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1 QUANTITATIVE BIOLOGY AND MEDICAL GENETICS FOR THE WORLD PROGRAM ANNOUNCEMENT The "Quantitative Biology and Medical Genetics for the World" program at McGill is offering a number of prestigious Queen Elizabeth II scholarships for Commonwealth citizens to pursue a PhD at McGill University. The Program The Canadian Queen Elizabeth II Diamond Jubilee Scholarships (QEII) program is a new program established by the Association of Universities and Colleges of Canada to create a community of leading Canadian and Commonwealth scholars. For background see: "Quantitative Biology and Medical Genetics for the World" at McGill is supported by the QEII program and coordinated by the McGill University and Génome Québec Innovation Centre (MUGQIC), one of Canada s leading institutions for genome research. The goal is to provide interdisciplinary training at a PhD level interfacing between high-throughput biology and quantitative sciences. While applicants can be from any Commonwealth country, we will favour students with nationality from countries where similar training opportunities are not readily available. The following are currently designated QEII partners, and we particularly encourage students with undergraduate training conducted at, or in association with, one of these institutions to apply: University of Oxford Kenya Medical Research Institute (KEMRI) Uganda Virus Research Institute & MRC Unit Noguchi Institute for Medical Research, University of Ghana Clinical Infectious Diseases Research Initiative, University of Cape Town South Africa Scholarships The program will support scholars from the Commonwealth to pursue a PhD degree at the University of McGill in areas related to the project. QE II scholars will receive full tuition waiver and a stipend of 20,000 $CA annually for up to 4 years of studies at McGill leading to a PhD. QEII scholars will be provided with additional support for annual travel in order to develop research opportunities within their home countries. After graduation, they will be invited to participate in future activities and opportunities as QEII alumni. Organisation The program is designed to provide training interfacing between genetics, genomics and other high throughput experimental methodologies, and quantitative approaches to biology.

2 The following are some examples of research areas that would be eligible: Quantitative genetics Population genetics Genetic/genomic epidemiology High-throughput experimental methods in biology associated with quantitative analysis of data Bioinformatics and computational genomics QEII scholars will be expected to meet course and other requirements for a PhD within their department, typically the Department of Human Genetics, and participate in the QEII training activities. Each QEII scholars will have a McGill faculty member as a designated supervisor. Research that involves collaboration with another higher education and research institution in the Commonwealth, particularly those in our partnership list, are encouraged. Some currently available topics are described in the attachment to illustrate training opportunities. Students are also free to propose their own research topics subject to acceptance by a faculty supervisor. Potential candidates should send preliminary enquiries to the address given below, or directly contact potential McGill faculty supervisors to discuss the suitability of a proposed research theme before applying. Eligibility & application procedures Incoming QEII scholars must be citizens of a Commonwealth country other than Canada. They must apply to and be accepted as a PhD student in the McGill Department of Human Genetics or other McGill department, and qualify for an international tuition waiver. Further information on requirements, deadlines and other considerations for Human Genetics can be found on the Department s website: PhD students are admitted for studies at McGill commencing in January and September of each year. The first QEII scholarships will be available to start in January The deadline for applications for this start date in the Department of Human Genetics is September 20, Simultaneously with applying to a Department, applicants for a QEII award should also provide a letter of motivation that shows alignment with the overall goals of the QEII program. These can be found here: Enquires and applications should be addressed to QEII Project, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6105, Montreal, QC, H3A 0G1, and can be sent via to:

3 QUANTITATIVE BIOLOGY AND MEDICAL GENETICS FOR THE WORLD OPEN STUDENTSHIPS The "Quantitative Biology and Medical Genetics for the World" program at McGill is offering a number of prestigious Queen Elizabeth II scholarships for Commonwealth citizens to pursue a PhD at McGill University. This program aims to train a new generation of researchers passionate about quantitative approaches to medical and population genetics. The program provides funds for tuition, stipend, and travel, as well as unique training opportunities. Some projects currently available to successful applicants are described below. Applicants are also encouraged to propose their own projects that fall under the general theme of the program. The accompanying Program Announcement should be consulted for eligibility, application instructions, and other information about the program. Preapplication enquires can be addressed to QEII Project, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6105, Montreal, QC, H3A 0G1, or sent by to:

