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BK0002

Genome analysis

This course at master level gives in-depth knowledge on methods for studying DNA and structure and evolution of genomes. An important part is the lab project were students work with DNA. The course is given on campus Ultuna the second half of the autumn semester.

Information from the course leader

2021-09-07
Welcome to the course Genome Analysis
Due to the Covid-19 restrictions, the course will also this year run as a blended on campus/digital course to lower the number of staff and students present at campus. The mandatory group discussions, while some computer exercises, and lectures will be digital, and some on campus. The laboratory project is scheduled for most part of December and will be on campus in the large student laboratory Ymer in VHC.

Course evaluation

The course evaluation is now closed

BK0002-20159 - Course evaluation report

Once the evaluation is closed, the course coordinator and student representative have 1 month to draft their comments. The comments will be published in the evaluation report.

Additional course evaluations for BK0002

Academic year 2023/2024

Genome analysis (BK0002-10019)

2023-08-28 - 2023-10-30

Academic year 2022/2023

Genome analysis (BK0002-20164)

2022-11-01 - 2023-01-15

Syllabus and other information

Grading criteria

Grading criteria* and type of examination for the different learning outcomes

5

Understand the functionality of eukaryotic genome organizations

Understand the concept of genome plasticity

Analytically interpret molecular evolutionary events

Explain the function of transcription factors and regulatory elements

Understand how to use advanced molecular technologies to resolve scientific questions

In depth understanding of principles for genetic mapping techniques

Understanding basic statistics relevant to genetic mapping

Understand the concept of systems biology and biological interactions.

Develop strategies to identify genes and genetic variation underlying phenotypic traits

Evaluate consequences resulting from causative and regulatory mutations underlying complex traits

Use population genetics and polymorphisms in the context of phenotypic variation

Explain how epigenetic mechanisms control chromatin structure and gene expression

Write reports with in depth analysis and scrutiny of the obtained results during laboratory project, computer exercises, and group discussions

4

Understand how genes and genomes are organized in eukaryotes

Understand fundamental principles of molecular evolution and phylogeny

Understand important mechanisms underlying gene expression

In detail describe different molecular genetic laboratory techniques and understand how to analyze and interpret the data produced

Understand principles for genetic mapping

Understand genotype-environment interactions and how genes within a genome interacts and controls the phenotype

Understand principles for methods used to study complex traits and diseases

Understand how gene interactions control complex traits in different environments

Understand the distinction on how genetic and epigenetic mechanisms influence phenotype

Compare genetic and epigenetic regulation of gene expression

Write reports showing understanding of the scientific tasks presented during mandatory parts of the course

3

Describe the architecture of eukaryotic genes and genomes

Understand principles of Mendelian and mitochondrial inheritance

Basic understanding of the principles of evolution and phylogenetics

Describe important mechanisms of gene expression

Describe the architecture of a eukaryotic nucleus and the role of its components

Ability to perform basic molecular genetic laboratory techniques

Describe the principles for genetic mapping

Describe advanced molecular techniques, modern DNA sequencing technologies and its applications

Understand the link between structure and function of biomolecules

Describe the different types of nucleic acids and other biomolecules important for a functional genome

Describe principles for methods used to study complex traits and diseases

Describe how gene interactions and environment control complex traits

Describe the histone code

Describe how chromatin structure is regulated

Following instructions, write reports about subjects in mandatory parts of the course

Learning outcomes

1. Knowledge about the organization structure of eukaryotic genome and genes

Understand the evolutionary mechanisms that shape eukaryotic genomes

2. Knowledge about principles for control of gene expression and how it influences phenotypic variation in animals

3. Knowledge about genetic recombination, and its importance for different gene mapping strategies and technologies

Understand how gene mapping is used to identify underlying disease and phenotypic variation

4. Knowledge about complex biological systems and functional genomics

5. Knowledge about complex traits and how they are influenced by genotype and environment

6. Knowledge of how epigenetic mechanisms control chromatin structure and gene expression

7. Skills in how to write scientific reports and how to perform an oral presentation of individual as well as group work(s)

Type of examination

Written reports and exam(s)

Written reports and exam(s)

Written reports and exam(s)

Written reports and exam(s)

Written reports and exam(s)

Written reports and exam(s)

Written reports and exam(s)

Activity in group discussions and activities

Oral presentation(s)

* Criteria for Grade 4 and 5 that defines the additional requirements besides the underlying grading level(s)

Litterature list

  1. Genomes 4 Författare: Brown T ISBN: 9780815345084 [Genomes 4] (https://www.garlandscience.com/product/isbn/9780815345084) Kommentar: Genomes 4 has been completely revised and updated. It is a thoroughly modern textbook about genomes and how they are investigated. As with Genomes 3, techniques come first, then genome anatomies, followed by genome function, and finally genome evolution. The genomes of all types of organism are covered: viruses, bacteria, fungi, plants, and animals including humans and other hominids.

