Module 1: Lesson 4 – Molecular Diagnostics and Bioinformatics Techniques

Trainers

Name: Prof Faisal Mohamed Fadlelmola
Affiliation: Centre for Bioinformatics and Systems Biology (CBSB) at the Faculty of Science, University of Khartoum
Location: Sudan

Prof. Faisal Mohamed Fadlelmola, PhD, FBCS, FIBMS, CTDP, University of Khartoum, Sudan. Experienced Principal Investigator with a demonstrated history of working in the higher education industry. Skilled in Genomics, Bioinformatics, Computer Science, Information Technology, and Life Sciences. Strong research professional with a Postdoctoral Fellowship Training focused in Cancer Genomics and Bioinformatics from the Centre for Translational and Applied Genomics (CTAG), BC, Vancouver, Canada. Since August 2012, he works as the Principal Investigator for the H3ABioNet Sudan Node. H3ABioNet, the NIH funded Pan African Bioinformatics Network for Human Heredity and Health in Africa, is being developed to support H3Africa research projects through the development of bioinformatics capacity on the continent. Currently, he is the chair of the H3ABioNet Research Working Group (January 2015-Present) as well as active member of Education and Training Working Group and the H3ABioNet Management Committee (January 2013-Present) and some of the H3Africa Working Groups. In October 2014, he started working as the head and founder of the newly established Centre for Bioinformatics and Systems Biology (CBSB) at the Faculty of Science, University of Khartoum, Sudan. He has been involved in a variety of research projects on topics such as cancer genomics, bioinformatics, molecular epidemiology of cancer, translational and applied genomics, mobile health and mobile learning, among many others. For further information: Website: http://cbsb.uofk.edu/ LinkedIn ID: https://www.linkedin.com/in/faisal-mohamed-fadlelmola-phd-fbcs-fibms-ctdp-56433539/recent-activity/

Name: Prof Nicola Mulder
Affiliation: Computational Biology Group, University of Cape Town & H3ABioNet
Location: Cape Town, South Africa

Prof Mulder heads the Computational Biology Division at the University of Cape Town, and leads H3ABioNet, a large Pan African Bioinformatics Network of over 30 institutions in 14 African countries. H3ABioNet aims to develop bioinformatics capacity to enable genomic data analysis on the continent by developing and providing access to and skills and computing infrastructure for data analysis. Prior to her position at UCT, she worked for 9 years at the European Bioinformatics Institute (EBI) in Cambridge, as a Team Leader, responsible for development of one of the most heavily used bioinformatics resources at the Institute. At UCT her research focuses on genetic determinants of susceptibility to disease, African genome variation, and microbial genomics and infectious diseases from both the host and pathogen perspectives. Her group also provides bioinformatics services for the local researchers, through which they develop visualization and analysis tools for high-throughput biology. Her team led the design of the H3Africa genotyping array and has also been involved in the development of new and improved algorithms for the analysis of complex African genetic data as well as for downstream analysis and interpretation of GWAS data. Prof Mulder is actively involved in training and education as well as curriculum development in Bioinformatics and Genomic Medicine.

Summary
This module/session provides the participant with an understanding of the molecular diagnostics and bioinformatics techniques for research and diagnostic purposes. The emphasis is to provide the participants with both theoretical knowledge and practical skills in molecular diagnostics and how to use bioinformatics to find information on genes and variants and their relations to diseases. A variety of learning and teaching methods will be used and include lectures, problem based learning, case studies, Exercises, eLearning material and tasks, as well as private study.

Learning Outcomes
● Explain how advances in diagnostic platforms in genetics and genomics testing can be translated into new approaches for risk assessment and molecular diagnostics;
● Appreciate the limitations, pros and cons in current molecular diagnostic approaches;
● Identify validated genetic tests available within their own institutes;
● Demonstrate the ability to search databases such as OMIM and ClinVar to find genes or mutations of interest for a disease.

Class Videos

Module1_Lecture4_Video1_Fadlelmola

Module1_Lecture4_Video2_Fadlelmola

Module1_Lecture4_Video3_Fadlelmola

Module1_Lecture4_Video1_Mulder

Module1_Lecture4_Video2_Mulder

Module1_Lecture4_Video3_Mulder

Class Slides

Module1_Lecture4_Slides1_Fadlelmola

Module1_Lecture4_Slides2_Mulder

Assessments – Pre-Class Exercise
Question 1: Read the following article (Credit: Ugandan Radio Network). What other genetic conditions/diseases are likely to be misdiagnosed in your clinic or hospital? Support/Explain your suggestions.
Click here to read article

Question 2: Watch the following videos and answer the question below.
Genetic Tests: Types and Uses
Prenatal Genetic Testing Credit – Reporter: Wendy Suares Photographer/Editor: Colleen Wilson
Diagnosis of Down Syndrome Credit – Lalita Josh
Please investigate diagnostic platforms/services available within your institute or neighbouring institutes that you could potentially refer patients to for testing of genetic diseases. Highlight the current nurses’ role in this process. Indicate what you think the ideal nurses’ role could be if it is different from the current?

Question 3: Watch the following videos and answer the questions below.
SNPs Video (Credit Khan Academy & 23andMe)
Sickle Cell Anemia Video Credit – CR King: Essential Cell Biology, Second Edition by Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, Walter copyright 2004 by Garland Science Publishin
What new knowledge or information about Sickle Cell did you learn from the Genetics Home Reference website: Click here to access the site

Assessments – Class Exercise
Case Study # 1:
Paper: Grotta et al. Advantages of a next generation sequencing targeted approach for the molecular diagnosis of retinoblastoma. BMC Cancer (2015) 15:841 DOI 10.1186/s12885-015-1854-0.

Read the paper authored by Grotta et al. above. Then, answer the following questions:

1. The authors reported that “All 65 patients were previously tested with conventional cytogenetics and MLPA techniques”. Explain what is meant by the conventional techniques?
2. Describe in more details the MLPA technique?
3. What is the accession number, OMIM ID, and cystoband of the RB1 gene?
4. Why are mutations in both alleles of the RB1 gene required for the development of this neoplasm?
5. Explain how this paper is a perfect example of translational medicine (i.e. Bench to Bed approach)!
6. What is the function and role of “The MiSeq Reporter software”?
7. What does GATK stands for and what is its usage in NGS?

Quiz
To be released during the session

Class Evaluation
See course evaluations section.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Extra Reading
Tang W, et al. Quality assurance of RNA expression profiling in clinical laboratories. J Mol Diagn. 2012;14(1)1-11.
Human Genetics: Concepts and Applications, Lewis 2015 11th Edition. McGraw-Hill Education.
Delanty N, Goldstein DB. Diagnostic exome sequencing: a new paradigm in neurology. Neuron. 2013 Nov 20;80(4):841-3. doi: 10.1016/j.neuron.2013.09.011. Review. PMID: 24267646
Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet. 2013 Jul;14(7):460-70. doi: 10.1038/nrg3455. Review. PMID: 23752795
Brookes AJ, Robinson PN. Human genotype-phenotype databases: aims, challenges and opportunities. Nat Rev Genet. 2015 Dec;16(12):702-15. doi: 10.1038/nrg3932. Review. PMID: 26553330