JCSMR School Seminar Series - Detecting selection signals in plasmodium with relatedness analysis of whole genome sequencing

Professor Melanie Bahlo, Co-Division Head, Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research. Parkville, VIC

Most of the human morbidity and mortality due to malaria is caused by two plasmodium species: falciparum and vivax. Drugs that treat malaria have developed treatment failure as plasmodium generates drug resistance through mutations which can arise independently in different populations or can spread. Since Plasmodium recombines in the mosquito midgut recombinants can achieve this resistance spread very effectively, especially when a population is put under strong selection pressure. We have developed an algorithmic approach that probabilistically enables the detection of genetic relatedness, also known as identity by descent (IBD) between pairs of malaria isolates.  This can also measured at specific SNPs. We further developed this into a test statistic to detect excessive IBD. Application of this method to a set of >2,500 whole genome sequences generated by the MalariaGen Consortium identified both known, for example pfCRT, and novel genomic loci likely to be under selection. Our network analysis is able to graphically summarise the inferred IBD sharing. We are now pursuing several new loci under selection with drug sensitivity tests. A preprint of some of the results can be found at biorxiv (http://biorxiv.org/content/early/2016/11/16/088039)

Division at the Walter and Eliza Hall Institute of Medical Research.  Her research covers statistical genetics, population genetics and bioinformatics. Her research lab performs advanced bioinformatics analyses and algorithmic development, producing software for next-generation sequencing data analysis, gene co-expression analyses and plasmodium next-generation sequencing data analysis.

Professor Bahlo is known for her genetic discoveries in neurogenetics, in particular epilepsy and ataxia. She has recently become interested in infectious diseases. In 2009 she won the Australian Academy of Science’s Moran Medal and in 2015 she won the Genetics Society of Australasia’s Ross Crozier Medal for mid-career researchers.

Date & time

12–1pm 12 May 2017

Location

The Finkel Lecture Theatre, The John Curtin School of Medical Research, Building 131 Garran Road, ANU

Speakers

Host: Professor Simon Foote

Contacts

 Ceri Flowers
 +61 2 6125 2589

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