Course catalogue doctoral education - VT20

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Title Rare Disease Genomics
Course number 2981
Programme Cellbiologi och genetik
Language English
Credits 1.5
Date 2019-11-25 -- 2019-11-29
Responsible KI department Institutionen för molekylär medicin och kirurgi
Specific entry requirements
Purpose of the course The purpose of this course is to provide the participants with knowledge and practical experience about current research strategies and tools for analysis of DNA-sequencing data in the field of rare disease genomics. The participants will also be made aware of ethical issues in relation to rare disease genomics.
Intended learning outcomes After the course, the participants should be able:
1. To select adequate genomic technologies and data analysis strategies to answer research questions in the field of rare disease genetics or in their field of research;
2. To evaluate candidate variants and genes using publicly available databases and tools;
3. To understand functional validation of candidate variants and genes;
4. To reflect on ethical issues arising from large-scale sequencing studies.
Contents of the course This is a course aimed at students actively involved or planning genetic analysis of rare diseases. The course is also appropriate for those working with complex diseases and cancer whose projects involve high throughput DNA sequencing. The focus of the course is the use of current DNA-sequencing methods and bioinformatics tools to understand the genetic basis of rare genetic diseases. Within the overall theme of clinical and experimental approaches to diagnostics of rare genetic diseases, particular attention will be paid to annotation and classification of different types of genetic variants (single nucleotide variants and structural variants). The course will cover the use of different in-silico pathogenicity scores, phenotype ontology terms, and population and family data for variant and gene interpretation. The course will cover selected experimental strategies to validate genetic findings. The course will also cover current clinical best practice guidelines concerning ethical issues such as report of incidental findings and acquisition of informed consent.
Teaching and learning activities The course consists of lectures, research seminars, group discussions, hands-on computer-based exercises, self-studies, and a journal club seminar. Students are required to bring their laptops.
Compulsory elements All teaching and learning activities are compulsory. Absence from compulsory parts is compensated according to the instructions from the course leader.
Examination It will be assessed whether each individual doctoral student has reached all the learning outcomes of the course through a take-home examination. Anti­plagiarism tools will be used according to KI guidelines.
Literature and other teaching material Reference literature:
- Wright CF et al. Paediatric genomics: diagnosing rare disease in children. Nat Rev Genet. 2018 May;19(5):253-268.
- Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet. 2017 Oct;18(10):599-612.
- Green RC et al. American College of Medical Genetics and Genomics. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013 Jul;15(7):565-74.
- MacArthur DG et al. Guidelines for investigating causality of sequence variants in human disease. Nature. 2014 Apr 24;508(7497):469-76.
- Strande NT et al. Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource. Am J Hum Genet. 2017 Jun 1;100(6):895-906
Number of students 12 - 16
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given to earlier registration date)
More information The course will be held in Bioclinicum, Solna. Students are required to bring their laptops, to have the Integrative Genomics Viewer (IGV) installed and to have access to Eduroam wi-fi. More information will be provided before the beginning of the course.
Additional course leader The course director is Anna Lindstrand (anna.lindstrand@ki.se). The course co-director is Ann Nordgren (ann.nordgren@ki.se). Additional course leaders are Fulya Taylan (fulya.taylan@ki.se) and Bianca Tesi (bianca.tesi@ki.se).
Latest course evaluation Course evaluation report
Course responsible Anna Lindstrand
Institutionen för molekylär medicin och kirurgi

Anna.Lindstrand@ki.se
Contact person Bianca Tesi
Institutionen för molekylär medicin och kirurgi

bianca.tesi@ki.se