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Advanced Courses in Life Sciences

6th Edition

Introduction to Genomic Data Analysis Using HapMap and 1000 Genomes Projects

February 13th-17th, 2017, Barcelona (Spain)

Introduction to Genomic Data Analysis Using HapMap and 1000 Genomes Projects

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.

LOCATION

Institut Català de Paleontologia Miquel Crusafont

C/ de l’Escola Industrial, nº 23
08201 Sabadell, Barcelona.

Spain – ICP – Sabadell

LANGUAGE

English

COURSE LENGHT & ECTS

35 hours on-site.

This course is equivalent to 3 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

Marc Via instructor for Transmitting Science

Dr. Marc Via
Universitat de Barcelona
Spain

Robert Carreras-Torres instructor for Transmitting Science

Dr. Robert Carreras-Torres
International Agency for Research on Cancer
France

Coordinators

Juan Vicente Bertó-Mengual coordinator at Transmitting Science

Juan Vicente Bertó-Mengual
Transmitting Science
Spain

Judit Marigó coordinator at Transmitting Science

Dr. Judit Marigó
Muséum national d’Histoire naturelle / Institut Català de Paleontologia Miquel Crusafont
France / Spain

Requirements

Graduate or postgraduate degree in Biological Sciences, Medicine or Anthropology, basic knowledge in genetics. All participants must bring their own personal laptop (Windows, Macintosh, Linux).

Program

Monday, February 13th, 2017.

Basic population genetics theory: Genetic polymorphisms, strand conventions, allele and genotype frequencies, Hardy-Weinberg equilibrium, haplotypes, linkage disequilibrium (LD), LD measurements, tag SNPs.

File formats (PED, INFO, MAP, DAT, VCF).

Visualization of LD and Tag SNPs (HaploView & HAPLOT).

Introduction to R: Becoming familiarized with the R working environment, creating data frames, using qualitative and quantitative variables, summary statistics in genetics using PED and VCF file formats.



Tuesday, February 14th, 2017.

Introduction to the International HapMap and the 1000 Genomes Projects: phases, data generated and main results.

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. Summary statistics in genetics using PLINK and visualization using R.

Wednesday, February 15th, 2017.

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, February 16th, 2017.

Genotype imputation: practical considerations and quality control. Strategies for admixed populations.

Single genetic region vs whole genome imputation.

IMPUTE2 software vs Michigan Imputation Server.


Friday, February 17th, 2017.

Association analyses: complex phenotypes; association tests; corrections for multiple comparisons (Bonferroni and permutation tests) and for population stratification (genomic-control, clustering, or admixture adjustments). Polygenicity assessment.

Other databases and resources.

Literature

  • 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.

Testimonials

You will find below some testimonials from former participants to previous editions of this course:

Dr. Xavier Turon

“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!” (2nd Edition)

Dr. Xavier TuronCentro de Estudios Avanzados de Blanes - CSIC, Spain

Fees

  • Course Fee
  • Early bird (until July 31st, 2016)
  • 550
  • Regular (after July 31st, 2016)
  • 770
  • This includes course material, coffee breaks and lunches.

We offer the possibility of paying in two instalments (contact the course coordinators).

Accommodation

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.

Funding

Former participants will have a 5 % discount on the Course Fee.

Unfortunately there are no scholarships available for this course. However 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).

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative.

Schedule

Course Schedule
Monday, February 13th through Friday, February 17th, 20179:30 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.

Organizers

Transmitting Science Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo

Registration

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