1. Introduction to genomes & genome browsers
Content
Introduction to genomes
The human genome
Human genetic variation
SNPs
CNVs
Alternative splicing
Browsing the human genome
Celia van Gelder
CMBI
UMC Radboud
December 2014

2. Exponential Growth in Genomic Sequence Data
# of genomes
First eukaryote
complete
(yeast)
First metazoan
complete
(flatworm)
First 2
bacterial
genomes
complete

4. 4

5. Ebola

6. The human genome Genome: the entire sequence of DNA in a cell
3 billion basepairs (3Gb)
22 chromosome pairs + X en Y chromosomes
Chromosome length varies from ~50Mb to ~250Mb
About protein-coding genes (average gene length 3000 bases, but largest known gene is 2.4 Mb (dystrophin))
Human genome is 99.9% identical among individuals This means that every 2 persons differ in 3 million nts!!

7. Eukaryotic Genomes: more than collections of genes
Genes & regulatory sequences make up 5% of the genome
Protein coding genes
RNA genes (rRNA, snRNA, snoRNA, miRNA, tRNA)
Structural DNA (centromeres, telomeres)
Regulation-related sequences (promoters, enhancers, silencers, insulators)
Parasite sequences (transposons)
Pseudogenes (non-functional gene-like sequences)
Simple sequence repeats

8. The human genome cntnd Only 1.2% codes for proteins
Long introns, short exons
Large spaces between genes
More than half consists of repetitive DNA
Alu repeat ~300 bp > million copies
From: Molecular Biology of the Cell (4th edition) (Alberts et al., 2002)

9. Non coding DNA

10. Human Genetic Variation
Genetic variation explains some of the differences among people, such as:
Blood group
Eye color, Skin color, Hair color
Length
Higher or lower risk for getting particular diseases
Cystic fibrosis, Sickle cell disease, Diabetes, Cancer, Arthritis, Asthma etc

11. Variations in the Genome
Common Sequence
Variations
Polymorphism
Deletions
Insertions
Chromosome
Translocations

12. Today’s focus Single Nucleotide Polymorphisms (SNPs)
Copy number variations (CNV)
Alternative transcripts

13. Single Nucleotide Polymorphisms (SNPs)
SNPs are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered.
For a variation to be considered a SNP, it must occur in at least 1% of the population.
SNPs make up about 90% of all human genetic variation and occur every 100 to 300 bases.
SNPs can occur in coding (gene) and non coding regions of the genome; <1% alter the protein sequence

14. SNPs
determine properties like eye color, hair (curly or straight), or if you can taste bitter or not.
are used for identification and forensics
are used for estimating predisposition to disease
can cause drug side–effects and/or non responsiveness for the drug
have impact on how humans respond to environmental factors like bacteria, viruses, toxins and chemicals
are used to predict specific genetic traits
are used for classifying patients in clinical trials
are used for mapping and genome-wide association studies of complex diseases

15. SNP - Bitter tasting, TAS2R38

16. SNP & disease, Alzheimer
Alzheimer's disease (AD) & apolipoprotein E (APOE)
Apolipoprotein E is a cholesterol carrier that is found in the brain and other organs. APOE is suspected to be involved in amyloid beta aggregation and clearance, influencing the onset of amyloid beta deposition.
APOE contains 2 SNPs that result in 3 possible alleles: E2, E3, E4.
Variant rs rs7412
E2 T T
E3 T C
E4 C C
A person who inherits at least one E4 allele will have a greater chance of developing AD.

