Genome analysis
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.
Information from the course leader
Updated preliminary schedule
Please find a new updated preliminary schedule. Zoom-links will be available in the schedule published in Canvas.
2020-10-27
Corona restrictions
I had hoped to see you all live at least the first day of the course, but due to the current corona restrictions in Uppsala most lectures will be digital. I will post an updated version of the schedule as soon as possible.
2020-08-31
Welcome to the course Genome Analysis
Due to the Covid restrictions, the course will this year run as a semi-digital course to lower the number of students present at campus. The mandatory group discussions, and computer exercises will be digital, while some lectures will be on campus, and some will be digital. 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
HV0187-20030 - 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.
Syllabus and other information
Syllabus
HV0187 Genome analysis, 15.0 Credits
GenomanalysSubjects
Animal Science Biology Animal science BiologyEducation cycle
Master’s levelAdvanced study in the main field
Second cycle, has only first-cycle course/s as entry requirementsMaster’s level (A1N)
Grading scale
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.
Language
EnglishPrior knowledge
Knowledge equivalent to- 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.
Grading form
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.Formats and requirements for examination
Passed written and oral examination. Passed participation in compulsory course modules.
- If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.
- The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.
- If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and 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 submission. Read more in the Education Planning and Administration Handbook.
Transitional provisions
• Exams: At least three retake sessions (renewed exams) must be offered within two years of the decision to cancel the course. • Compulsory elements: At least one opportunity for a retake session must be offered within two years of the decision to cancel the course.Other information
The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.
If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.
Additional information
The course assumes good prior knowledge of basic genetic mechanisms (the structure of the genetic make-up and the genetic code, DNA replication, transcription), RNA-processing, translation, regulation of gene expression, general genetics and population genetics, equivalent to 7.5 credits.Further information
Grading criteria
Grading criteria* and type of examination for the different learning outcomes
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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 |
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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 |
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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 |
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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) |
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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) |
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* Criteria for Grade 4 and 5 that defines the additional requirements besides the underlying grading level(s)
Litterature list
- 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.
- 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.