The Journal Club aims to provide an opportunity to keep up with recent and impactful articles in the field of complex disease human genetics and to connect with colleagues.
In each session, one participant will present a research article that could be anything from a translational study to a methods paper. Other participants will familiarize themselves with the article beforehand, and a discussion will follow the presentation.
Felix Vaura (felix.vaura@helsinki.fi) coordinates the Journal Club. If you are interested in presenting, please get in touch with him!
The Journal Club is hosted monthly on Thursdays from 12:30-13:30 in the 3rd-floor coffee area at FIMM. The Journal Club is primarily on-site only.
ECTS: 5 attendances and one presentation = 1 ECTS. Max. 2 ECTS (=10 attendances and two presentations). Course code: DOCPOP-133. For enquiries and more information, please contact felix.vaura@helsinki.fi
Speakers - Spring 2024
January 25th (Thursday): Joonas Kartau: "Improving fine-mapping by modeling infinitesimal effects"
February 22nd (Thursday): Linda Ottensmann: "PheWAS-based clustering of mendelian randomisation instruments reveals distinct mechanism-specific causal effects between obesity and educational attainment"
March 21st (Thursday): Sebastian May-Wilson: "Accurate proteome-wide missense variant effectprediction with AlphaMissense"
April 25th (Thursday): Sannimari Suhonen: "Associations of a breast cancer polygenic risk score with tumor characteristics and survival"
May 23rd (Thursday): Zhiyang Wang: "Childhood exposure to non-persistent endocrine disrupting chemicals and multi-omic profiles: a panel study"
DATE: Friday, January 20, 2023
LOCATION: Ossian Lecture Hall, Folkhälsan, Topeliuksenkatu 20 00250 Helsinki
ORGANIZERS: Centre of Excellence in Complex Disease Genetics, Stephanie Zellers, Bradley Jermy, Julius Anckar
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 CoECDG coordinator (julius.anckar@helsinki.fi).
07:45-08:00 Coffee and sandwich
| 08:00-08:10 | Opening words | Samuli Ripatti |
| 08:10-09:00 | Keynote: From identification of mutations to targeted therapies for vascular malformations | Miikka Vikkula |
| 09:00-09:20 | Cohort effects on regular use of tobacco and quantity of tobacco used: Longitudinal twin modeling in the Older Finnish Twin Cohort | Stephanie Zellers |
| 09:20-09:40 | Polygenic risk of BMI and BMI trajectories in twin pairs from Finland: A 26-year follow-up | Bram Berntzen |
| 09:40-10:00 | Systematic evaluation of the environmental effect on depressive symptoms in late adolescence and early adulthood: exposome-wide association study and twin modeling | Zhiyang Wang |
10:00-10:30 Coffee Break
| 10:30 -10:50 | Understanding chronic fatigue and dysautonimia | Hanna Ollila |
| 10:50-11:10 | Medication genetics | Tuomo Kiiskinen |
| 11:10-11:30 | Health, socioeconomic and genetic predictors of COVID-19 vaccination uptake: a nationwide machine-learning study | Tuomo Hartonen |
| 11:30-11:50 | Tackling Long COVID with the global Host Genetics Initiative collaboration | Vilma Lammi |
12:00-13:00 Lunch
| 13:00-13:20 | Phenome-wide perspective into the role of Finnish Y chromosome variation in complex diseases | Anniina Preussner |
| 13:20-13:40 | Genetic contribution to disease-course development in psychotic disorders | Anders Kämpe |
| 13:40-14:00 | The effect of incomplete X chromosome inactivation on complex trait genetics | Yu Fu |
14:00-14:10 Break
| 14:10-14:30 | The synthetic Genome | Zhiyu Yang |
| 14:30-14:50 | Finemapping with missing data | Joonas Kartau |
| 14:50-15:00 | Closing remarks | Tiinamaija Tuomi |
End of programme
DATE: Thursday, January 20, 2022
LOCATION: Online (Zoom link will be sent to all registered participants)
REGISTRATION: via e-form
Registration deadline January 17, 2022!
