All NIH T32 trainees must have an account within eRA Commons. Once the account is active, trainees need to complete the Personal Profile within the eRA Commons xTrain system. For trainees with existing accounts, please verify personal profile information is complete and up-to-date. Personal profiles must be current and complete before the appointment form, PHS 2271 (link contains form instructions), can be routed to the trainee. The eRA Commons Help System and User Guide provide detailed instructions on setting up personal profiles. Instructions for trainees on how to route the form back to the PI can be found in pages 38-42 of this PDF. Trainees must respond to emails from NIH’s eRA Commons in a timely manner and complete and route forms as instructed within the xTrain system.

T32 Grant Support Acknowledgement

Trainees appointed on this federally-funded training grant are required to acknowledge this T32’s support as detailed in the NIH Notice of Grant Award. Each publication, press release, or other document about research supported by an NIH award must include an acknowledgment of NIH award support and a disclaimer such as “Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number 1T32HG008961-08. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”

Trainees should cite the T32 as a source of support if the publication, abstract or presentation resulted from work conducted while the individual was supported by the grant (i.e., receiving a stipend) as per NOT-OD-15-091.

NIH Public Access Policy

All publications and abstracts resulting from NIH support must be in compliance with the NIH Public Access Policy. Lack of compliance can jeopardize the funding of this T32 grant. Notification of accepted publications and abstracts acknowledging T32 support must be emailed by the trainee and/or mentor to Shaila Handattu within 30 days of acceptance. Details of the NIH Public Access Policy can be found here: http://publicaccess.nih.gov/

FAQs: https://publicaccess.nih.gov/faq.htm

My NCBI Bibliography

Trainees must keep their My NCBI Bibliography up-to-date. Trainees should always use their eRA Commons login to access My NCBI. The My NCBI Bibliography should be a complete list of all of the trainee’s publications to date. Trainees should ensure that the appropriate grants are associated with each publication, matching those listed in the acknowledgments/funding source section the publication. A My NCBI Bibliography “how to” reference can be found here: http://www.ncbi.nlm.nih.gov/books/NBK53595/ as well as a YouTube video here: https://www.youtube.com/watch?v=9gApmLHdCSM as well as FAQs here: http://publicaccess.nih.gov/my-bibliography-faq.htm

NIH Biosketch

It is also highly recommended that trainees create and maintain a NIH formatted biosketch. Information including examples and formats (for pre and postdocs) can be found in this NIH Notice: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-15-032.html

Genetics and Genomics Seminar (Fridays 12-1 pm)

This weekly seminar is attended by all trainees and faculty in the UAB Department of Genetics.  It consists of invited speakers from UAB, HudsonAlpha, as well as outside invited speakers.  

HudsonAlpha Institute for Biotechnology Research Seminars

The HudsonAlpha Research Seminars bring together experts in genetics, genomics, biotechnology, bioinformatics, medicine and immunology for public presentations and debate among the scientific community. The seminars also provide valuable academic learning and discussion opportunities for scientists training in labs at HudsonAlpha and at universities across Alabama. Seminars are hosted by researchers at the HudsonAlpha Institute for Biotechnology from October through May, and they are typically held on Wednesdays at noon in the Wayne R. Widener Auditorium at HudsonAlpha as well as via zoom.

Multidisciplinary/Molecular Tumor Board

Weekly conference on Thursdays at 7:15am organized and run by Sushanth Reddy, MD.

All trainees will attend this conference. 

2024 NHGRI Research Training and Career Development Annual Meeting

April 7-9, 2024

Seattle, WA

Click here for more information

UAB has a strong commitment to the responsible conduct of research (RCR) at all levels, including the postdoctoral level. Indeed, UAB is among six prestigious institutions whose best practices in the teaching of research integrity at the graduate school level are considered a model for universities across the country. UAB participated in The Project for Scholarly Integrity, a multi-year Council of Graduate Schools initiative supported by the U.S. Office of Research Integrity. The data, published in 2012 in Research and Scholarly Integrity in Graduate Education, highlights the need for a more comprehensive approach to teaching research integrity in graduate education. Subsequent to this activity, UAB was one of eight institutions to be awarded funding by the Council of Graduate Schools and the Office of Research Integrity to integrate RCR educational materials throughout the graduate curriculum. Such material, which encompasses all subject matter specified by NOT-OD-10-019 (Training in the Responsible Conduct of Research), is currently in use by faculty, postdoctoral fellows, and graduate students in promoting discussion of scholarly integrity. UAB has posted their policy at http://www.uab.edu/policies/content/Pages/UAB-RA-POL-0000263.aspx. All new postdocs at UAB (including all new trainees on this training grant) are required to attend a Postdoc Orientation during their first year; orientations are offered twice a year. Orientation sessions include information from UAB administrators in the offices of the OPE, Institutional Review Board, Conflict of Interest Review Board, Institutional Animal Care and Use Committee, Occupational Health and Safety Office, Grants and Contracts Administration, Research Foundation, among others. In addition, these sessions include a 2-hour introductory workshop in the RCR.

