Events, seminars and courses organized by the Centre of Excellence in Complex Disease Genetics.
Centre of Excellence in Complex Disease Genetics Journal Club (ongoing)
The aim of the Journal Club is to give the participants an opportunity to learn about recent and impactful articles of interest. The participants will also have an opportunity to present an article of their own choosing to the other participants and network with other researchers and PhD candidates. The Journal Club is open to all interested in the field of complex disease genetics.
In each session one of the participants will present a relevant, recent research article. The papers can be method-based, translational or relevant resources. The articles will be made available to all participants beforehand, so everyone can familiarize themselves with the article and the topic before the session. The presentation will be followed by discussion.
The meetings will take place on the first Friday of each month (this can vary somewhat), at 12:30-13:30, excluding the summer months. We will meet in Biomedicum 2, 3rd floor, FIMM lunch area.
Pizza will be served!
Autumn 2019 schedule:
In the first meeting of autumn 2019 (September 13), Nina Mars will present:
A global overview of pleiotropy and genetic architecture in complex traits (Watanabe et al. 2019)
For enquiries and more information, please contact firstname.lastname@example.org
ECTS: 5 attendances and one presentation = 1 ECTS. Max. 2 ECTS (=10 attendances and two presentations). Course code: DOCPOP-133.
Complex Disease Genetics Day
Time: Thursday, January 17, 2019
Place: Lecture hall 3, Biomedicum 1
Organizer: Centre of Excellence in Complex Disease Genetics
Doctoral candidates: Certificate of participation can be provided
Chair: Elisabeth Widén
Welcoming words: Samuli Ripatti, CoECDG director
|9:10||Søren Brunak (University of Copenhagen)
Disease progression in a life-long perspective
Juha Karjalainen (Broad Institute of MIT and Harvard): IBD in FinnGen
Heidi Hautakangas (FIMM, University of Helsinki): Meta-analysis of migraine with over 102,000 cases
Nina Mars (FIMM, University of Helsinki): High polygenic risk provokes an early disease onset in common cardiometabolic diseases and cancers
Sini Kerminen (FIMM, University of Helsinki): Geographic variation and bias in polygenic scores of complex diseases and traits in Finland
|11:30||Andrea Ganna (Broad Institute of MIT and Harvard/ FIMM): Scalable stratified LDscore regression to probe biology|
Chair: Matti Pirinen
|13:00||Om Prakash Dviwedi (FIMM, University of Helsinki): How does loss of ZNT8 protect from Type 2 diabetes|
|13:20||Vidya Velagapudi (FIMM, University of Helsinki): Plasma metabolites reveal distinct profiles associating with different metabolic risk factors in monozygotic twin pairs|
|13:40||Zoltan Kutalik (University of Lausanne)
From genome-wide association studies to causal inference and back
|14:15||End of seminar|
Building Bridges 2018: Large scale Sequencing Initiatives and Precision Medicine in Clinical and Translational Research
September 10-11, 2018
Lecture hall 2, Biomedicum 1, Helsinki, Finland
For more information, please see: https://www.helsinki.fi/en/conferences/building-bridges-2018
On August 14th 2018 the CoECDG at the University of Helsinki will be hosting a coding workshop on
Hail — an open-source, scalable framework for exploring and analyzing very large genomic data.
With the introduction and evolution of next-generation sequencing platforms, it is now feasible to analyze exomes and genomes of thousands and soon millions of people. This remarkable development is accompanied by great computational challenges to analyze the huge data sets. Alongside the new challenges there are also new opportunities. A team from the Neale lab at the Broad Institute of Harvard and M.I.T., US has developed the Hail Project. The aim of the Hail project is to harness the flood of sequenced genomes in order to unravel the genetic architecture of disease. Their open-source framework is already being used to analyze the largest genetic data sets available, to power dozens of major academic studies, and to meet the exploding needs of hospitals, diagnostic labs, and industry.
What is the course about?
In this course, participants will gain an overview of the functionality of Hail and hands-on experience using Hail. Hail is a library for data analysis in Python and runs on Apache Spark. Because it can scale from one computer to thousands, Hail has had enormous impact in the analysis of the largest sequencing and genotyping datasets, but Hail is useful for analyzing data of any scale.
