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Ph.D. Graduate Program

Ph.D. Graduate Program

The Department of Genetics Genome Sciences embraces a unified program devoted to outstanding research and teaching in all areas of genetics, with particular emphases on genetics and genomics, human and model system genetics, animal models of human disease, stem cell models of human disease, epigenetics and the regulation of gene expression, therapeutic targets of human genetic disease, as well as developmental genetics. Faculty conduct internationally recognized research programs in each of these areas. They also are committed to training the next generation of leading genetics researchers. The Department has several affiliated programs that provide additional research and training opportunities, including the Center for Human Genetics at University Hospitals and the Genomics Medicine Institute at the Cleveland Clinic.

The GGS graduate program has maintained an active student body for many years and consistently has 25-30 students enrolled. The student body provides the momentum and driving force for research in the department. During the last six years, GGS students published 1st author papers in Cell Stem Cell, Genome Research, Nature, Nature Biotechnology, Nature Genetics, Science, and Proceedings of the National Academy of Sciences. Since 2012, eight GGS students have been awarded pre-doctoral fellowships from American Heart Association and the National Institutes of Health. A 2015 graduate, Olivia Corradin, was recently selected to be a Whitehead Fellow, a highly selective and prestigious program at the Whitehead Institute and MIT that provides support for her own independent research program right out of her graduate studies without further postdoctoral training.

The department has a strong, long-standing commitment to providing excellence in graduate education. The department offers a well-developed training program that integrates courses, workshops, journal clubs and student seminars to help students to develop research capabilities as well as other crucial skills such as oral and written presentations. Students are expected to present a research seminar annually to the department followed by a brief session that critiques the presentation by faculty members. The graduate program directors, the department chair and the thesis committee chair formally review students' academic progress annually. The time to degree in 2011-2016 is 5.25 years. The program supports students' career development by advising students on teaching opportunities, obtaining clinical laboratory experience, etc.

Overview of the Program

The following summary pertains to most incoming Ph.D. students, regardless of the route through which they enter the program. Exceptions are occasionally made to reflect previous educational experiences (e.g., a prior M.S. degree). Note that combined M.D./Ph.D. students must meet all of the requirements for the Ph.D. degree; requirements for the M.D. degree are described on the MSTP website.

The First Year

Course work, rotations in at least three laboratories, and participation in seminars, journal clubs, and research meetings are the major activities of first year students. During the Fall term, most students take a core course in Cell and Molecular Biology (CBIO 453/455) that is offered jointly for all participating Biomedical Sciences Training Program departments. Laboratory rotations begin in early July and the choice of a thesis advisor is usually made by the end of December (see below for more details on Choosing an Advisor).

During the Spring term, students take the Genetics core course, Advanced Eukaryotic Genetics (GENE 500/504). This core course is designed to acquaint students with fundamental principles and methodologies used in modern genetic research. The focus is on similarities and differences between different model organisms used in genetics research. During the Spring term and continuing into the Summer, students begin formulating a doctoral research proposal.

The Second Year and Beyond

During the second year, students participate in a Proposal Writing Workshop (GENE 511) and take other advanced elective courses. The academic background and interest of the student largely determines his/her course schedule. The remaining elective credits can be satisfied by choosing from the courses offered by departmental faculty or participating training faculty from other departments (see List of Courses below). At the end of the second academic year, students must pass an oral proposal defense in order to advance to candidacy for the Ph.D. degree. An outline of the typical course of study is shown below.

Typical Course of Study

Year 1:
First semesterC3MB (CBIO 455/IBMS 450/CBIO 453/456)8 credit hrs
Complete 3 lab rotations(July 1 to Dec 15)
Choose Ph.D. mentor(end December)
Second semesterGENE 500/5046 credit hrs
Summer semesterProgram Directors meet with students to discuss status, mentor, and next steps. Students begin assembling Ph.D. thesis committee
Year 2:
First semesterGENE 5113 credit hr
1 elective course (Genetics or other)3 credit hrs
Second semester1 elective course (Genetics or other)1-3 credit hrs
Oral Defense of Thesis Proposal(to be completed by June 30)
Advancement to Ph.D. Candidacy
Year 3:
Full time research

Other Requirements

Students meet twice per year with Thesis Committee
Students meet once per year with Genetics and Genome Sciences Graduate Education Committee
Genetics Student Seminar (weekly attendance, yearly presentation)
Genetics Journal Club (weekly attendance, yearly presentation)
Genetics Retreat (yearly participation, organized by students)
Two first-author, peer-reviewed publications (see below)

