HUMAN GENETICS AND GENOMICS

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1 Human Genetics and Genomics HUMAN GENETICS AND GENOMICS Overview The Interdepartmental PhD Program in Human Genetics and Genomics is a multi-disciplinary program aimed at training scientists broadly in areas of human genetics and genomics relevant to human health and disease. The emerging practice of precision medicine, whereby clinical treatment decisions are based in part on an individual s genomic profile, depends on genomic literacy among practitioners, researchers and patients. Human Genetics and Genomics is a multidisciplinary field that requires training in three core competencies: clinical, molecular, and statistical genetics. Individuals earning PhDs in Human Genetics and Genomics will have various career options, including clinical laboratory (after fellowship training and board certification), research laboratory or computational research in academia, healthcare, and the biotechnology industry. During the first year PIBS curriculum, students will have the opportunity to take two introductory short courses: Variation & Disease and Family Studies & Genetic Analysis. Rotations through faculty laboratories provide students with hands-on experience in various research areas. The rotations also provide the student the background necessary to select their dissertation advisor and area of research. During the second year, the curriculum focuses on core coursework in molecular and computational genetics, biostatistics, and seminars and journal clubs. Also, during the second year, students choose to pursue one of two tracks within the program: molecular genetics or computational genetics. Course requirements differ slightly between these two paths: students in the molecular genetics track will take Advanced Topics in Molecular Genetics while the Computational Genetics track students take Fundamentals of Genetic Epidemiology and Medical Biostatistics II. During the second and third years of study, students formulate and defend a dissertation proposal. All students participate in a -credit hour clinical rotation and complete a teaching practicum during their fourth or fifth years. Contact Information We would be pleased to respond to any questions you may have and look forward to your inquiry. William K. Scott, PhD ( Graduate Program Director Dori McLean, ( Senior Program Coordinator University of Miami, Miller School of Medicine The Dr. John T. Macdonald Foundation Department of Human Genetics Interdepartmental PhD Program in Human Genetics and Genomics 50 N.W. 0 th Avenue, BRB 4 (M860) Miami, FL Admission Applying to the Program Admission Requirements Applicants to biomedical programs should have a bachelor degree in a biological or related discipline (e.g., psychology, chemistry, engineering, physics). Although there are no prerequisite requirements, courses in general biology, cell/molecular biology, calculus, general physics, organic chemistry, physical chemistry, and biochemistry are encouraged. Applications are generally accepted from September to December for fall entry only. Select applicants will be offered an interview. Competitive candidates will have the following: Excellent academic record Competitive GRE exam scores Research experience in a laboratory setting Publications of abstracts and / or papers Co-authorship in a peer-reviewed journal is recommended Strong letters of recommendation from research scientists who know the candidate well Motivation to pursue state-of-the-art biomedical research Applicants must submit the following: Online Application Application Fee Official Academic Transcripts GRE General Test English Proficiency Exam (non-native speakers) Statement of Purpose Resume / CV Full application instructions can be found at: biomed.med.miami.edu/ apply ( Program Plan Program Plan The PhD in Human Genetics and Genomics (HGG) curriculum allows candidates to pursue a track in molecular or computational genetics by their second year of training; however, all students complete a core curriculum in the first three years of graduate study. Students will also participate in seminars and journal clubs in the fall and spring semesters, through all years of study. First-year students interested in Human Genetics and Genomics are strongly encouraged to take two introductory HGG short courses in the spring semester: HGG 60 Variation and Disease and HGG 640 Family Studies and Genetic Analysis which are requirements for completing the HGG degree. Courses in computational / quantitative skills, including biostatistics and bioinformatics will also form part of the first year PIBS curriculum. Each PIBS student completes at least three lab rotations of nine weeks each and chooses a dissertation laboratory (and graduate program) during the latter half of the spring semester. If necessary a fourth rotation may be possible, and in this case a laboratory choice may be deferred until June. All first year students will make short presentations to a group of faculty after each lab rotation. For these presentations the students will be divided into four groups with related research interests.

