Genome graph for variant genotyping in cattle

Linear reference genome is an oversimplification as it fails to account for the segregated variants in the populations, resulting in overreporting the alleles in the reference, widely known as reference allele bias.

A natural data structure that can represents these variants jointly is genome-graph. In this work, I showed that using cattle WGS (the first of its kind in livestock population) genome-graph genotyper is comparable, and even has better quality metrics (e.g genotype concordance, mendelian accuracy) than the current standard variant-calling tools that are strictly limited to the linear reference genome.

Publication

Danang Crysnanto, Christine Wurmser, Hubert Pausch. 2018. Accurate sequence variant genotyping in cattle using genome graphs. Genetics Selection Evolution. Github repository. bioRxiv from 4th November 2018.

Conference

Genome Informatics. Wellcome Genome Campus Cambridge. 17-20 September 2018

Cambridge Livestock Genomics Meeting. Wellcome Genome Campus Cambridge. 21-22 September 2018 (Oral Presenter, Long talk)





Past

The evolution of RNAi gene duplicates in Drosophila

Genes involved in RNA inteference pathway are prevasively duplicated in D obscura group.
I analysed the 35 genomes across species in Drosophilidae and showed that the duplication are adaptive and occurred independently across Drosophila lineages, implying that many selective agents may be responsible.

Publication

Danang Crysnanto, Darren Obbard. 2018. Widespread gene duplication and adaptive evolution in the RNA-interference pathways of the Drosophila obscura group. BMC Evolutionary Biology. Github repository. bioRxiv from 29th September 2018.

Conference

52nd Population Genetics. Oxford. 3-6 January 2019 (Invited Oral Speaker)