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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.

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.

The course evaluation is not yet activated

The course evaluation is open between 2022-01-09 and 2022-01-30

Additional course evaluations for BK0002

Academic year 2021/2022

Genome analysis (BK0002-M2159) 2021-11-02 - 2022-01-16

BK0002 Genome analysis, 15.0 Credits

Genomanalys

Syllabus approved

2020-11-12

Subjects

Bioinformatic Biology

Education cycle

Master’s level

Modules

Title Credits Code
Laboratory project 5.00 1002
Computer exercises 2.00 1003
Home exam 8.00 1004

Advanced study in the main field

Second cycle, only first-cycle courses as entry requirements(A1N)

Grading scale

5:Pass with Distinction, 4:Pass with Credit, 3:Pass, U:Fail The requirements for attaining different grades are described in the course assessment criteria which are contained in a supplement to the course syllabus. Current information on assessment criteria shall be made available at the start of the course.

Language

English

Prior knowledge

- 180 credits at first cycle level, of which
- 60 credits biology, animal science, equine science, veterinary nursing or veterinary medicine
or
- 60 credits agricultural sciences (of which at least 30 credits animal and dairy science/zoology)
and
- English 6

Objectives

The course intends to provide advanced knowledge of methods for studies of eukaryotic genomes, including their organization and evolution. There is a focus on animal genomics, but methodological and theoretical aspects of the course are applicable on many different organisms.
On completion of the course, the student should be able to:
- in detail describe structure, diversity and evolution of eukaryotic genomes and genes,
- in detail describe various types of genetic variation,
- in detail explain state of the art and large-scale methods to analyze genetic variation (eg. whole genome sequencing), and gene expression analysis (eg. RNA-seq),
- apply and critically process basic molecular phylogenetic / -genomic and evolutionary analysis,
- in detail describe the different types of RNA in the transcriptome and their function,
- describe principles for transcriptional regulation,
- describe and plan different approaches for functional analysis of genes and genomes,
- summarize genetic recombination and its applications within genome analysis,
- summarize and evaluate the principles of whole genome mapping and comparative genomics to identify genes and loci underlying mendelian and quantitative inherited diseases as well as important phenotypic traits,
- explain epigenetic and epigenomic markers and methods for the analysis of these,
- explain the concept of genome editing and transgenic animals,
- compile data and apply basic statistics relevant to genome analysis,
- use and evaluate molecular genetic laboratory methods and basic bioinformatics methods.

Content

The course is based on lectures, exercises, discussions and laboratory sessions. The contents build largely on animal genome research. Both laboratory and theoretical teaching is for the most part directly applicable also within eg. human or plant genetics. The course is based on current state-of-the-art methodology and research.

Computer exercises and group discussions will cover:
- molecular evolution and phylogenetics/-genomics,
- genetic variation, sequence analysis and primer design,
- gene mapping and genomewide association analysis,
- QTL analysis,
- whole genome sequencing,
- epigenetics/-genomics,
- copy-number variation analysis
The aim of the computer exercises is to give the students useful tools for basic genetic and genomic analyses. Therefore the computer exercises use free and open source software that the student can download to their own laptop. Apart from in the written and the oral examination, compulsory components occur within eg. exercises, group assignments and laboratory sessions.

In the course the following general skills are trained: oral and written communication, problem solving and critical thinking.

Formats and requirements for examination

Passed written and oral examination. Passed participation in compulsory course modules.
  • If the student fails a test, the examiner may give the student a supplementary assignment, provided this is possible and there is reason to do so.
  • If the student has been granted special educational support because of a disability, the examiner has the right to offer the student an adapted test, or provide an alternative assessment.
  • If changes are made to this course syllabus, or if the course is closed, SLU shall decide on transitional rules for examination of students admitted under this syllabus but who have not yet passed the course.
  • For the examination of a degree project (independent project), the examiner may also allow the student to add supplemental information after the deadline. For more information on this, please refer to the regulations for education at Bachelor's and Master's level.

Other information

  • The right to take part in teaching and/or supervision only applies to the course date to which the student has been admitted and registered on.
  • If there are special reasons, the student may take part in course components that require compulsory attendance at a later date. For more information on this, please refer to the regulations for education at Bachelor's and Master's level.

Additional information

The course presupposes good prior knowledge of basic genetic mechanisms (genome structure and the genetic code, DNA replication, transcription), RNA processing, translation, regulation of gene expression, general genetics and population genetics, corresponding to 7.5 credits.

Responsible department

Department of Animal Breeding and Genetics

Further information

Determined by: Programnämnden för utbildning inom veterinärmedicin och husdjur (PN - VH)
Biology field: Genetik
Replaces: BI1218, HV0122, HV0164, HV0187

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)

1) Genomes 4
Author: Brown T
ISBN: 9780815345084
Comments: 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.
2) Genetics and Genomics in Medicine
Author: Tom Strachan, Judith Goodship, Patrick Chinnery
ISBN: 9780815344803
Comments: 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.
3) Human Molecular Genetics 5th edition
Author: Tom Strachan and Andrew P Read
ISBN: 978-0-815-34589-3
Comments: 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.

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
Subject: Bioinformatic Biology
Course code: BK0002 Application code: SLU-20159 Distance course: No Language: English Responsible department: Department of Animal Breeding and Genetics Pace: 100%