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Translational Bigenomics - from the bedside to the bench and back again

Organizer: Maria Manuela M Grazina

The course schedule and programme can be found here


Background and Goals:

This course is directed to students aiming to understand the molecular basis of translational bigenomic analysis and to put into practice nucleic acids research in advanced biomedical key areas. We will teach the basic concepts and principles of the techniques used in translational genetics of both human genomes, nuclear and mitochondrial, and will focus on ‘hands on’ training in the practical steps required to design, establish, run and validate assays to obtain nucleic acids samples, perform amplification by PCR and carry out post-PCR analysis, both to analyse DNA sequences and measure expression of specific genes. Analysis by quantitative real time PCR (q-RT-PCR) will also be accomplished. Modern and advanced techniques such as arrays of combined genome applications will be also presented. The bioinformatics and biostatistics tools will be presented and discussed for each type of application.

The bigenomic interaction will be stressed out and the role of the genetic diversity will be discussed under the scope of aging, geographic distribution and pathology. Additionally, one of the main goals is to translate the bedside pathologies to the bench experiments and back again to the application into clinical practice.

A special emphasis will be given to ethical and legal issues concerning management of genetic information.

A “meet the expert” session is included to provide the students to interact with top international scientists specialized in different areas of knowledge and research related to Translational Human Genetics.

Paper club and brainstorm discussions are organized for achieving the most relevant and up-to-date findings in current literature and international guidelines.

Students are asked to propose a guideline for the application of genetic testing, particularly predictive, in the clinical practice management of dual genome diseases, in an open discussion special sessionFaculty:

Manuela Grazina (PhD - FMUC)

Henriqueta Silva (MD, PhD - FMUC)

Jorge Saraiva (MD, PhD - FMUC, CHC)

Emília Telo (PhD, ACT)

Luísa Pereira (PhD - IPATIMUP)

Catarina R. Oliveira (MD, PhD - FMUC)

Natércia Conceição (PhD – UALG)

Leonor Cancela (PhD - UALG)

Paulo Santos (CNC/UC)

Lina Carvalho (MD, PhD - FMUC, HUC)

Eduardo Silva (MD, PhD - HUC, IBILI)

Alda Sousa (PhD - ICBAS, IBMC)

Carolina Lemos (PhD - ICBAS, IBMC)

Guiomar Oliveira (MD, PhD - FMUC, CHC

Isabel Santana (MD, PhD - FMUC, HUC)

Lina Ramos (MD - CHC)

Teresa Almeida Santos (MD, PhD - FMUC, HUC)

Luísa Diogo (MD, PhD - FMUC, CHC)

Maria do Carmo Macário (MD - HUC)

Lee-Jun Wong (PhD - Baylor College of Medicine, Houston – Texas, USA)


Evaluation dates: see programme and calendar.

Form of evaluation: Final Mark= A + B + C

A- Task 1- Presentation of scientific papers – groups of 2-3 students: max 6 val

a. The coordinator distributes papers to be prepared in groups and presented – max 15 min each. The presentation should follow the scheme (maximum 15 slides):

i. Introduction

ii. Objectives

iii. Methods

iv. Results

v. Conclusions

vi. Critical analysis

The speakers ask questions to the students for discussion.

B- Task 2- Autonomic search and present major guideline based on peer-

reviewed papers – one from each student: max 8 val

a. According to the subject in the programme (Ethics and genetic testing, particularly predictive, in Diseases involving two genomes), the students should prepare a ppt slide with one guideline that should be followed. The reference(s), in which the guideline was(were) based on, has(have) to be also included. The slide and pdf of paper(s) have to be sent to the coordinator by email until the end of day 6 (10:00 a.m.) during the course, with the identification of the student (name of the file “name_task2 TBiGen2013”).

b. The guidelines will be presented at the OPEN DISCUSSION Session, day 7 (~17:30 p.m.).

C- Task 3- Delineate 2 questions based on given papers and discuss with the

expert – groups of 2-3 students: max 6 val

a. According to the paper (published by the expert team) sent to the group, the students are asked to prepare a ppt slide with 2 questions. The reference, in which the questions were based on, has to be also included. The slide has to be sent to the coordinator by email until the end of day 9 (10:00 a.m.) during the course, with the identification of the students and group number (name of the file “groupN_task3 TBiGen2013”).

b. The questions will be presented at the MEET THE EXPERT Session, day 10 (~16:30 p.m.).


References:

Brodsky MC. Highlights of the 32nd Annual Meeting of the European Pediatric Ophthalmological Society. Journal of American Association for Pediatric Ophthalmology and Strabismus 2007; 11: 1-2.

Chinault AC, Shaw CA, Brundage EK, Tang LY, Wong LJ. Application of dual-genome oligonucleotide array-based comparative genomic hybridization to the molecular diagnosis of mitochondrial DNA deletion and depletion syndromes. Genet Med. 2009;11(7):518-26.

Graça B, Lunet C, Coelho AS, Monteiro G, Freire P, Speidel A, Carvalho L. Angiogenesis and cancer: from biopathology to therapy. Acta Med Port. 2004;17(1):76-93.

Grazina M, Pratas J, Silva F, Oliveira S, Santana I, Oliveira C. Genetic basis of Alzheimer's dementia: role of mtDNA mutations. Genes Brain Behav. 2006;5 Suppl 2:92-107. Review.

Grazina MM, Diogo LM, Garcia PC, Silva ED, Garcia TD, Robalo CB, Oliveira CR. Atypical presentation of Leber's hereditary optic neuropathy associated to mtDNA 11778G>A point mutation--A case report. Eur J Paediatr Neurol. 2007;11(2):115-8.

Howard KL, Filley CM. Advances in genetic testing for Alzheimer's disease. Rev Neurol Dis. 2009;6(1):26-32.

Lafferty-Whyte K, Cairney CJ, Jamieson NB, Oien KA, Keith WN. Pathway analysis of senescence-associated miRNA targets reveals common processes to different senescence induction mechanisms. Biochim Biophys Acta. 2009;1792(4):341-52.

Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. The diversity present in 5140 human mitochondrial genomes. American journal of human genetics 84: 628-40, 2009.

Zhang W, Cui H, Wong LJ.Application of Next Generation Sequencing to Molecular Diagnosis of Inherited Diseases. Top Curr Chem. 2012 May 11.

Bai RK, Chang J, Yeh KT, Lou MA, Lu JF, Tan DJ, Liu H, Wong LJ. Mitochondrial DNA content varies with pathological characteristics of breast cancer. J Oncol. 2011;496189.

Wong LJ. Molecular genetics of mitochondrial disorders. Dev Disabil Res Rev. 2010;16(2):154-62.