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Genotype - phenotype associations for biologists

Informacje ogólne

Kod przedmiotu: WB.SD.VP-5 Kod Erasmus / ISCED: (brak danych) / (brak danych)
Nazwa przedmiotu: Genotype - phenotype associations for biologists
Jednostka: Instytut Nauk o Środowisku
Grupy:
Punkty ECTS i inne: (brak)
Język prowadzenia: angielski

Zajęcia w cyklu "Semestr letni 2019/2020" (w trakcie)

Okres: 2020-02-24 - 2020-06-14
Wybrany podział planu:


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Typ zajęć: Wykład z elementami konwersatorium, 15 godzin, 6 miejsc więcej informacji
Koordynatorzy: Dominika Włoch-Salamon
Prowadzący grup: Matteo De Chiara
Lista studentów: (nie masz dostępu)
Zaliczenie: Przedmiot - Zaliczenie
Efekty kształcenia:

The students will understand the complexity of the relationship between genotype and phenotype. Genetic sources of phenotypic variation will be discussed, together with a theoretical overview of the methods to link genetic variant and phenotypes and potential confounding factors. Fundaments of Next-generation sequencing (NGS) analyses will be given as preparatory for the practical lessons. These will be dedicated to the full run of GWAS (genome-wide association study).

Skills:

The students will be able to chose the adequate method to link genotype to phenotype, depending on the available dataset. They will be able to run a basic set of NGS analyses and the necessary data preparation to run GWAS, as well as the downstream result interpretations.

Social competence and attitude:

The students will learn how to interpret and correctly communicate the GWAS results. Importance will be given to avid overestimate results implications.

Wymagania wstępne:

Practical ability in a Unix-based system, use of the bash terminal. Basic understanding of statistical concept and tests and basic of R language would be useful.

Forma i warunki zaliczenia:

80% attendance and completing homework(s)

Metody sprawdzania i kryteria oceny efektów kształcenia uzyskanych przez studentów:

evaluation of short homework exercises

Bilans punktów ECTS:

1 ECTS point

15 contact hours plus 5 hours self-study

Pełny opis:

conservatory lecture

• NGS (X hours): Students will receive a general explanation of the current sequencing methods, the kind of data provided and the subsequent bioinformatics analyses

• Population genomics (X hours): The module will focus on population genomics, explaining basic fundamental concepts regarding the population stratification and the bias it could introduce in linking genotypes with phenotypes.

• Linkage and QTLs (X hours): The students will be with alternative methods to the GWAS , either older and modern, with explanation of specific contest in which specific methods could be more suitable then others.

• GWAS (X hours): This module will guide the student through the principles of the genome-wide association study, with practical exercises and final data analyses.

• Downstream functional validation analyses (X hours): Potential methods to test and validate the identified variant will be shown and explained.

Literatura:

Xinkun Wang (2016) "Next-Generation Sequencing Data Analysis", CRC Press.

Karl W. Broman & Saunak Sen (2009) “A Guide to QTL Mapping with R/qtl”, Springer.

Hoon Sul et al. “Population structure in genetic studies: Confounding factors and mixed models” PLOS Genetics 2018

Ott et al. “”Genetic linkage analysis in the age of whole-genome sequencing” 2015

Goodwin et al. “Coming of age: ten years of next-generation sequencing technologies” Nature Reviews Genetics volume 2016

Uwagi:

18th May 2020- 22 th May 2020

Timetable


Monday, 18th May 2020 3 x 45min 10:00 -13:00 room 2.0.2

Tuesday, 19th May 2020 3 x 45 min 10:00 - 13:00 room 2.0.2

Wednesday, 20th May 2020 3 x 45 min 12:00 – 15:00 room 2.0.2

Thursday, 21th May 2020 3 x 45 min 10:00 – 13:00

Friday, 22 th May 2020 1 x 45 min + 2 x 45 min(open hours) 10:00 – 13:00

IES Seminar: 21th May 2020 13:00 – 14:00 (45’ seminar + discussion 15 min)

Opisy przedmiotów w USOS i USOSweb są chronione prawem autorskim.
Właścicielem praw autorskich jest Uniwersytet Jagielloński w Krakowie.