Genome sequencing and assembly methods have been thoroughly revised including a survey of four genome projects: human, Neanderthal, giant panda, and barley. Coverage of genome annotation emphasizes genome-wide RNA mapping, with CRISPR-Cas 9 and GWAS methods of determining gene function covered. The knowledge gained from these techniques forms the basis of the three chapters that describe the three main types of genomes: eukaryotic, prokaryotic (including eukaryotic organelles), and viral (including mobile genetic elements). Coverage of genome expression and replication is truly genomic, concentrating on the genome-wide implications of DNA packaging, epigenome modifications, DNA-binding proteins, non-coding RNAs, regulatory genome sequences, and protein-protein interactions. Also included are applications of transcriptome analysis, metabolomics, and systems biology. The final chapter is on genome evolution, focusing on the evolution of the epigenome, using genomics to study human evolution, and using population genomics to advance plant breeding. Established methods of molecular biology are included if they are still relevant today and there is always an explanation as to why the method is still important.

Each chapter has a set of short-answer questions, in-depth problems, and annotated further reading. There is also an extensive glossary. Genomes 4 is the ideal text for upper level courses focused on genomes and genomics.

  1. Human Molecular Genetics 5th edition Författare: Tom Strachan and Andrew P Read ISBN: 978-0-815-34589-3 [Human Molecular Genetics 5th edition] (https://www.taylorfrancis.com/books/mono/10.1201/9780429448362/human-molecular-genetics-tom-strachan-andrew-read) Kommentar: Human Molecular Genetics has been carefully crafted over successive editions to provide an authoritative introduction to the molecular aspects of human genetics, genomics and cell biology. Maintaining the features that have made previous editions so popular, this fifth edition has been completely updated in line with the latest developments in the field. Older technologies such as cloning and hybridization have been merged and summarized, coverage of newer DNA sequencing technologies has been expanded, and powerful new gene editing and single-cell genomics technologies have been added. The coverage of GWAS, functional genomics, stem cells, and disease modeling has been expanded. Greater focus is given to inheritance and variation in the context of populations and on the role of epigenetics in gene regulation. Key features: Fully integrated approach to the molecular aspects of human genetics, genomics, and cell biology Accessible text is supported and enhanced throughout by superb artwork illustrating the key concepts and mechanisms Summary boxes at the end of each chapter provide clear learning points Annotated further reading helps readers navigate the wealth of additional information in this complex subject and provides direction for further study Reorganized into five sections for improved access to related topics Also new to this edition – brand new chapter on evolution and anthropology from the authors of the highly acclaimed Human Evolutionary Genetics A proven and popular textbook for upper-level undergraduates and graduate students, the new edition of Human Molecular Genetics remains the ‘go-to’ book for those studying human molecular genetics or genomics courses around the world.
  2. Genetics and Genomics in Medicine Författare: Tom Strachan, Judith Goodship, Patrick Chinnery ISBN: 9780815344803 [Genetics and Genomics in Medicine] (https://www.garlandscience.com/product/isbn/9780815344803) Kommentar: Genetics and Genomics in Medicine is a new textbook written for undergraduate students, graduate students, and medical researchers that explains the science behind the uses of genetics and genomics in medicine today. Rather than focusing narrowly on rare inherited and chromosomal disorders, it is a comprehensive and integrated account of how genetics and genomics affect the whole spectrum of human health and disease. DNA technologies are explained, with emphasis on the modern techniques that have revolutionized the use of genetic information in medicine and are indicating the role of genetics in common diseases. Epigenetics and non-coding RNA are covered in-depth as are genetic approaches to treatment and prevention, including pharmacogenomics, genetic testing, and personalized medicine. Cancers are essentially genetic diseases and are given a dedicated chapter that includes new insights into its molecular basis and approaches to its detection gained from cancer genomics. Specific topics, including multiple examples of clinical disorders, molecular mechanisms, and technological advances, are profiled in boxes throughout the text.

Course facts

The course is offered as an independent course: Yes Tuition fee: Tuition fee only for non-EU/EEA/Switzerland citizens: 38054 SEK Cycle: Master’s level (A1N)
Subject: Bioinformatics Biology Bioinformatic Biology
Course code: BK0002 Application code: SLU-20159 Location: Uppsala Distance course: No Language: English Responsible department: Department of Animal Breeding and Genetics Pace: 100%