We’ve asked Clara Grazian, post-doc with a double PhD in Applied Mathematics and Statistics from Université Paris-Dauphine and Sapienza Università di Roma, to tell us how the annual committee meeting in Dubai went. Clara’s role in CRyPTIC is to understand the development of TB drug resistance mechanisms using genome-wide association studies (GWAS). Grazie Clara!!
It was a great occasion for all the members to meet up and discuss past and future of the project in the beautiful setting of the Shangri-La Hotel in Dubai.
So, where are we?
First of all, we welcomed three new CRyPTIC partners: Ruwen Jou from the Centers for Disease Control in Taiwan, Jim Werngren from the Public Health Agency of Sweden and Nick Paton from the National University of Singapore. We are very excited with the extension of our collaboration to these new centres!
The day started with Derrick welcoming us all and Sarah giving updates on the project completion. One of the very important achievements so far has been the microtitre plate validation study.
Tim Walker, from Oxford, presented the results. There were good levels of agreement between the results obtained by the participating centres (Milan, Gauting, Birmingham, Lima, Mumbai, Johannesburg and Ho Chi Minh City), suggesting good reproducibility. The study also helped optimize the plate design—a new drug layout was presented, without PAS and with adjustments to the concentrations of other drugs. This will enhance the microtitre plate value for the project and was accepted without reservations by all members.
After that, Daniela Cirillo, from Milan, and Kayzad Nilgiriwala, from Mumbai, presented the results of the first block of clinical strains entering CRyPTIC: approximately 1500 in total from Pakistan, India and Italy.
Martin Hunt, CRyPTIC’s bioinformatician based at the European Bioinformatics Institute, presented the impressive work he and Zam Iqbal are undertaking in Cambridge in order to prepare the analytical pipelines to process the wealth of CRyPTIC data. Data storage hubs are being created and a very accurate variant calling pipeline is near completion.
Finally, Yang Yang, who runs Oxford’s Computational Health Informatics Lab’s second site in Suzhou, China, presented the machine learning techniques for classifications of mutations, and I presented the challenges we will face when applying the genome-wide association studies within CRyPTIC’s high dimension.
The morning was quite intense, with talks from 9am to 1.15pm, and were followed by the executive committee meeting and afterwards by a workshop led by Oxford Nanopore Technologies.
This all happened in a very cold room—quite shocking, if you think that out of the hotel there were 30 degrees!
CRyPTIC’s 2017 meeting was characterized by a great exchange of ideas and shared experiences and difficulties. CRyPTIC turned out to be a really collaborative environment; we have achieved a lot despite logistic difficulties inherent to an international collaboration with hands-on work developed in four different continents with their own processes and systems and time zones. Our next steps will be moving toward the definition of MIC breakpoints for each drug. What a challenge!
I would like to thank Sarah Hoosdally and Ana Gibertoni Cruz for their tireless organisational work for CRyPTIC and this meeting. Everything went really smoothly, something that cannot be taken for granted when trips and accommodation for almost 30 people from all around the world need organising! Grazie mille!