Research Rotations

The main purpose of research rotations is to facilitate the selection of a thesis advisor. A minimum of three rotations of four-to-six-week duration must be completed within the first year. Rotations are arranged by the student with prospective research advisors selected from Genetics and Genome Sciences (for students who elected Genetics and Genome Sciences as their priority program) or from any member of the BSTP program (for other students). Because an additional rotation is sometime needed, and since it is desirable to begin thesis work as soon as possible, students are encouraged to begin rotations in July of their entrance year. It ensures that rotations are completed and a thesis research laboratory is chosen by the end of the first semester.

Choosing a Thesis Advisor

First-year students choose a thesis advisor by the end of the first semester, as a joint decision by the student, the prospective advisor, and the Genetics Graduate Student Program Committee. The student's interest is the primary factor in this decision. By choosing a thesis advisor affiliated with the Genetics Training Program the student becomes a member of this program and must satisfy the specific program requirements to earn the Ph.D. degree.

Proposal Defense

Students must pass the oral defense of a written thesis proposal. This written proposal is defended orally by the student and judged by a thesis committee composed of at least four faculty with related interests and expertise. The student must pass the proposal defense by the end of the second year (by the end of the fall semester of second year for MSTP students), and all other requirements for advancement to candidacy should have been completed by this time. The defense process is designed to ensure that the successful student has a basic foundation in genetics and biomedical science, exposure to and understanding of the development of a research program, and a well-designed thesis research project. If a student does not perform sufficiently well in the oral defense, the student's thesis committee and Genetics Training Program Graduate Committee will meet and decide if the student will be asked to withdraw from the program.

Seminars and Journal Clubs

Students are expected to participate in ongoing journal clubs and research seminars that provide regular opportunities for developing oral presentation skills and the ability to analyze experimental work critically. A program of departmental and interdepartmental seminars by outstanding visiting scientists provides regular exposure to a broad range of current research.

Doctoral Research and Publication Requirements

Dissertation research and publication are the most important aspects of graduate education. Writing a scientific paper as the lead author is an essential pedagogical experience in research training. Trainees must be accomplished in the effective communication of novel and significant results of their research. Graduates of Case School of Medicine Ph.D. programs are expected to have two or more first-authored primary research publications in peer-reviewed scientific journals. As a minimum, at least one such paper must be accepted for publication prior to award of the Ph.D. In certain cases, the publication requirement may be reduced from 2 to a minimum requirement of one first-authored publication, upon approval of the Chair of the Department or Graduate Program Director, particularly if that publication is clearly substantial. Research is done in the laboratory of the thesis advisor in a close collaboration. After completion of research objectives, a formal written thesis, oral defense, and formal seminar presentation complete the program of study, and a Ph.D. in Genetics is awarded by Case.

List of Courses

(cross-listed courses in parentheses)