4 Open project topics Advanced statistical analysis tools for single cell cancer genomics (Supervisor Pr. I. Ragoussis) In cancer, tumor cells are shed from the primary tumor into the blood circulation and then spread to distal sites to give rise to metastasis. These circulating tumor cells (CTCs) are a form of liquid biopsy shown to be prognostic indicators in some cancers. These CTCs are heterogeneous and comprise small but critically important subpopulations known as cancer stem cells with an epithelial phenotype (referred to as CSCs) or a mesenchymal phenotype (referred to as EMT). These CSCs/EMT subpopulations are now the target of drug development. The major challenge is to capture these CTCs and their subpopulations in sufficient number to fully characterize their molecular profile for the design of novel molecules and to follow their fate in real time during the course of therapy. This latter point is crucial in the design of future clinical trials. RNA sequencing at the single cell level is being used to look at CTCs heterogeneity prior to and following chemotherapy in combination with our large-scale isolation to provide a reliable and reproducible assay suitable for drug development and monitoring. The student will work on new computer tools and quantitative methods that are necessary for the analysis of these data. Statistical genetics with applications to minority populations (Supervisor Pr. S. Gravel) Recent genomic events, such as migrations, rare mutations, or founding events have an important effect on the apportionment of human genomic diversity. This is particularly true in minority populations whose genetic history can be strongly affected by interactions with neighboring populations. In North America, we can think of First Nations/Native Americans, African-Americans, and Hispanics who often derive ancestry from multiple continental populations. The goal of this project is to improve our understanding of genomic diversity in minority populations through the development of new mathematical approaches and the combined analysis of genetic, historical, linguistic, and epidemiological data. This project aims to improve our fundamental understanding of human biology, diversity, and history, as well as our ability to perform medical genetics studies in minority populations around the world.

5 Trans-ethnic mapping for identifying susceptibility genes in infection and chronic disease (Supervisor Pr. M. Lathrop) The association of atopy, asthma and malaria has long been recognized, and recent genetic investigations suggest that malaria and dengue share common genetic determinants with atopy and asthma. The project will focus on developing and using advanced statistical methods for analyzing large, complex datasets involving sequencing targeting regulatory regions of the genome in these diseases. The goal is to apply trans-ethnic sequencing studies to identify genetic determinants of malaria and dengue fever, and examine their pleitropic relationships to Immunoglobulin E levels, atopy, and asthma. The project will draw upon detailed epidemiological and clinical data with longitudinal surveillance in multiple ethnic groups, and apply novel approaches to study both frequent and rare genetic variants systematically in coding and important regulatory regions of the genome. The student will work on one the richest dataset presently available to examine the effects of demographic history on genetic diversity. New methods to assess the contribution of repetitive elements in functional genomics studies (Supervisor Pr. G. Bourque) It is increasingly being recognized that repetitive elements and in particular transposable elements (TEs) are not simply parasitic passengers but that they have contributed functional elements to the human genome. In particular, it has been shown that endogenous retroviruses, a class of TEs with viral origins, have had a major impact on early developmental programs across a number of mammalian lineages. Endogenous retroviruses not only contribute new proteins but also remodel early gene regulatory networks. One challenge in studying TEs and their contribution to transcriptional regulation is the repetitive nature of their sequences, which makes them difficult to be studied using regular short read protocols. The student involved in this project will work on developing new analysis methods to study the impact of TEs on gene regulation by taking into account ambiguously mapped reads and incorporating other sources of information. The student will have the chance to work with unique functional genomic datasets that have been generated across a number of primate species (including human, chimpanzee, gorilla, etc.) in different cell types to characterize for the first time the impact of TEs on primate gene regulation.

6 Optimization of the Oxford Nanopore GridION technology for pathogen genome sequencing and assembly (Supervisor Pr. I. Ragoussis) The project involves the development of protocols for sample preparation and data analysis suitable for rapid DNA sequencing for disease surveillance in the field. The project will use the Oxford Nanopore Technologies GridION sequencing technology, which uses nanopores to analyze single DNA molecules. Key points of the technology are long sequence reads - with up to 120kb achieved by us and rapid turn around. The technology has been used to sequence pathogen genomes and due to its small size and portability as a USB device, it has the potential to be used anywhere in the world. In this project, the performance of the GridION will be evaluated for microbiome and pathogen genome analysis and its ability to characterize repeats and complex DNA structures. Bioinformatics and analysis tool development and application will be a major component of the work.

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