Who is the course instructor?
Cotton Seed is a Senior Principal Software Engineer and Institute Scientist at the Broad Institute of Harvard and M.I.T., the co-founder and technical lead of the Hail project, and an institute member in the Neale lab.
Course details: The course will be held August 14th and will take place in Biomedicum. It will start with a seminar giving an overview on “Hail — an open-source, scalable framework for exploring and analyzing very large genomic data” open to everyone, in Lecture hall 3. Right after the seminar the workshop will begin in Meeting room 3, however, this will be open to registered participants only.
More information about Hail: More background including tutorials can be found on the official Hail.is homepage.
Talk (12:00-12:45), Lecture hall 3, open to everyone:"Hail — an open-source, scalable framework for exploring and analyzing very large genomic data"
Workshop (13:00-), Meeting room 3, open only for registered participants (the workshop will take around 2hrs and there is time for questions and troubleshooting afterwards if needed)
Please note! The workshop is now full! You can still register for the lecture.
Target audience: Doctoral candidates, postdoctoral scholars, clinical scientists, and principal investigators currently working with genomic data, or about to embark on projects that require analysis of such data.
Prerequisites: Basic familiarity with UNIX/Linux environments is required. Participants should be comfortable with Python (more than basic familiarity). Important: For individuals with no training/preparation in Python nor strong coding skills in a related language this hands-on workshop will not be useful. However, interested individuals can still join the seminar before the course.
Please note that you will need a laptop at the workshop. We strongly encourage you to bring your own laptop, but there are also university laptops available in Meeting room 3, if needed. If you have a Mac/Linux laptop, feel free to install Hail to there before the workshop! Instructions can be found here: https://hail.is/docs/devel/getting_started.html
Unfortunately, Hail does not work in Windows.
Costs: Attendance at the course is free.
Doctoral candidates: Certificates for the course will be provided (available only for those who will attend both the lecture and the workshop).
Finnish Diabetes Research Society’s Summer Meeting
August 17 – 18th, 2018, Hanasaari Culture Center, Espoo, Finland
Organized by Finnish Diabetes Research Society & Centre of Excellence in Complex Disease Genetics (FIMM, University of Helsinki)
Centre of Excellence in Complex Disease Genetics (CoECDG)
Thursday February 8th 2018, at 9:00-16:00, Lecture Hall 2, Biomedicum 1
Registration is closed. Thank you all for a great Kick-Off!
Session I: Genetic discovery
|9:00||Samuli Ripatti: The CoECDG vision for complex disease genetics|
|9:20||Jukka Koskela: Running phenomewide GWAS using Hail in Google Cloud|
|9:35||Om Dwivedi: Genetic architecture of type 2 diabetic families|
|9:50||Rubina Tabassum: Genetics of human plasma lipidome|
Mark Daly: Genetic studies on large-scale biobanks
Session II: Statistical and computational methods
|11:00||Christian Benner: Fine-mapping of trait-associated genomic regions|
|11:15||Hande Topa: Searching for genetic variants matching a given multivariate target profile|
|11:30||Priit Palta: Accurate and high-throughput genotype imputation with population-specific reference panels|
Session III: Translation
|13:00||Martti Färkkilä: Genetics and environmental factors of disease outcomes in two IBD cohorts|
|13:30||Jarno Kettunen: Rare RFX6 variants and diabetes|
|13:45||Antti Latvala: Complex traits: Genomics and causality|
|14:00||Pietari Ripatti: Polygenic hyperlipidemias and coronary artery disease risk|
|14:15||Emma Ahlqvist: Novel subgroups of adult-onset diabetes sharpen genetic associations and improve prediction of outcome|
|14:45||Andrea Ganna: Insights from the largest genetic study of sexual orientation|
|15:00||Tiinamaija Tuomi: Closing words|
|15:15-16:00||Wine & Cheese|
For doctoral candidates:
University of Helsinki Course Code: DOCPOP-127, Complex Disease Genetics - From Discovery to Precision Medicine seminar
ECTS Credits: 1-2 ECTS (1 ECTS for participation, 2 ECTS for participation + talk)