2 Human Genetics and Genomics After choosing a mentor and laboratory at the end of the first year, a student becomes a member of the HGG Program. Students select and follow a track in molecular genetics or computational genetics in the first semester of year. At this point course requirements differ slightly between these two paths: Students in the molecular genetics track take Advanced Topics in Molecular Genetics (HGG 650) in the second semester, while the computational genetics track students take a second course in biostatistics (EPH 60) and a course in genetic epidemiology (HGG 6). In addition to the required core courses, all students participate in a clinical rotation and serve one semester as a teaching assistant for a core course, in their fourth or fifth year. It is expected that on average, students will complete the program in five years. Please review the complete course descriptions on the COURSE tab above. The general core curriculum is shown in the Plan of Study below: Plan of Study - Molecular Track Course Title Credit Hours Year One PIB 70 Introduction to Biomedical Sciences 5 PIB 70 Scientific Reasoning PIB 7 Laboratory Research ( credit per lab rotation) PIB 700 Journal Club PIB 780 Research Ethics PIB 78 Success I Credit Hours PIB 700 Journal Club PIB 7 Laboratory Research - PIB 78 Success II EPH 60 Medical Biostatistics I HGG 60 HGG 640 Variation and Disease (HGG program elective - I) Family Studies and Genetic Analysis (HGG program elective - II) Credit Hours 0- PIB 80 Doctoral Dissertation Year Two Credit Hours HGG 60 Seminar/Journal Club HGG 6 Genes in Populations. HGG 60 Seminar/Journal Club HGG 650 Advanced Topics in Molecular Genetics (Molecular Track Requirement) HGG 660 Bioinformatics Theory and Practice Year Three.. Credit Hours HGG 60 Seminar/Journal Club HGG 680 Genome Ethics and Public Policy. HGG 60 Seminar/Journal Club Year Four Credit Hours Credit Hours HGG 60 Seminar/Journal Club HGG 68 Human Genetics Clinical Rotation (Can be taken in or - Year 4 or 5) HGG 60 Seminar/Journal Club Human Genetics and Genomics Teaching Practicum (Can be taken in or - Year 4 or 5) Credit Hours

3 Human Genetics and Genomics Year Five HGG 60 Seminar/Journal Club Credit Hours HGG 60 Seminar/Journal Club HGG 850 Research in Residence (Final Semester) Total Credit Hours 6-6 Plan of Study - Computational Track Course Title Credit Hours Year One PIB 70 Introduction to Biomedical Sciences 5 PIB 70 Scientific Reasoning PIB 7 Laboratory Research ( credit per lab rotation) PIB 700 Journal Club PIB 780 Research Ethics PIB 78 Success I Credit Hours PIB 700 Journal Club PIB 7 Laboratory Research - PIB 78 Success II EPH 60 Medical Biostatistics I HGG 60 HGG 640 Variation and Disease (HGG program elective - I) Family Studies and Genetic Analysis (HGG program elective - II) Credit Hours 0- PIB 80 Doctoral Dissertation Year Two Credit Hours HGG 60 Seminar/Journal Club HGG 6 Genes in Populations HGG 6. Fundamentals Of Genetic Epidemiology HGG 60 Seminar/Journal Club HGG 660 Bioinformatics Theory and Practice EPH 60 Year Three. Biostatistics II (Computational Track Requirement). Credit Hours HGG 60 Seminar/Journal Club HGG 680 Genome Ethics and Public Policy. HGG 60 Seminar/Journal Club Year Four Credit Hours Credit Hours HGG 60 Seminar/Journal Club HGG 68 Human Genetics Clinical Rotation (Can be taken in or - Year 4 or 5) HGG 60 Seminar/Journal Club Year Five Human Genetics and Genomics Teaching Practicum (Can be taken in or - Year 4 or 5) Credit Hours HGG 60 Seminar/Journal Club