Mentoring By Example

One of the best modes of training in scientific integrity and ethical research principles is for trainees to be exposed to such principles from outstanding and well-respected research scientists. Trainees work closely with principal investigators, funded by the NIH and other public and private funding agencies, in their research efforts. Mentors are advised that their mentorship should include a focus on ethical and legal aspects of research in addition to focusing on the scientific subject matter.

Written Materials

All trainees will receive copies of the following ethics resources: 1) "On Being a Scientist" published by the National Academy of Sciences; and 2) the UAB misconduct policy.

Periodic Seminars & Symposia

UAB routinely offers seminars and symposia on research ethics that emanate from multiple entities, including the UAB Center for Ethics and Values in Science (EVIS) and the UAB Center for Clinical and Translational Sciences (CTSA). For example, recent symposia hosted by these Centers have examined the topics of scientific misconduct, fraud, and ethics involving information communication in science as well as the bioethics of health disparities. Postdoctoral scholars and their mentors will be encouraged to attend and/or participate in the training opportunities offered through the Center.

Required Didactic Training

All postdoctoral trainees in this program are required to take a more detailed and structured instruction in the RCR training in the first year of appointment.  RCR training is documented in the annual progress report of the trainees in their Individual Development Plan. Faculty members are required to have completed an initial course in RCR and a refresher course every four years. In addition to the ethics training included during the required orientation session, all trainees will be required to take the Principles of Scientific Integrity (GRD 717).  This is a semester-long course consisting of (10) 2.0 hour sessions that provides a survey of ethical issues and principles in the practice of science. This course is offered on Friday afternoons and all trainees, including those located at HudsonAlpha, will take this class at UAB. 

Optional Research Ethics Training

Postdoctoral scholars may also choose to take systematic instruction about the responsible conduct of science via a series of formal courses including:

• IRB training: Trainees who will perform research on human subjects will complete an approved training course on human subjects protection and will update their training annually. There are a number of avenues for fulfilling this training requirement, including on-line opportunities and seminars. For example, scholars may fulfill this requirement via completion of the web based training program Collaborative IRB Training Initiative (CITI). The CITI Program includes courses in the ‘Protection of Human Research Subjects for Biomedical as well as for Social/Behavioral Research’. Each training module focuses on different aspects of bio-ethics and human subjects research.

• IACUC training: Trainees who will be involved in research that utilizes animals will complete IACUC training via on-line coursework combined with individualized instruction from IACUC veterinarians. Specifically, IACUC training will review the humane use of animals in research together with related ethical issues. In addition, scholars will receive species-specific direction in the appropriate techniques of drug administration, specimen collection, and surgery.

(per NIH Policy NOT-OD-14-113)

At the beginning of the research training period, mentors work with trainees to develop a written individualized development plan (IDP), which includes a set of activities and goals including didactic courses, ongoing conferences and seminars, as well as the mentored research project. UAB provides all trainees with information about the benefits of individual development plans for their desired career outcomes. Training sessions for new and continuing trainees are provided throughout the year, including an introduction to the myIDP website. This IDP provides the framework for periodic assessment of progress in the training relationship and is reviewed twice a year with the Program Directors and the Executive Committee.

Postdocs being supported by NIH funding must maintain an Individual Development Plan (IDP). An IDP is a dynamic document that identifies career goals, sets a path and helps trainees manage their career development plans. The IDP should be drafted by the trainee and discussed and reviewed with their mentor(s), at minimum, every 6 months. Input from secondary mentors and beyond is encouraged. A recommended resource dedicated to the development and maintenance of an IDP is the Science Centers myIDP resource.

NOTE: Trainees are only required to email IDPs to Shaila Handattu (hande@uab.edu) twice a year. It is up to the trainee and mentor(s) to determine the format. 

