20. March 2015 · Comments Off on Genetic study sheds new light on TB pathogenesis · Categories: Papers, Science · Tags: , , ,

One of the world’s most ancient diseases

Tuberculosis, also known as consumption, was first recorded in Greek literature around 460 BCE. Hippocrates identified it as the most widespread and fatal disease of his time. Tuberculosis (TB) is caused by a pathogen called Mycobacterium tuberculosis (M.tb). In Greek myco refers to a mushroom-like shape, vividly describing these fungal looking bacterium that float into the human system through the airways.

TB accounted for approximately 25% of total deaths in Europe from the 17th to 19th centuries. Many of the writers and artists of the Victorian era suffered and died from the disease and painted it with a pathological – yet somehow romantic – extreme: febrile, unrelenting and breathless.

Experiment eleven

It was not until 1943 when a young Ph.D. student called Albert Schatz, from Professor Selman Waksman’s lab at Rutger’s University in the US, discovered the first effective cure for treating TB. On Schatz’s eleventh experiment on a common bacterium found in farmyard soil, the first antibiotic agent for treating TB, streptomycin, was discovered. The battle for the ownership of streptomycin became a famous scientific scandal [Experiment Eleven], when Waksman took credit and the Nobel prize for the discovery, downplaying Schatz’s contributions. Thanks to a sustained effort from the government and society, including better nutrition, housing, improved sewage systems and ventilation, the number of TB cases was reduced significantly by the 1980s. The efforts to seek cures for TB have not only brought TB mortality down, but also helped to shape modern medicine and our understanding towards infectious illness.
More »

28. October 2013 · Comments Off on A neat idea to tell polygenic signal from stratification noise · Categories: Conferences, Science · Tags: , , ,

One of my favorite presentations at ASHG this year was a poster given by Brendan Bulik-Sullivan from the Broad. Brendan and his colleagues attempted to answer a puzzling question which has come up quite often recently: “If we see an inflation of GWAS test statistics, is it because of polygenic risk (good) or population stratification (bad)?”
More »

06. February 2013 · Comments Off on Moving from common to rare · Categories: Conferences, Editorial · Tags: , , ,

One of the main research focuses of the Barrett group is to understand genetic associations with Inflammatory Bowel Disease (IBD), in particular with its two most common subtypes, Crohn’s disease and ulcerative colitis (UC).

Back in November 2012, in preparation for the ASHG meeting, I did a brief literature review on the development of IBD based on a number of selected publications. The motion chart below (created in R as used in the well-known Hans Rosling TED talk) shows an overview of the discovery of IBD disease loci since 2001, when three independent groups identified a CD risk gene on chromosome 16q12, NOD2, using linkage techniques.

Plot: IBD Motion Chart
R version 2.15.2 (2012-10-26) • googleVis-0.2.17Google Terms of UseData Policy

More »

16. May 2012 · Comments Off on Genomic Epidemiology in Africa 2012 · Categories: Outreach · Tags: , , ,

Students on the course Last week I was in Malawi to teach on a Wellcome Trust Advanced Course on Genomic Epidemiology in Africa, along with Inês Barroso and Manj Sandhu from the Sanger, and Chris Spencer, Gavin Band and Kirk Rockett from Oxford. This is the second time we’ve run this course (the previous instance was in Kilifi, Kenya in 2010), which involves lectures on epidemiology, genomics, GWAS and study design in Africa as well as computer practicals using PLINK and R.

More »