Archana Bhardwaj

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2020 – Bioinformatics Applications – Systems Medicine

Special topics course within “Bioinformatics”: Systems Medicine

Location: ULg / COVID-10 online

Course schedule changes: CELCAT calendar – second semester

Lecturer: Prof Dr Dr Kristel VAN STEEN 


Course themes

I: Genome-wide association studies

  • Components of GWAS
  • Case studies via assignments
  • Assignment I: GWAS

-          different disease traits -- infectious disease, cardiovascular …, intermediate phenotype;

-          different genetic info -- rare variants;

-          different software tools;

-          different study designs incl. families, meta-analysis, replication, …

II: Systems medicine

  • Interactions
  • Patient-to-patient heterogeneity
  • Case study on pancreatic cancer
  • Assignment II: Systems medicine / Precision medicine

-          Translational aspects of GWAS;

-          Individual heterogeneity;

-          Subnetwork discovery;

-          Omics integration tools;

-          Disease subtyping (omics, missingness, …)


Classes


Dates

Themes

GoToMeeting ID

Course materials

 March 4 (2-6pm)

 I: GWAS

 Face to face

 April 1  (2-6pm)

 II: Systems Medicine

 185-433-821

 Assignment:

  • Go to https://www.disgenet.org/ and the SEARCH button
  • Go to “General links” and “Summary of All Variant-Disease Associations”
  • Click on ADD/REMOVE FILTER
  • Type in the DISEASE of your choice (make sure you use the convention suggested by the data bases)
  • Select in addition SOURCE GWASCAT if you wish to have GWAS studies from the GWAS catalogue; alternatively select SOURCE GWASDB
  • Take most recent studies “Last Ref” and/or those with a good number of evidences via “N PMIDs”
  • GO!

 

Examples:

 

 

 

To prepare

Evaluated*

 April 22  (2-6pm)

I: presentations with  discussions

 

 ID: 175-601-917

 

 1. Slides (max 50) addressing

 2. Selection of slides addressing 3 Q in depth to present in 15 min

 Oral slides presentation   with  Q&A

 April 27  (2-6pm)

II: presentations with discussions

 

ID: 290-828-045

 

1. Slides (max 50) addressing

 2. Selection of slides addressing 3 Q in depth to present in 15 min

 Oral slides presentation with  Q&A

 

 Compilation of 1. before

 Written exam: Compilation  of slides into a  comprehensible “story” (details to be discussed: slides or doc)

 

*Evaluation

Dates

Themes

To prepare

Evaluated*

Proposed scoring

 April 22  

  (2-6pm)                

I: presentations with educative discussions

1. Slides (max 50)  addressing the Qs

2. Selection of slides addressing 3 Q in depth to present in max 15 min

Oral slides presentation

with Q&A

 

 

 

30

  April 27 

  (2-6pm)

II: presentations with educative discussions

 1. Slides (max 50) addressing the Qs

 2. Selection of slides addressing 3 Q in depth to present in max 20min + results of group work: overlap between two topics

Oral slides presentation

with Q&A

20

 

 

10

 

Compilation of 1. before

Written exam: Compilation of slides into a comprehensible “story” (max 50 slides)

40 (based on accurateness and critical evaluation with links to literature and classes)


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