GENE 451
(EPBI 451, MPHP 451)
Principles of Genetic EpidemiologyWilliam Bush3.0
This course introduces the foundational concepts of genomics and genetic epidemiology through four key principles: 1) Teaching students how to query relational databases using Structure Query Language (SQL); 2) Exposing students to the most current data used in genomics and bioinformatics research, providing a quantitative understanding of biological concepts; 3) Integrating newly learned concepts with prior ones to discover new relationships among biological concepts; and 4) providing historical context to how and why data were generated and stored in the way they were, and how this gave rise to modern concepts in genomics.
GENE 452 (EPBI 452)Statistical Methods in Genetic EpidemiologyRobert Igo3.0
Analytic methods for evaluating the role of genetic factors in human disease, and their interactions with environmental factors. Statistical methods for the estimation of genetic parameters and testing of genetic hypotheses, emphasizing maximum likelihood methods. Models to be considered will include such components as genetic loci of major effect, polygenic inheritance, and environmental, cultural and developmental effects. Topics will include familial aggregation, segregation and linkage analysis, ascertainment, linkage disequilibrium, and disease marker association studies. Recommended preparation: EPBI 431 and EPBI 451.
GENE 488
(MBIO 488, CLBY 488, PATH 488)
Yeast Genetics/Cell BiologyAlan Tartakoff3.0
This seminar course provides an introduction to the genetics and molecular biology of the yeasts S. cerevisiae and S. pombe by a discussion of current literature focusing primarily on topics in yeast cell biology. Students are first introduced to the tools of molecular genetics and special features of yeasts that make them important model eukaryotic organisms. Some selected topics include cell polarity, cell cycle, secretory pathways, vesicular and nuclear/cytoplasmic transport, mitochondrial import and biogenesis, chromosome segregation, cytoskeleton, mating response and signal transduction.
GENE 500Advanced Eukaryotic Genetics IHelen Salz3.0
Fundamental principles of modern genetics; transmission, recombination, structure and function of the genetic material in eukaryotes, dosage compensation, behavior and consequences of chromosomal abnormalities, mapping and isolation of mutations, gene complementation and genetic interactions. Recommended preparation: BIOL 362.
GENE 504Advanced Eukaryotic Genetics IIHelen Salz3.0
Fundamental principles of modern genetics: population and quantitative genetics, dissection of genome organization and function, transgenics, developmental genetics, genetic strategies for dissecting complex pathways in organisms ranging from Drosophila and C. elegans to mouse and human. Recommended preparation: GENE 500 or permission of instructor.
GENE 505Genetics Journal ClubAhmad Khalil1.0
Genetics Journal Club is a graduate level course designed to facilitate discussion of topics in Genetics. Students choose "hot" papers in Genetics and present them to their peers. Group presentations are designed to encourage audience participation. The intent of this class is to expose students to cutting edge topics in Genetics and to instill teaching and leadership skills.
GENE 467(LAWS 5341, MGMT 467, EBME 467 and EECS 467)Commercialization and Intellectual Property Management3.0
This interdisciplinary course covers a variety of topics, including principles of intellectual property and intellectual property management, business strategies and modeling relevant to the creation of start-up companies and exploitation of IP rights as they relate to biomedical-related inventions. The goal of this course is to address issues relating to the commercialization of biomedical-related inventions by exposing law students, MBA students, and Ph.D. candidates (in genetics and proteomics) to the challenges and opportunities encountered when attempting to develop biomedical intellectual property from the point of early discovery to the clinic and market. Specifically, this course seeks to provide students with the ability to value a given technological advance or invention holistically, focusing on issues that extend beyond scientific efficacy and include patient and practitioner value propositions, legal and intellectual property protection, business modeling, potential market impacts, market competition, and ethical, social, and healthcare practitioner acceptance. During this course, law students, MBA students, and Ph.D. candidates in genomics and proteomics will work in teams of five (two laws students, two MBA students and one Ph.D. candidate), focusing on issues of commercialization and IP management of biomedical-related inventions. The instructors will be drawn from the law school, business school, and technology-transfer office. Please visit the following website for more information:
GENE 511Grant Proposal WorkshopZhenghe Wang3.0
This is an introductory graduate course in grant writing and reviewing skills. During this course each student will write a research grant on a topic of his or her choice. Proposals may form the basis for the written component of the preliminary examination in the Genetics and Genome Sciences Department. Students will also participate in editing and reviewing the proposals of their classmates.
GENE 513Adv. Developmental GeneticsRon Conlon3.0
This course covers the mechanisms of development in the context of the major events of mammalian embryogenesis. The focus is on how genes act in cells to create and pattern the tissues and organs of the adult. Students can expect to acquire a deep understanding of the embryology of mammals, and how genetic manipulations have led to our current understanding of pattering mechanisms. The material will be taught by a combination of self-study exercises, discussions of the primary literature, student presentations, and facilitator guided, student-led, problem-based learning.
GENE 524Advanced Medical Genetics: Molecular & CytogeneticsAnne Matthews2.0-3.0
An in-depth forum for discussion of fundamental principles regarding clinical cytogenetics and molecular genetics and their relevance to medical genetics, genomics and genetic counseling. Following a historical overview, topics include a discussion of numerical and structural aberrations, sex chromosome abnormalities, issues regarding population cytogenetics, clinical relevance of such findings as marker chromosomes, mosaicism, contiguous gene deletions and uniparental disomy. The course will cover principles of molecular genetics including structure, function and regulations of genes (DNA, RNA, proteins), genetic variation, inheritance patterns and both cytogenetic and molecular laboratory techniques (fluorescence in situ hybridization, micro-array, SNP analyses, sequencing) in the clinical laboratory.
GENE 525/GENE 516Advanced Medical Genetics: Clinical GeneticsAnne Matthews2.0-3.0
Fundamental principles regarding congenital malformations, dysmorphology and syndromes. Discussion of a number of genetic disorders from a systems approach: CNS malformations, neurodegenerative disorders, craniofacial disorders, skeletal dysplasias, connective tissue disorders, hereditary cancer syndromes, etc. Discussions also include diagnosis, etiology, genetics, prognosis and management.
GENE 526Advanced Medical Genetics: Quantitative Genetics & GenomicsAnna Mitchell/Becky Darrah2.0-3.0
This course provides a foundation in quantitative genetics as well as genomic approaches and technologies which have greatly expanded our understanding of not only rare genetic disorders but common ones as well. Concepts related to risk assessment and calculation and its application to medical genetics including principles and application of Hardy Weinberg equilibrium and applying Bayes' Theorem as a mechanism to refine risk assessment based on patient specific data are covered. The clinical implications of interpreting next generation sequencing results, identifying limitations of genomic technologies, and practicing annotation and interpretation of genomic testing results are also covered. In addition, resources and bioinformatics tools including national databases and clinical labs to aid in the interpretation of genomic test results including variants of uncertain significance are discussed.
GENE 527Advanced Medical Genetics: MetabolismArt Zinn2.0-3.0
Fundamental principles of metabolic testing; amino acid disorders; organic acid disorders; carbohydrate disorders; peroxisomal disorders; mitochondrial disorders; etc. Discussion of screening principles and newborn screening as well as approaches to diagnosis, management and therapy for metabolic diseases.
GENE 503Readings & Discussion in GeneticsFaculty0.0-3.0
GENE 601Research in GeneticsFaculty1.0-9.0
GENE 651Master's ThesisFaculty1.0-9.0
GENE 701Dissertation Ph.D.Faculty1.0-9.0
Last update on: September 2016

