News & Events

Centre of Excellence in Complex Disease Genetics Journal Club

CoECDG is hosting a Journal Club starting this autumn! Welcome!

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.

Ari Ahola-Olli (ari.ahola-olli@helsinki.fi) and Jake Lin (jlin212@gmail.com) 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. We will meet in Biomedicum 2, 3rd floor, FIMM lunch area.
Pizza will be served!

Autumn 2018 schedule:

September 7
October 12 - Note the changed date!
November 2
November 30

Spring 2019 schedule:

January 11
February 1
March 1
April 5
May 3

In the first meeting (September 7), Ari will present:
Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (Khera et al.)

In the second meeting (October 12), Jake will present:
Decoding the genomics of abdominal aortic aneurysm (Li et al.)

In the third meeting (November 2), Pyry Helkkula will present:
Type 2 diabetes genetic loci informed by multi-trait associations point to disease mechanisms and subtypes: A soft clustering analysis (Udler et al.)

In the fourth meeting (November 30), Meri Kaustio will present:
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome (Zhernakova et al.)

Please note! You are welcome to join the Journal Club at any point, but if you want pizza, you need to register at least 3 days before the session you are planning to join!

If you need to cancel, 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.

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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

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Hail Workshop

hail

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).

How to apply: Due to space constraints, we can only accept a limited number of participants to the workshop.
Please register at the following link by August 12: https://elomake.helsinki.fi/lomakkeet/90881/lomake.html
Please note! The workshop is now full! You can still register for the lecture.

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Genes behind Diabetes

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)

More information and registration: https://www.diabetes.fi/ammattilaiset/ammatilliset_yhdistykset/diabetestutkijat_ja_diabetologit/summer_meeting_17.-18.8.2018

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Upcoming Genomics Conferences:

2018 PQG Conference
BIOBANKS: Study Design and Data-analysis

November 1-2, 2018
Harvard Medical School Conference Center | Boston, MA 
#HarvardPQG18
Conference website

Keystone Symposia Genomics Meeting
One Million Genomes: From Discovery to Health

June 4-8, 2018
Herrenhausen Palace, Hannover, Germany
Discounted registration ends April 11!
Conference website

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Centre of Excellence in Complex Disease Genetics (CoECDG)

Centre of Excellence Academy of Finland logo

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
10:50 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)