Each spring this T32 grant is required to submit a progress report to NIH NHGRI. Each trainee will prepare individual progress reports detailing their course work, training, skills, and research project experiences twice a year and review them with their mentor(s) and program directors. Any work on publications or conference presentations and honors or fellowships, etc. should also be mentioned. A listing of publications, abstracts and presentations accomplished during the reporting period will also be collected. Publications must be in NIH Public Access format. A listing of the grants the trainee is involved with is also required and all grants must be provided in the following format: Name of grant, funding institution, grant number(A01 AA123456-01), last name(s) of grant PI/co-PI(s), UAB IRB or IACUC number(s) XXXX or XX-XX-XX approval through date(s) (xx/xx/xx).

It is highly recommended trainees keep their T32 training grant progress report documents and publications/presentations listings up-to-date at all times.

Genomic Medicine Research Project(s)

Provide a detailed description of the genomic medicine research project(s) you are involved with or have initiated during your time of support on this T32. Include the methodology, utility/significance of the proposed results, and how it fits into your career trajectory. Include the support information for the project beyond your support from the T32 – ex. your mentor’s R01 grant number.

Peer-Reviewed Papers (in print or press)

– Must be compliant with the NIH Public Access Policy!
Format Example: Vander Velde, J.J. and Riley, E.P.[List all authors] Title of the paper. Journal Name, 20xx[year];X[issue number]:123-127[page numbers]. PMCID: PMC9999999

Submitted Manuscripts

Format Example: Vander Velde, J.J. and Riley, E.P. Title of the paper. Journal Name, Submitted Month 20xx.

Manuscripts in Preparation

Format Example: Vander Velde, J.J. and Riley, E.P. (In Preparation). Title of the paper.

Conference Abstracts and Presentations

Format Example: Vander Velde, J.J. and Riley, E.P. Title. Presented at the Name of the Meeting, City, State, Month 20xx. [If it is a published abstract also include: Journal Name, 20xx;X(Supplement SX):123A.]

We have developed a six-part evaluation to assure the progress of trainees and to help identify and correct weaknesses.

1. Weekly evaluation is conducted informally by the Program Directors based on trainees’ participation in the weekly seminar series (Genetics and Genomics Grand Rounds and other conferences);

2. Monthly evaluation will be conducted in formal meetings of each trainee with the mentor. These meetings will supplement more frequent meetings on the mentored research project and will address how didactic courses are proceeding, career planning, and will provide an opportunity for reflection and feedback on progress. Any issues that arise during these meetings will be relayed to the Executive Committee for review and input.

3. Semi-annual review will be conducted at a meeting with the one or both of the co-directors. These meetings will provide formative evaluation based on input from mentors and will inquire specifically about problems or weaknesses in the training program and suggestions for improvement.

4. Annual review: All trainees will be asked to evaluate the program on a yearly basis in the form of a survey. Questions asked will include: 1. satisfaction with mentor; 2. satisfaction with Executive Committee interactions; 3. satisfaction/benefit of advanced courses; 4. satisfaction with opportunities for presentation of data, attendance at meetings, and interaction with relevant seminar speakers; 5. level of preparation for next step in career, (i.e., postdoctoral position, junior faculty, industry, etc.); and 6. what can be improved about the program?  This is not an inclusive list of all questions, but reflects some of what will be captured on a yearly basis. 

5. Exit interviews with the Executive Committee will be conducted with each trainee upon completion of their training, asking similar questions in person. We recognize that trainees sometimes may leave the program before completion, for example due to personal circumstances or that their passion lies in areas other than research. In addition to proactively addressing these circumstances through the mechanisms listed above, when a trainee decides to leave we will conduct an extensive exit interview and discuss the case within the Executive Committee to identify any lessons to be learned and opportunities for improvement in our processes of admissions, ongoing and mentorship.

6. Evaluation by Past Trainees: Outcomes will be tracked by maintaining contact with the trainees to determine what positions they have taken and to note future achievements. 

As described in the application, we identify competencies that fall into four broad areas: (A) ELSI; (B) genomics; (C) quantitative sciences; (D) Clinical Applications. Every trainee will be required to acquire competencies in each of these areas as determined on an individualized basis by the trainee, the trainee’s mentor, and the mentoring committee.

