This course is entitled to teach the main concepts of genomic data analysis using real data from two of the most important international projects describing human genetic variation: The HapMap and the 1000 Genomes Projects. In this course you will get familiar with general results emerged in these two projects, focusing in the genomic information displayed in the Ensemble version of 1000 Genomes Project Browser; but not in the transcriptomic and proteomic applications. You will also learn how to manage and deal with huge genetic datasets and which strategies and analysis are used to answer genetic, demographic and evolutionary questions. The course will alternate theory with practical computer exercises but it will focus on hands-on training.
Although examples will be based on single-nucleotide polymorphism (SNP) data in human individuals, most topics covered in this course can be extended to other types of markers and organisms. Basic use of the R statistical package and command-line based environments will be introduced in the course and previous knowledge is not required.
Dr. Marc Via
(Universitat de Barcelona, Spain).
Dr. Robert Carreras-Torres
(International Agency for Research on Cancer, France).
Dr. Soledad De Esteban-Trivigno
(Transmitting Science, Spain).
Dr. Judit Marigó
(Muséum national d’Histoire naturelle, France; and Institut Català de Paleontologia Miquel Crusafont (ICP), Spain).
Graduate or postgraduate degree in Biological Sciences, Medicine or Anthropology, basic knowledge in genetics and personal computers. All participants must bring their own personal laptop (Windows, Macintosh, Linux).
Monday 1st to Friday 5th February 2016.
Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont (ICP), C/ de l’Escola Industrial, 23, 08201 Sabadell, Barcelona (Spain). GPS Coordinates: Latitude 41.547346 (41° 32’ 50.4459’’N), Longitude 2.106325 (2° 6’ 22.7712’’E). How to arrive.
Monday 1st February 2016.
Basic genetic theory: Genetic polymorphisms; allele frequencies; Hardy-Weinberg equilibrium; linkage disequilibrium (LD); LD measurements; haplotypes; tag SNPs.
Visualization of LD and Tag SNPs (HaploView).
Introduction to the International HapMap and the 1000 Genomes Projects: Phases, data generated and main results.
Tuesday 2nd February 2016.
Navigating the HapMap and 1000G Browsers: Search regions of interest; visualize LD patterns; add custom data onto browser plots; download sets of SNPs and indels; create images and reports;…
Bulk data download and file formats (PED, MAP and DAT). Summary statistics in genetics using PLINK and visualization using R.
Wednesday 3rd February 2016.
Data Management: Conceptual aspects of Quality Control; merging datasets; removing sets of SNPs / individuals; pruning based on LD;…
Detecting structure in your genetic data: Genetic distances; identity-by-descent (IBD); detection of cryptic relatives; outlier detection; multidimensional scaling (MDS); admixture analysis (quantification of ancestry).
Thursday 4th February 2016.
Phasing genetic data with MACH software and generating haplotype reference datasets.
Genotype imputation: Practical considerations and quality control. Strategies for admixed populations.
Friday 5th February 2016.
Association analyses: Complex phenotypes; association tests; corrections for multiple comparisons (Bonferroni and permutation tests) and for population stratification (genomic-control, clustering, or admixture adjustments).
Other databases and resources.
- The International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467: 52-58.
- Via M, Gignoux C, González Burchard E (2010) The 1000 Genomes Project: new opportunities for research and social challenges. Genome Medicine, 2: 1-3.
- The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature, 491: 56-65.
- Fejerman L, Chen GK, Eng C, Huntsman C, Hu D, Williams A, Pasaniuc B, John EM, Via M, Gignoux C, Ingles S, Monroe KR, Kolonel KL, Torres-Mejía G, Pérez-Stable EJ, González Burchard E, Henderson BE, Haiman CA and Ziv E (2012) Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas. Human Molecular Genetics, 21 (8): 1907-1917.
35 hours on-site. This course is equivalent to 3.5 ECTS (European Credit Transfer System). Participants who have completed the course will receive a certificate at the end of it.
Monday 1st to Friday 5th February 2016:
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.
- There will be two coffee breaks each day, halfway through each lesson session.
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.
You will find below some testimonials from former participants to previous editions of this course:
“Not being myself involved in human research, I was a bit concerned as to whether the course would provide useful information for application to my favourite, non-model organisms (benthic invertebrates). I was happy to discover that the course provided a very good methodological overview and that we learned to use basic programs applicable to all kind of organisms. The teachers were great and beared nicely with our non-specialist naive questions. I recommend the course to everyone interested in applications of SNP data, no need to be a computer wizard!”
Dr. Xavier Turon, Centro de Estudios Avanzados de Blanes - CSIC, Spain (2nd Edition).
Places are limited to 20 participants and will be occupied by strict registration order.
Reduced registration fee until July 31, 2015: 490 €. Full registration fee after July 31, 2015: 655 €. This includes course material, coffee breaks and lunches.
Former participants will have a 5 % discount** on the current course fee.
We offer the possibility of paying in two instalments (contact us at email@example.com).
Please complete and submit your Registration Form (see below); we will confirm your acceptance by e-mail. If you do not receive any confirmation by e-mail after registration, please contact us at firstname.lastname@example.org.
If you wish to cancel your participation in this course, cancellations up to 20 days before the course start date will incur a 30 % cancellation fee. For later cancellations, or non-attendance, 75 % of the fee will be charged.
If Transmitting Science must cancel this course due to unforeseen circumstances beyond the control of Transmitting Science, you will either be entitled to a full refund of the course fee, or your fee can be credited toward a future course / workshop. Transmitting Science is not responsible for travel fees, or any expenses incurred by you as a result of such cancellation. Every effort will be made to avoid the cancellation of any planned course / workshop.
The course will take place in the city of Sabadell, Barcelona (Spain).
You may stay in Barcelona city or Sabadell. You will find information about Hotels and Hostel in Sabadell here. It takes about 45 minutes by public transport to arrive to Sabadell from the centre of Barcelona city. The place of the course is about 15 minutes walking from the train stop.
How to arrive to Sabadell from Barcelona city.
Unfortunately there are no internal grants available for this course. However some discounts are offered to people belonging to some of the Associations, Institutions or Universities listed here. If you want to apply to this discount please state the name of your Association, Institution or University in the “Comments” field of the Registration Form (proof will be asked later).
Spanish unemployed scientists, as well as Spanish PhD students without any grant to develop their PhD, could benefit from a 40 % discount** on the course fee. If you want to ask for this discount, please contact us at email@example.com. That would apply for a maximum of 2 places and they will be covered by strict inscription order.
For further information contact: firstname.lastname@example.org.
** Discounts are not cumulative.