4 4 Human Genetics and Genomics Credit Hours HGG 60 Seminar/Journal Club HGG 850 Courses HGG Core Course Listing ~ Research in Residence (Final Semester) Total Credit Hours For additional information, please review the General Core Curriculum Plan of Study on the PROGRAM PLAN page. HGG 60 Seminar/Journal Club (/ - Years -5) HGG 6 Fundamentals Of Genetic Epidemiology ( - Year / Computational Track Requirement) HGG 60 Variation and Disease ( I - During PIBS Year ) HGG 6 Genes in Populations ( - Year ) HGG 640 Family Studies and Genetic Analysis ( II - During PIBS Year ) HGG 650 Advanced Topics in Molecular Genetics ( - Year / Molecular Track Requirement) HGG 660 Bioinformatics Theory and Practice ( - Year ) HGG 680 Genome Ethics and Public Policy ( - Year ) HGG 68 Human Genetics Clinical Rotation (/ - Years 4 or 5) Human Genetics and Genomics Teaching Practicum (/ - Years 4 or 5). - - HGG 850 Research in Residence (Final Semester) EPH 60 Biostatistics II ( - Year / Computational Track Requirement) HGG Course Descriptions HGG 60. Seminar/Journal Club. Credit Hour. All registered students must participate in the Seminar/Journal Club. Students are required to review published papers and discuss in detail the findings des cribed therein. Components: SEM. Typically Offered: &. HGG 6. Fundamentals Of Genetic Epidemiology. Credit Hours. This class is a survey of introductory topics in genetic epidemiology and statistical genetics. Basic concepts and methods will be covered including introduction to genetic linkage and genetic association including candidate gene analysis and genome-wide studies, geneenvironment interactions, quantitative trait analysis, and rare variant analysis. The course will consist of a combination of lectures and computational laboratory assignments, with some discussion from the primary scientific literature. There will be several lab assignments (requiring use of laptops), one exam, and two in-class paper discussions. Details on the assignments will be posted to BlackBoard. Typically Offered:. HGG 60. Variation and Disease. Credit Hours. This course provides an overview of the science of genetics, including historical and modern approaches, with emphasis on the underlying mechanisms of human genomic variation and their relation to human disease. After taking this course the student will be able to list the different types of human genomic variation, explain the mechanism by which each occurs, and discuss the consequences of the variation. Where appropriate, specific examples of human disorders will be related to the variation. Topics include: chromosomal, biochemical, and DNA sequence variation, mitochondrial genome variation and epigenetic effects. The course structure consists of a combination of lectures and discussion of primary literature. Typically Offered:. HGG 6. Genes in Populations. Credit Hours. The course explores the relevant history and principals governing the behavior of genes in human populations. Topics include Hardy-Weinberg equilibrium; Mendelian, complex and quantitative traits; principals of selection and change in populations, neutral theory; and molecular evolution of gene families. The course is lecture based with supplemental readings. Components: LAB. Typically Offered:. HGG 640. Family Studies and Genetic Analysis. Credit Hours. This course will cover the analysis of genetic data in family based data sets. Topics include: heritability, segregation analysis and linkage analysis. This course includes a computer lab component in which students will learn to use the relevant analytic programs. Typically Offered:. HGG 650. Advanced Topics in Molecular Genetics. Credit Hours. Topics include human micrornas, the neurobiology of aging, structural varation, modern genome technology, among others. The course structure consists of disc ussions and analysis of primary literature. Typically Offered:.

5 Human Genetics and Genomics 5 HGG 660. Bioinformatics Theory and Practice. Credit Hours. This course covers a gradient of basic to advanced bioinformatics theory, data mining, and analysis. Each class will include a lecture to explain the concepts, followed by a hands-on lab session with worksheets and exercises. Early lectures will cover in-depth searching of the major databases, alignments, and motif discovery. These themes will recur with the applications of these and other algorithms to gene expression analysis, next generation sequencing data and its analysis, and analysis of variation. Freely available web resources will be used wherever possible, and the students will learn how to use Python for some bioinformatics applications. Typically Offered:. HGG 680. Genome Ethics and Public Policy. Credit Hours. This course explores current and future applications of human genetics as they pertain to the health and identity of individuals and society. Topics to be covered will include the science of genetic testing, the ethical, legal and social issues related to such testing, living with a genetic diagnosis, the factors influencing the use of human genetic information, and evolving direct-to-consumer genetic testing services. The emphasis will be on real life examples and experiences, with a primary goal of helping students explore how their life, and the society in which we live, will be affected by genetic information. Policy themes include: the role of society in regulating the use of genetic testing and genetic information, implications of genetic testing for people with disabilities, role of the media in public genetic education, legal issues associated with the use of genetic information (e.g. discrimination, duty to warn, wrongful birth), and the role of eugenics in today's society. Typically Offered: &. HGG 68. Human Genetics Clinical Rotation. Credit Hour. The HGG graduate students participate in medical genetics clinic post clinical rounds, metabolic-sign out and journal clubs. During clinic students observe clinical evaluations and counseling, and participate in weekly didactic sessions with faculty and residents. Components: CLN. Typically Offered: &.. Human Genetics and Genomics Teaching Practicum. Credit Hour. HGG students serve one semester as a teaching assistant for a core course. This experience will include giving at least one lecture, leading small group discussions, and holding regular office hours to discuss student questions. This will generally take place in the student?s third or fourth year, and will be graded as a one-credit pass-fail course. Components: PRA. Typically Offered:,, & Credit Hours. - credit course for Doctoral candidates working on pre-candidacy dissertat ion. Typically Offered:,, &... - Credit Hours. - credit course for Doctoral Candidates working on dissertation post candida cy. Typically Offered:,, &. HGG 850. Research in Residence. Credit Hour. Used to establish research in residence for Ph.D, after the student has been enrolled for the permissible cumulative total in appropriate doctoral research. Credit not granted. May be regarded as full-time residence as determined by the Dean of the Graduate School. Typically Offered:,, &.

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