Application Information
BSTP (Ph.D.) & MSTP (M.D./Ph.D.) Pathways

The Department of Genetics and Genome Sciences accepts students into its Ph.D. program via two pathways: the interdepartmental Biomedical Sciences Training Program (BSTP) or the Medical Scientist Training Program (MSTP).

Applications to the PhD program in Genetics and Genome Sciences are through the Biomedical Sciences Training Program, which provides access to most of the biomedical science Ph.D. programs at CWRU during the first semester. Students who wish to join Genetics and Genome Sciences directly should apply to the BSTP by selecting "Biomedical Sciences Training Program" as their Academic Program in the "Enrollment Information" section. Then, select Genetics and Genome Sciences as a Priority Program of Interest (PPI) in the Supplemental portion of the BSTP application form. Selecting the PPI option will identify you as an BSTP applicant who seeks admission only to the Genetics and Genome Sciences PhD program. In general, selecting Genetics and Genome Sciences as a Priority Program of Interest (PPI) in the Supplemental portion of the BSTP application is reserved for students who already have identified Genetics as their field of study, and who have had considerable exposure to genetic research, either in undergraduate school or the workplace. All full time Ph.D. students receive a competitive stipend, health insurance, and all academic tuition fees are waved.

Priority will be given to applications received by December 1. We will continue to review applications received after the priority deadline, but not beyond the final application deadline of January 15. Your application will be reviewed by the Admissions Committee as soon as it is complete. A completed application has all of the following parts:

  • Application form completed by the student
  • Official transcripts of all previous work
  • Three GRE scores (Institutional code 1105)
  • TOEFL Score for international applicants (Institutional code 1105).
  • Three letters of recommendation
  • Personal Statement
  • A $50.00 Application Fee (check or money order in US $ payable to CWRU)

Applications are completed online, using the links above. Please have your transcripts sent directly to BSTP.

For further information, please contact the Genetics and Genome Sciences Graduate Program Assistant, Clarice Young - (216) 368-3431 or email:

Admission Requirements and Process

Applicants who have completed undergraduate courses in mathematics, physics, chemistry (preferably organic chemistry), and biology may apply. Applicants are required to take the Graduate Record Examination. Advanced GRE subject examination is not required. No minimum GRE or TOEFL score is required. Prior research experience is highly desirable and strongly recommended. Personal statement in the application should discuss interest in genetics, prior research experience, research interest for graduate study, and future goals. Perspective students who meet the requirements will be invited for an interview in January, February or March. Acceptance letters will be sent out shortly after the interview, which will be confirmed by students as soon as possible. We strongly recommend that the incoming students start in early July.

Last update on: 20th October 2017