1. Ethical, Legal, and Social Issues in Genomic Medicine

   1. Informed consent, including both for return of genomic results as well as broad consent for the use of biobanks and data repositories

   2. The demarcation of clinical and research duties and their implications for research and clinical practice

   3. Privacy and the special challenges of de-identification for genomic data

   4. Appropriate uses of genomic technologies, including preconception, preimplantation, and prenatal genomic testing, as well as diagnostic, pharmacogenomic, and population screening

   5. Normative and social risks and the role of community consultation and engagement, including for development of biobanks and data repositories

   6. Health disparities and the fair distribution of benefits and risks from genomic research, as well as fair access to, and coverage of, genomic medicine services

   7. Ethical issues pertinent to vulnerable populations, including implications of genomic research for understanding race, ethnicity, and other relationships within and among human populations

   8. Role of genomics in preventive care and public health, including patient and research participant understanding of genomic results, risks of undue anxiety and false reassurance, and the limitations of genomic information for drawing deterministic conclusions

   9. Intellectual property issues, including the status of patents and ownership of an individual’s genomic information

   10. The scope and limitations of the Genetic Information Nondiscrimination Act (GINA), as well as other legal, legislative, and policy initiatives designed to protect individuals

2. Genomics

   1. Structure and common uses of the human reference genome assembly:

      • Technologies and methods used to generate the human reference sequence and assembly

      • Size, scope, and quality of the reference assembly

      • Landscape of coding and non-coding genes

      • Nature, types, and distributions of regulatory elements and other functional features

      • Distribution and relevance of mobile elements and other repetitive sequences

      • Use of genome browsers to learn about loci, genes, variants, annotations, or other relevant features

      • Strengths and weaknesses of a single reference genome in both clinical and research genomics

      • How annotations of genomic structure, function, and evolution can help to evaluate the potential role(s) of variants and genes in a given phenotype

   2. Human population genetics:

      • Nature and distributions of genetic variation, including SNVs, CNVs,

      • Allele frequency spectra in individual human genomes, in populations of human genomes, and in datasets from varying experimental/technological strategies (e.g., GWAS, exome, genome, )

      • Haplotype structure and linkage disequilibrium, and the mechanisms and value of genotype imputation

      • Influence of ancestry and demography on observed patterns of variation

      • Rates of new mutations of various categories, how genomic sequence and structural features can influence mutation rates, and expected patterns of de novo mutations in individual genomes

      • Influence of selection on variation properties and patterns and the predominance of neutrality among common variants

   3. High-throughput sequence generation and analysis:

      • Sizes and scopes of typical sequence-based experiments, g., numbers and lengths of reads and their expected enrichments or other properties

      • The importance and relevance of read depth to various genomic experiments

      • Differences in strategy, interpretation, and utility of single- and paired-end sequencing

      • How variants of differing classes are identified, at a conceptual level, from multiple data types, including germline DNA resequencing, somatic tissue resequencing, and RNA sequencing

      • How variants of differing classes are identified in common pipelines (e.g., GATK), and the key parameters and thresholds relevant to evaluating the quality and reliability of those variants

      • The influence of batch effects

      • The influence and importance of various “normalization” schemes to evaluate sequence-based counts and other statistics

   4. The basics of sequence alignment:

      • Differences between alignment strategies (e.g., local vs global, BLAT vs BLAST, ) and how and why those differences are relevant to common tasks in genomics

      • Impact of read lengths on alignment results

      • Influence of algorithm choice, thresholds, parameters, on factors like alignment sensitivity and specificity and how those decisions may affect interpretation of results

      • Impact of repetitive sequences on alignment results and interpretations

      • Goals, parameters, and performances of computational tools commonly used in genomics

   5. Common genomic experimental designs or strategies relevant to clinical genomic result interpretation:

      • Germline sequencing to identify high-penetrance contributions to disease

      • Germline sequence or array-based genotyping to identify genotype-phenotype correlations, especially pharmacogenomic studies

      • Tumor sequencing of DNA and/or RNA to identify causal mutations or other features with diagnostic, prognostic, or therapeutic value

      • Functional genomics experiments (e.g., ChIP-seq, RNA-seq, Methyl-seq, etc.) used to annotate human genomes

      • Application of genomic data sharing systems (e.g., AnVIL)

   6. Translational Genomics

      • Obtaining and interpreting family histories for Mendelian and non-Mendelian traits

      • Classification of genetic variants in terms of likelihood of contribution to a specified phenotype (including use of ACMG/AMP criteria)

      • Application of diagnostic approaches, including cytogenomic microarrays, exome sequencing, and genome sequencing in clinical assessment

      • Application of genomic technologies to assess tumor genotype

      • Uses and limitations of SNP genotyping in assessment of risk of common disease

      • Significance and technical analysis of somatic mosaicism

      • Use of human phenotype ontology and major databases of clinical genetic disorders (e.g., OMIM)

      • Use of data sharing components of Matchmaker Exchange

3. Quantitative Sciences

   1. Basic statistical concepts and methods:

      • Nature of distributions and importance of features like means, medians, and variance

