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Manipulation of NGS Data for Genomic and Population Genetics Analyses
February 4-7, 2020 (Spain)
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Genetics and Genomics
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.
DATE
November 25th-29th, 2019
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 and ForBio.
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.
Instructors
Dr. Gerard Muntané
Universitat Rovira i Virgili / Universitat Pompeu Fabra
Spain
Dr. Juan Rodríguez
CNAG · CRG
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).
Program
Monday, November 25th, 2019.
- 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, November 26th, 2019.
- Morning:
- Quality Control (QC) for GWAS
- Variant identification
- Population stratification
- HWE
- MAF
- Afternoon:
- Imputation (Michigan Imputation Server)
Wednesday, November 27th, 2019.
- 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, November 28th, 2019.
- Morning:
- Annotation of Genomic Variants (LocusZoom, CADD)
- Use of summary statistics
- Afternoon:
- Genetic risk scores (LDSC, Heritability explained, PRS)
Friday, November 29th, 2019.
- Morning:
- Wrap-up
- Hands-on training. Perform an association test from scratch
Fees
- Course Fee
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- Early bird (until October 31st, 2019):
- 538 € *
(430.40 € for Ambassador Institutions)
- Regular (after October 31st, 2019):
- 672 € *
(537.60 € 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
- {{content-1}}
- Early bird (until October 31st, 2019):
- 538 € * + 350 € = 888 €
(780.40 € for Ambassador Institutions)
- Regular (after October 31st, 2019):
- 672 € * + 350 € = 1,022 €
(887.60 € 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 HERE. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.org.
Discounts (see Funding below) are not cumulative and apply only on the fee.
We offer the possibility of paying in two instalments (contact the course coordinators).
Accommodation
Accommodation Package
If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.
If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.
A supplemental charge will be added if you prefer to stay in a single room.
Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).
Other accommodation options
If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.
Rural House Can Carol
Rural House Can Carol
Rural House Can Carol
Schedule
Course Schedule
- Monday to Friday:
- 9:30 to 13:30 Lessons.
- 13:30 to 15:00 Lunch (included).
- 15:00 to 18:00 Lessons.
Accommodation Package Schedule
- Sunday:
- 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information in How to get there.
- 20:00 Registration in the Hotel.
- 20:30 Dinner.
- Monday to Thursday:
- 8:00 to 9:00 Breakfast.
- 20:30 Dinner.
- Friday:
- 8:00 to 9:00 Breakfast.
- 15:00 Meeting point in the Hotel to take the bus to Barcelona city.
- 16:30 Arrival to Plaza Catalunya (Barcelona).
The 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.
Funding
Discounts
Former participants will have a 5 % discount on the Course Fee.
Furthermore, a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).
Unemployed scientists living in Spain, as well as PhD students based in Spain 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.
Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.
Organizers
Collaborators
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Transmitting Science started in 2012 to manage specialized courses and workshops we were already organizing within our own Partnerships. Up to date, we have already run more than 120 advanced courses in different topics related to Life Sciences.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.
All the courses are self-financed with participant’s fees and we strive to keep the fees to the minimum necessary for running them.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.