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Targeted NGS in patients with cancer, mendelian or complex diseases

19 – 23 September 2016 | Krakow, Poland

Registration deadline

17 June 2016

Abstract submission deadline

17 June 2016

Selected participants will be notified by

1 July 2016

Payment deadline

15 July 2016

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About the practical course

The cost of sequencing large genomes is still significant. Besides the cost, whole genome sequencing or whole exome sequencing generates a large amount of data that can complicate interpretation of the results. Depending on the goal of study, targeted NGS may be more cost effective and time efficient. Several clinical studies are focused only on a limited number of genes, for example in cancer research, oriented towards driver mutations across cancer-associated genes. To access the genomic region of interest, companies have developed methods which rely on various ways of capturing selected sequences. The main idea of the course is to show different ways of doing targeted NGS experiments.


The EMBO Practical Course, which will be held at the Center for Medical Genomics – OMICRON, Jagiellonian University Medical College from 19 to 23 September 2016, will consist of lectures and a hands-on part. Lectures will be given by invited speakers who are experts in the discussed topics. OMICRON staff will lead the practical part. This one week course will introduce young scientists to next generation sequencing methodology, mainly to targeted DNA analysis. Students will have an opportunity to learn how different library preparation methods – eg. PCR amplicon, capture enrichment - work. During the course we will perform several experiments based on predesigned or custom panels of different sizes in the area of cancer, mendelian and complex diseases. We will show how to analyse and interpret the data from all above mentioned panels. Sequencing experiments will be complemented by small set of qPCR experiments to demonstrate how to validate the obtained results.


After completion of this course, students should easily recognize the method of library preparation and point out its advantages and disadvantages. They should also be able to choose both the appropriate wet lab method and bioinformatics analysis pipeline for their requested study design.








Registration deadline

17 June 2016

Abstract submission deadline

17 June 2016

Selected participants will be notified by

1 July 2016

Payment deadline

15 July 2016












Registration includes:

  • Accomodation (6 nights)
  • Course materials
  • Meals, coffee breaks
  • Social events, excursion


Selection Criteria

  1. Research topic – preferences will be given to researchers studying human diseases.
  2. Place of work – preferences will be given to neighbouring countries (Central Europe)
  3. Career stage – preferences will be given to young scientists, PhD students or early postdocs.



Candidates must provide an abstract related to the project proposed for the course. The abstract should be one paragraph and should not exceed 200 words.



All participants must present a poster about their current project. Format A0.


Travel grants

A limited number of travel grants are available for eligible participants. Applicants do not need to apply separately for travel grants for this event. Selection of awardees is handled directly by the organizer who will notify all eligible participants. More information is available at EMBO Travel Grants' page.




Krystyna Witek

Phone +48 12 37 04 320





venue map


Center for Medical Genomics - OMICRON,
Jagiellonian University Medical College

ul. Kopernika 7c

31-034, Krakow, PL


The venue of the course (Center for Medical Genomics – OMICRON) is in Krakow, Poland. Krakow is the second largest city in Poland, very well connected with the world. Krakow can be reached by train, bus or plane. The closest international airport – Krakow Airport – is located about 16 km from the OMICRON lab.

More information about the city on:



All participants will be housed together (shared rooms) at Przegorzały Guesthouse. The Guesthouse is located on a hill, in the beautiful secluded spot of the Wolski Woods, 6,5 km away from the venue of the course. Free WIFI is available. The organizers will provide shuttle bus service between the venue and the Guesthouse.