On-site course – 2nd Edition
Introduction to GWAS (Genome-Wide Association Studies)
July 6th-10th, 2020, Crete (Greece)
Genetics and Genomics
Manipulation of NGS Data for Genomic and Population Genetics Analyses
October 2nd-11th, 2023 (ONLINE)
REGISTRATION IS CLOSED
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Course Overview
Genome-wide association studies have become increasingly popular to identify associations between genetic risk factors and phenotypic traits.
This introductory course is addressed to medical students, social scientists and biologists without formal training in the field. The aim of the course is to provide a guideline for conducting genetic analyses. In addition to the illustration of the standard GWAS process, we will also show how to perform functional enrichment and apply polygenic risk score (PRS) analysis in order to provide individual‐level scores of genetic risk.
A mix of theoretical background and hands‐on experience will walk students through a series of increasingly complex data manipulation and visualization tasks. These exercises will be based on PLINK, PRSice, and R, among others, which are commonly used, freely available software tools that are accessible for novice users.
Requirements
Graduate or postgraduate degree in any Biosciences discipline. All participants must bring their own personal laptop (Windows, Macintosh, Linux). Basic knowledge of programming (basic level) is required, you do not need any previous experience with genomics analyses.
All participants must bring their own personal laptop (Windows, Macintosh, Linux).
Contact
LOCATION
Gerakári, Municipality of Amari, 74 061
Rethymno
Crete, Greece
DATE
July 6th-10th, 2020
LANGUAGE
English
COURSE LENGTH & ECTS
35 hours on-site.
This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.
The recognition of ECTS by other institutions depends on each university or school.
PLACES
Places are limited to 20 participants and will be occupied by strict registration order.
Participants who have completed the course will receive a certificate at the end of it.
Program
Daily Program
Monday
- Morning:
- Introduction to Unix and R (theoretical)
- The process of GWAS (Introduction, Study designs, genomic controls, LD, sample size, power)
- GWAS Catalog
- Afternoon:
- Getting the data and starting (SNP array genotyping)
Tuesday
- Morning:
- Quality Control (QC) for GWAS
- Variant identification
- Population stratification
- HWE
- MAF
- Afternoon:
- Imputation (Michigan Imputation Server)
Wednesday
- Morning:
- Basic association analyses
- Statistical tests (PLINK, multiple testing, binary or continuous phenotype, covariates, etc)
- Discovery and replication studies
- Gene-based analysis. Bioinformatic follow-up of results to explore functional mechanism (Pascal, Magnum, FUMA GWAS)
- Afternoon:
- Practical
Thursday
- Morning:
- Annotation of Genomic Variants (LocusZoom, CADD)
- Use of summary statistics
- Afternoon:
- Genetic risk scores (LDSC, Heritability explained, PRS)
Friday
- Morning:
- Wrap-up
- Hands-on training. Perform an association test from scratch
Fees
- Course Fee
- Early bird (until April 30th, 2020):
- 530 € *
(424 € for Ambassador Institutions)
- Regular (after April 30th, 2020):
- 640 € *
(512 € for Ambassador Institutions)
- This includes course material, coffee breaks and lunches (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
- Course Fee + Accommodation Package
- Early bird (until April 30th, 2020):
- 880 € *
(774 € for Ambassador Institutions)
- Regular (after April 30th, 2020):
- 990 € *
(862 € for Ambassador Institutions)
- This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
* Participants from companies/industry will have an extra charge of 100 €.
You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com
Schedule
Course Schedule
Participants will make their own way
- Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 18:00 Lessons.
The class schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.
Course + Accommodation Package Schedule
- Sunday:
- 18:30 Meeting at Heraklion Archaeological Museum to take the bus to Gerakári. If you are planning to arrive later, you can find more information on how to get there.
- 20:00 Registration in the Hostel.
- 20:30 Dinner.
More information
- Monday to Thursday:
- 08:00 to 09:00 Breakfast
- 9:30 to 13:30 Lessons
- 13:30 to 15:00 Lunch (included)
- 15:00 to 18:00 Lessons
- 20:00 Dinner
- Friday:
- 8:00 to 9:00 Breakfast.
- 9:30 to 13:30 Lessons
- 13:30 to 14:30 Lunch (included)
- 15:00 to 17:30 Lessons
- 18:30 Meeting at Alexander Hotel to take the bus to Heraklion.
- 20:15 Arrival at Heraklion Archaeological Museum.
The class schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.
Accommodation
If you choose the Accommodation Package you will be hosted at Alexander Hotel in Gerakári village, in shared en-suite rooms, although you will only share rooms with other course participants (male or female only).
If you prefer to stay in a single en-suite room, you can do so with a supplementary charge.
More information
The Accommodation Package includes transportation from the centre of Heraklion to the venue and back, at the start and end of the course, respectively. The trip takes around 1 hour 50 minutes each way. If you require transportation from or to Chania (the other city of Crete with an airport), please contact the course coordinator who can arrange it at an additional cost.
If you do not wish to take the Accommodation Package, you can find a few other options in the surrounding area. However, please be aware that access to and travelling around the area requires a private vehicle as public transport is scarce. Therefore, course participants will find choosing the Accommodation Package more convenient.
Funding
Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).
5 % Discount
Former participants will have a 5 % discount on the Course Fee.
20 % Discount
20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
40 % Discount
Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
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