SIGU on-line training tutorial on “Data analysis and interpretation for clinical genomics” using Galaxy

sigu


In years 2018-2019, on behalf of the Italian Society of Human Genetics (SIGU) an itinerant Galaxy-based “hands-on-computer” training activity entitled “Data analysis and interpretation for clinical genomics” was held four times on invitation from different Italian institutions (Università Cattolica del Sacro Cuore in Rome, University of Genova, SIGU 2018 annual scientific meeting in Catania, University of Bari) and was offered to about 30 participants each time among clinical doctors, biologists, laboratory technicians and bioinformaticians. Topics covered by the course were NGS data quality check, detection of variants, copy number alterations and runs of homozygosity, annotation and filtering and clinical interpretation of sequencing results.

Realizing the constant need for training on NGS analysis and interpretation of sequencing data in the clinical setting, we designed an on-line Galaxy-based training resource articulated in presentations and practical assignments by which students will learn how to approach NGS data quality at the level of fastq, bam and VCF files and clinically-oriented examination of variants emerging from sequencing experiments.


Requirements

This tutorial is based on the Galaxy platform, therefore a basic knowledge of Galaxy is required to get most out of the course. In particular, we’ll use European Galaxy server running at https://usegalaxy.eu.

Registration is free, and you get access to 250GB of disk space for your analysis.

  1. Open your browser. We recommend Chrome or Firefox (please don’t use Internet Explorer or Safari).
  2. Go to https://usegalaxy.eu
    • If you have previously registered on this server just log in:
      • On the top menu select: User -> Login
      • Enter your user/password
      • Click Submit
    • If you haven’t registered on this server, you’ll need to do now.
      • On the top menu select: User -> Register
      • Enter your email, choose a password, repeat it and add a one word name (lower case)
      • Click Submit

Datasets used in this course are available:

To familiarize with the Galaxy interface (e.g. working with histories, importing dataset), we suggest to follow the Galaxy at a Glance tutorial.

Contributors


Italian Society of Human Genetics

The Italian Society of Human Genetics (SIGU) was established on November 14, 1997, when the pre-existing Italian Association of Medical Genetics and the Italian Association of Medical Cytogenetics joined. SIGU is one of the 27 member societies of FEGS (Federation of European Genetic Societies). Animated by a predominant scientific spirit, SIGU wants to be reference for all health-care issues involving human genetics in all its applications. Its specific missions are to develop quality criteria for medical genetic laboratories, to promote writing of guidelines in the field of human genetics and public awareness of the role and limitations of genetic diagnostic techniques. SIGU coordinates activities of several working groups: Clinical Genetics, Cytogenetics, Prenatal Diagnosis, Neurogenetics, Fingerprinting, Oncological Genetics, Immunogenetics, Genetic Counseling, Quality Control, Medical Genetics Services, Bioethics. More than 1000 medical geneticists and biologists are active members of the society.