17. Today’s focus Single Nucleotide Polymorphisms (SNPs)
Copy number variations (CNV)
Alternative transcripts

18. Copy Number Variation
Copy Number Variations (CNVs): segment of DNA (> 1 kB) which is present at variable copy number in two or more genomes
When there are genes in the CNV areas, this can lead to variations in the number of gene copies between individuals
CNVs contribute to our uniqueness.
CNVs can also influence the susceptibility to disease.
CNVs may either be inherited or caused by de novo mutation

19. Copy Number Variation Normal cell CN=2 deletion amplification
CN= CN= CN= CN=4

20. CNVs and their possible effects on gene expression.
Cabianca D S , Gabellini D J Cell Biol 2010;191:
© 2010 Cabianca and Gabellini

21. CNVs & disease Many inherited genetic diseases result from CNVs;
Gene copy number can be elevated in cancer cells
Autism
Schizophrenia (dept. human genetics)
Mental retardation (dept. human genetics)
Parkinsons disease
There are CNVs that protect against HIV infection and malaria.
The contribution of CNV to the common, complex diseases, such as diabetes and heart disease, is currently less well understood

22. Today’s focus Copy number variations (CNV)
Single Nucleotide Polymorphisms (SNPs)
Alternative transcripts

23. Alternative splicing

24. Alternative splicing
Defects in alternative splicing have been implicated in many diseases, including:
neuropathological conditions such as Alzheimer disease
cystic fibrosis, those involving growth and developmental defects
many human cancers, e.g. BRCA1 in breast cancer
Beta-globin in Beta-thalassemia
Parkinsons Disease

25. Annotating & Browsing the Human Genome

26. Annotating the genome
Annotation: attaching biological information to sequences.
Two main steps:
identifying elements on the genome
attaching biological information to these elements.

27. Basic & Advanced Genome Annotation
Genomic location
Gene features: Exons, Introns, UTRs
Transcript(s)
Pseudogenes, Non-coding RNA
Protein(s)
Links to other sources of information
Advanced
Cytogenetic bands
Polymorphic markers
Genetic variation, including SNPs & CNVs
Repetitive sequences
cDNAs or mRNAs from related species
Genomic sequence variation
Regulation sequences (enhancers, silencers, insulators)

28. [Human] Genome Browsers
Not limited to
only human data
EBI
Ensembl
NCBI
Map Viewer
UCSC Genome Browser

29. Ensembl
©EMBL-EBI

30. Other Ensembl Installations
©EMBL-EBI (2013)

31. Organized Data Based on Chromosome Location
Gene X
Description
Transcript data
Structure
Gene Ontology
Pathway Data
Homologous Genes
Expression Data
Etc….
genes & predictions
tracks
variations &
repeats
cross-species
comparative data
& many more types of data from expression
& regulation to mRNA and ESTs…

33. ENSG### Ensembl Gene ID
ENST### Ensembl Transcript ID
ENSP### Ensembl Peptide ID
ENSE### Ensembl Exon ID
HGNC – a unique name and symbol for every gene in human

34. Ensembl: An Example
Click for
more
details
tracks
tracks

35. Direction of transcription
Above blue line: forward strand
Below blue line: reverse strand

36. Ensembl Transcripts
A red transcript comes from Ensembl or VEGA/Havana.
A transcript from the Ensembl annotation pipeline starts with 2 (MYO6-201)
A transcript with Vega/Havana manual curation starts with 0 (MYO6-001)
A gold, or merged, transcript is identical between Ensembl automated annotation and VEGA/Havana manual curation. Only human, mouse, and zebrafish will have gold transcripts. This transcript can be thought of as stable (unlikely to change), and is coloured gold. It is assigned a number beginning with 0.
A blue, pink or grey transcript is non-coding. See the 'NON-CODING TRANSCRIPTS' section below for more.
©EMBL-EBI

39. Synopsis- What can I do with Ensembl?
View, examine & explore annotated information for any chromosomal region:
Genes,
ESTs, mRNAs, alternative transcripts
Proteins
SNPs, and SNPs across strains (rat, mouse), populations (human), or even breeds (dog)
homologues and phylogenetic trees across more than 40 species
whole genome alignments
conserved regions across species
gene expression profiles
Upload your own data and use BLAST/BLATagainst any Ensembl genome
Export sequence, or create a table of gene information

40. Help & Documentation -> Tutorials Save configuration
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FAQ
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