University of Cambridge > Talks.cam > Genetics Seminar  > Beyond the reference genome:  inference using prior knowledge of the diversity of a species.

Beyond the reference genome:  inference using prior knowledge of the diversity of a species.

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Host: Chris Illingworth

Encoding the genetic diversity of a species into a ³graph reference², with applications to antibiotic-resistance and antigenic variation

The choice of reference object used to represent the genome of a species has far reaching effects on biological inference. The use of a ³reference genome² made pragmatic sense when sequencing was expensive. However it can also lead to under-detection of non-reference alleles and various artefacts. The problem is substantial in regions of genomes of high diversity, such as the human MHC , or where unusual mutational mechanisms occur, as observed in the var genes in P. falciparum, for instance. Indeed, the limitations of a single reference genome have long been recognized in bacterial genomics, where the term pan-genome has been coined to refer to the full set of genes found across all individuals of a species. Recently progress has been made towards using an ensemble of genomes or variation data as a first-class object . However many algorithmic challenges remain and few implementations exist. I will discuss two lines of research from my group, based on the idea of building a reference graph of known sequence and variation in a species. The first relates to the prediction of antibiotic resistance in bacteria, recently published for S. aureus and M. tuberculosis (nature.com/ncomms/2015/151221/ncomms10063/full/ncomms10063.html). The second shows how a new data structure based on a generalised Burrows-Wheeler Transform and FM-index allow encoding of a graph of variation and read-mapping to the graph. I will show the impact of this method on the study of antigenic diversity in P. falciparum, the parasite responsible for the most deadly form of malaria.

This talk is part of the Genetics Seminar series.

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