ORGANIZERS: Centre of Excellence in Complex Disease Genetics, Claudia Schwarz, Rodos Rodosthenous, Julius Anckar
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 Claudia Schwarz (claudia.schwarz@helsinki.fi).
Chair: Samuli Ripatti
| 10:00-10:10 | Opening words | Samuli Ripatti |
| 10:10-10:50 | Keynote 1: Midlife factors in the aetiology of Alzheimer’s disease and other dementias | Mika Kivimäki |
| 10:50-11:05 | Lipidome- and genome-wide study to understand sexual dimorphism in lipid metabolism | Rubina Tabassum |
| 11:05-11:20 | Multi-omics integration and predictive modeling of blood pressure variability in twin cohort | Gabin Drouard |
| 11:20-11:40 | Catalogue of Finnish FH-causing variants | Elisabeth Widén |
| 11:40-12:00 | Quantifying the impact of genetic variation on disease burden across 80 diseases | Sakari Jukarainen |
12:00-13:00 Lunch break
Chair: TBC
| 13:00-13:20 | Covid risk alleles | Matti Pirinen |
| 13:20-13:40 | Assessing the utility and generalizability of polygenic risk scores – progress and opportunities in the INTERVENE consortium | Bradley Jermy |
| 13:40-14:00 | From one to 27 otosclerosis GWAS loci: Insights into a rare disease | Joel Rämö |
| 14:00-14:20 | Shared and distinct heritability of infectious and inflammatory upper respiratory diseases in FinnGen | Elmo Saarentaus |
| 14:20-14:40 | Finnish Pediatric Diabetes Registry | Jarno Kettunen |
14:40-15:00 Break
Chair: Tiinamaija Tuomi
| 15:00-15:40 | Keynote 2: TBC | Ramnik Xavier |
| 15:40-16:10 | Distinct contributions of genetic risk factors and metabolic dysfunction in the pathogenesis of non-alcoholic fatty liver disease | Panu Luukkonen |
| 16:10-16:30 | Exome sequencing reveals mechanistic insights into the etiology of schizophrenia | Tarjinder Singh |
| 16:30-16:50 | TBC | Amanda Elliott |
| 16:50-17:00 | Closing remarks | Tiinamaija Tuomi |
Date and time: Wednesday, 1 December 2021, at 9:00-16:00 CET/10.00-17.00 EET
The Building Bridges symposia series is arranged to bridge basic, translational and clinical research and provide examples of how teams of investigators are working together to advance molecular medicine. With the 10th Building Bridges symposium we shine the spotlight on technologies used to improve our understanding of health and disease. In particular, we will demonstrate research advances using infrastructure available in the Nordic region, bridging research and technology development as well as bridging researchers across borders. With an opening and closing keynote from EMBL Heidelberg and EMBL Hamburg, we highlight research infrastructure at EMBL, as well.
Join the symposium and learn more about the research technology and core facility services available within the Nordic EMBL Partnership!
Organizers: The Nordic EMBL Partnership for Molecular Medicine, a Nordforsk-funded Research Infrastructure Hub in collaboration with the CoECDG. The Nordic EMBL Partnership consists of four international research and technology centers:
More information and registration HERE!
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).
| 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 |
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
| 11:20 |
Speed talks Mattia Cordioli (FIMM, University of Helsinki): Genetic and environmental determinants of drug adherence and drug purchasing behaviour |
12:00 Lunch break
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)
DOCPOP-138, 1 ECTS
For more information, please see the seminar page.
American Society of Human Genetics (ASHG) Annual Meeting 2020
San Diego, USA
October 27-31, 2020
https://www.ashg.org/meetings/2020meeting/
Building Bridges 2019: Aging
Date: November 28, 2019
Location: Lecture hall 3, Biomedicum 1, Helsinki
https://www.helsinki.fi/en/conferences/building-bridges-2019
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.
#rethinkingoldage
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
Program
Session I
Chair: Elisabeth Widén
| 8:30 | Morning coffee |
| 9:00 |
Welcoming words: Samuli Ripatti, CoECDG director |
| 9:10 | Søren Brunak (University of Copenhagen) Disease progression in a life-long perspective |
| 9:45 |
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 |
| 10:50 |
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 — 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.
Agenda
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!
Program
| 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)