM, Meader S, Ponting CP and Lunter G

    PLoS genetics 2014;10;7;e1004525

  • The long non-coding RNA Paupar regulates the expression of both local and distal genes.

    Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL and Ponting CP

    The EMBO journal 2014;33;4;296-311

  • Considerations when investigating lncRNA function in vivo.

    Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA and Ponting CP

    eLife 2014;3;e03058

  • Diagnostically relevant facial gestalt information from ordinary photos.

    Ferry Q, Steinberg J, Webber C, FitzPatrick DR, Ponting CP, Zisserman A and Nellåker C

    eLife 2014;3;e02020

  • A transcriptomic atlas of mouse neocortical layers.

    Belgard TG, Marques AC, Oliver PL, Abaan HO, Sirey TM, Hoerder-Suabedissen A, García-Moreno F, Molnár Z, Margulies EH and Ponting CP

    Neuron 2011;71;4;605-16

  • Massive turnover of functional sequence in human and other mammalian genomes.

    Meader S, Ponting CP and Lunter G

    Genome research 2010;20;10;1335-43

  • Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa.

    Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS and Ponting CP

    PLoS genetics 2009;5;12;e1000753

  • Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain.

    Ponjavic J, Oliver PL, Lunter G and Ponting CP

    PLoS genetics 2009;5;8;e1000617

  • Lineage-specific biology revealed by a finished genome assembly of the mouse.

    Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, Ponting CP and Mouse Genome Sequencing Consortium

    PLoS biology 2009;7;5;e1000112

* quick link - http://q.sanger.ac.uk/21dpplul