      • Nature and utility of probabilities

      • Central limit theorem

      • Correlation quantification, linear regression, ANOVA, and related approaches

      • Parametric and non-parametric statistical testing

      • Specific tests, methods, and distributions commonly used in genomics and genetics, like t- and Wilcoxon-tests, Z-scores and other normalized statistics, Poisson, normal, and negative binomial distributions,

      • Common methods in high-dimensional genomic data analysis, such as principal component analysis

      • Command-line manipulation and R to perform basic tasks like importing and exporting data, generating summary statistics and plots, and developing and applying functions

   2. The role of “prior” probabilities, “multiple hypothesis testing”, and related concepts in genomics:

      • The ubiquitous nature of error in data, how errors are quantified and modeled, and ways in which they exhibit both random and non-random behaviors

      • Basic concepts like false positive and false negative rates, and how these relate to, but are distinct from, false discovery rates

      • Relationships between sample sizes, effect sizes, statistical power, and study design/expectation

      • How models, expectations, and prior knowledge influence interpretation of any given quantitative or statistical result

      • Bayes Theorem and some of its applications

   3. Statistical approaches, concepts, and tools used in the analysis of human genetic disease:

      • Penetrance

      • Linkage analysis

      • “Brute-force” resolution of Mendelian disease

      • Association studies

      • Influence and importance of genetic models on experimental design and results interpretation, especially with regards to anticipating the numbers, frequencies, penetrance, and functional consequences of casual variants for any given disease

4. Clinical Applications

   1. Rare Disease

      • Approach to the clinical assessment of rare disorders

      • Use of data systems (e.g., Phenotips, OMIM, Gene Reviews, Face-to-Gene, )

      • Principles of genetic counseling

      • Application and interpretation of cytogenomic microarrays, single gene testing, genomic panel testing, exome and genome sequencing

      • Use of cytogenetic and genomic nomenclature

      • Distinctions of variant classification, g., pathogenic, likely pathogenic, VUS, etc.

      • Interpretation and counseling of secondary genomic findings

      • Interpretation of a genomic laboratory report

      • Communication with patients and referring physicians

      • Access to patient-friendly sources of information

      • Principles of privacy and protection of privileged information

   2. Common Disease

      • Genetic architecture of disease

      • Theories of multifactorial inheritance

      • Concept of genetic association

      • Applications of GWAS, PheWAS, TWAS,

      • Concept and application of polygenic risk scores

      • Principles of population genomic screening

   3. Cancer

      • Identification of risk factors for familial predisposition to malignancy and application of genomic panels

      • Common genomic rearrangements and variants associated with major types of cancer

      • Application of tumor genomic sequencing to identify potential drivers and therapeutic approaches

      • Identification of clinical trials based on genomic profiling of a patient’s tumor

Spring 2020

GBSC 718 - Epigenetics

Course Directors: Runa Liu, M.D., Ph.D., Associate Professor of Genetics, and Lizhong Wang, Ph.D., Associate Professor of Genetics

Course Description: This course introduces the fundamentals of epigenetic controls and how epigenetic regulation is being investigated and utilized in basic and translational research. Specifically, students learn of changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. Students also gain an understanding of the differences between genetic and epigenetic influences on gene expression; epigenetic mechanisms that regulate gene expression; how epigenetic modifications are propagated; and the phenotypic consequences of normal versus abnormal epigenetic regulation in disease.

GBS 720 - Genomic Structure and Function

Course Director: Michael Crowley, Ph.D., Associate Professor of Genetics

Course Description: This course will cover the general concepts of genomics including gene structure and function, genomic technologies and their applications, comparative genomics and cancer genomics.

GBS 724 - Principles of Human Genetics

Course Director: Fady Mikhail, M.D., Ph.D., Professor of Genetics

Course Description:  This course will cover the general concepts of human genetics, including population genetics, dominant, recessive, X-linked, multifactorial, and mitochondrial inheritance and disease, as well as cytogenetics, chromosomal abnormalities, molecular genetics, and triplet repeat disorders.

Click here for more information about these courses.

Trainees generally are supported for 12-month full-time training appointments for which they receive a stipend to help defray living expenses during the research training experience (per the NIH Grants Policy Statement – section 11.3.8.2). Stipend levels are determined by NIH (2023 levels are used for appointments starting on or after 10/1/2022).

The training grant makes a considerable contribution towards each trainee’s health insurance coverage costs

The training program will cover the cost of six credit/hours per year.

Travel expense to attend the one scientific symposium and the Annual training meeting organized by NHGRI will be covered with a maximum of $2000.00 per year.  

Limited funds are available to assist with training related expenses such as reference materials, software, or research supply costs.