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.

Vasudha Ahuja (vasudha.ahuja@helsinki.fi) and Mart Kals (mart.kals@helsinki.fi) coordinate the Club. If you are interested in presenting, please contact them!

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.

Please note! The Journal Club sessions are currently organized ONLINE! Please register to receive more information by email.

In the third meeting of spring 2021 (May 7), Sini Kerminen (group Pirinen) will present: “Incorporating family history of disease improves polygenic risk scores in diverse populations” Hujoel et al. https://www.biorxiv.org/content/10.1101/2021.04.15.439975v1.full.pdf

In the second meeting of spring 2021 (February 12), Mari Niemi (group Ganna) will present: “Protein-coding repeat polymorphisms strongly shape diverse human phenotypes” Mukamel et al.  https://www.biorxiv.org/content/10.1101/2021.01.19.427332v1

In the first meeting of spring 2021 (January 22), Weilong Li will present: “LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method” Han et al. https://www.nature.com/articles/srep46566

Spring 2021 schedule:
January 22
February 12
March 5 - Cancelled!
April 9 - Cancelled!
May 7

For enquiries and more information, please contact ulla.tuomainen@helsinki.fi

ECTS: 5 attendances and one presentation = 1 ECTS. Max. 2 ECTS (=10 attendances and two presentations). Course code: DOCPOP-133.

Registration: https://elomake.helsinki.fi/lomakkeet/106423/lomake.html

CoE SA logo

DATE: Tuesday, January 19, 2021
LOCATION: Online (Zoom link will be sent to all registered participants)
REGISTRATION: via e-form
Registration deadline January 15, 2021!

Doctoral candidates: Please note! This is not an official course, and thus, no credits can be given. However, if a certificate of attendance is needed, please contact the coordinator (ulla.tuomainen@helsinki.fi).

Tuesday, January 19, 2021

9:00 Welcome words: Samuli Ripatti, CoECDG director
Centre of Excellence in Complex Disease Genetics (CoECDG)
9:10 Yukinori Okada (Osaka University)
Statistical genetics, disease biology, and drug discovery

Functional Genetics

Chairs: Alyce Whipp & Rubina Tabassum

9:50 Riikka Lund (University of Turku)
Epigenetic mechanisms as mediators and markers of complex diseases
10:10 Olli Pietiläinen (University of Helsinki)
Modeling biological processes underlying schizophrenia in human neurons
10:30 Helena Kilpinen (FIMM, University of Helsinki)
Taming biological variability in iPSC-based disease models

10:50 Break

Chairs: Sini Kerminen & Alyce Whipp


Speed talks

Mattia Cordioli (FIMM, University of Helsinki): Genetic and environmental determinants of drug adherence and drug purchasing behaviour
Heidi Hautakangas (FIMM, University of Helsinki): Stratifying migraine risk loci by subtypes
Viola Helaakoski (FIMM, University of Helsinki): Sleep disruption as a risk factor for increased alcohol consumption
Tuomo Kiiskinen (FIMM, University of Helsinki): Genetic predictors for trajectories of medication use in dyslipidemia, hypertension and type 2 diabetes
Maheswary Muniandy (University of Helsinki): Sustained weight loss and the adipose tissue mitochondria
Linda Ottensmann (FIMM, University of Helsinki): Multivariate genetic analysis of lipidome
Prima Sanjaya (FIMM, University of Helsinki): Interpretable feature extraction with deep learning to understand somatic mutagenesis in cancers

12:00 Lunch break

Personalized Medicine

Chairs: Rubina Tabassum & Alyce Whipp

12:50 Emma Ahlqvist (Lund University)
Subclassifying diabetes by clinical phenotyping and GWAS
13:10 Nina Mars (FIMM, University of Helsinki)
Why measure the genome for risk, when we can simply ask about family history of diseases?
13:30 Elisabeth Widén (FIMM, University of Helsinki)
Genome-based disease prediction & prevention – A practical approach

13:50 Break

Chairs: Sini Kerminen & Rubina Tabassum

14:00 Andrea Ganna (FIMM, University of Helsinki)
COVID-19 host genetics update
14:20 Martti Färkkilä (HUS & University of Helsinki)
Survival and new prognostic markers for PSC
14:40 Elina Sillanpää (FIMM & University of Jyväskylä)
Genetic and epigenetic scoring in physical activity
15:00 Henrike Heyne (FIMM, University of Helsinki)
Recessive effects of coding variants in 176,899 Finns

15:20 Break

15:35 Mark Daly (FIMM, University of Helsinki)
Progress in the genetics of IBD
15:55 Benjamin Neale (The Broad Institute of MIT and Harvard)
Progress in the genetics of mental illness

16:35 End of seminar

DATE: Wednesday, November 18, 2020
LOCATION: ONLINE (Zoom link coming)

REGISTRATION & PROGRAM: please follow this LINK.

The Building Bridges symposia series is arranged to bridge clinical and basic/translational research and provide examples of how teams of investigators are working together towards a better understanding of the pathophysiology of disease and improved options for patient treatment and care. 

PARTICIPANTS: The 9th Building Bridges symposium will highlight current progress in research on sex differences in human health and disease. As such, the events are open to the entire scientific community as well as clinicians.  

ORGANIZERS: Institute for Molecular Medicine Finland (FIMM), University of Helsinki Doctoral Programme in Population Health (DocPop), Centre of Excellence in Complex Disease Genetics (CoECDG)

Modern GWAS meets Classic HLA and latest advances in complex disease genetics

Time: Wednesday - Thursday, January 22-23, 2020
Place: Lecture hall 2 & 3, Biomedicum 1
Organizer: Centre of Excellence in Complex Disease Genetics (CoECDG)

For more information, please see the seminar page.

Building Bridges 2019: Aging

Date: November 28, 2019
Location: Lecture hall 3, Biomedicum 1, Helsinki


The Building Bridges symposia series is arranged to bridge clinical and basic/translational research and provide examples of how teams of investigators are working together towards a better understanding of the pathophysiology of disease and improved options for patient treatment and care.

The 8th Building Bridges will the highlight the current progress of age-related research focusing on physical activity, cognitive aging and the aging society.


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


Session I
Chair: Elisabeth Widén

8:30 Morning coffee

Welcoming words: Samuli Ripatti, CoECDG director
Centre of Excellence in Complex Disease Genetics (CoECDG)

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

10:25 Coffee break

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
12:00 Lunch break

Session II
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 logo

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)


Kick-Off Symposium

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!



8:30 Morning coffee

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
10:05 Keynote talk
Mark Daly: Genetic studies on large-scale biobanks
10:35 Break

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
11:45 Lunch break

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)