1. Introduction to genomes & genome browsers Content  Introduction  The human genome  Human genetic variation SNPs CNVs Alternative splicing  Browsing the human genome Celia van Gelder CMBI UMC Radboud December 2012 c.vangelder@cmbi.ru.nl

2. Exponential Growth in Genomic Sequence Data # of genomes Currently 1000+ completed genomes First 2 bacterial genomes complete First eukaryote complete (yeast) First metazoan complete (flatworm)

3. Exponential Growth in Genomic Sequence Data © Pevzner 2011

4. The cow genome Houston Chronicle Houston scientists milk cow genome for its secrets Weekly Times Now Bovine genome to revolutionise food production National Geographic Cow Genome Decoded -- Cheaper Beef for Everybody? BBC News Cow genome 'to transform farming

5. The pig genome

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 22000 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 From: Molecular Biology of the Cell (4 th edition) (Alberts et al., 2002) 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

9. Variation along genome sequence Nucleotide usage varies along chromosomes – Protein coding regions tend to have high GC levels Genes are not equally distributed across the chromosomes – Housekeeping generally in gene- dense areas – Gene-poor areas tend to have many tissue specific genes Karyotype: – Gene rich areas = light – Gene poor areas = dark From: Ensembl

10. Chromosome organisation From: Lodish (4 th edition) DNA packed in chromatin Non-active genes often in densely packed chromatin (30-nm fiber) Active genes in less dense chromatin (beads-on-a-string) Gene regulation by changing chromatin density, methylation/acetylation of the histones Genes that are OFF Genes that are ON

11. Introduction to genomes & genome browsers Content  Introduction  The human genome  Human genetic variation CNVs SNPs Alternative splicing  Browsing the human genome

12. Human Genetic Variation Every human has essentially the same set of genes, but there are different forms of each gene -- known as alleles Genetic variation explains some of the differences among people, such as: – Blood group – Eye color – Skin color – Hair color – Higher or lower risk for getting particular diseases Cystic fibrosis, Sickle cell disease, Diabetes, Cancer, Arthritis, Asthma Stroke, Heart disease Alzheimer's disease, Parkinson's disease Depression, Alcoholism

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

14. Today’s focus 1.Single Nucleotide Polymorphisms (SNPs) 2.Copy number variations (CNV) 3.Alternative transcripts

15. 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, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. SNPs can occur in coding (gene) and non coding regions of the genome; <1% alter the protein sequence

16. SNPs & medicine Although more than 99% of human DNA sequences are the same, variations in DNA sequence can have a major impact on how humans respond to: – disease; – environmental factors such as bacteria, viruses, toxins, and chemicals; – and drugs (& side-effects). This makes SNPs valuable for biomedical research and for developing pharmaceutical products or medical diagnostics.

17. SNP & disease, Alzheimer Alzheimer's disease (AD) & apolipoprotein E The APOE gene encodes the protein apolipoprotein E, a cholesterol carrier that is found in the brain and other organs. Its exact role in the development of AD is unclear. Several studies have indicated a role of APOE in amyloid beta aggregation and clearance, influencing the onset of amyloid beta deposition.

18. SNP & disease, Alzheimer (2) Two SNPs - three APOE variants APOE contains 2 SNPs that result in 3 possible alleles: E2, E3, E4. Variant rs429358 rs7412 E2 T + T E3 T + C E4C + C A person who inherits at least one E4 allele will have a greater chance of developing AD.

19. Today’s focus 1.Single Nucleotide Polymorphisms (SNPs) 2.Copy number variations (CNV) 3.Alternative transcripts

20. Copy Number Variation People do not only vary at the nucleotide level (SNPs) Copy Number Variations (CNVs): gains and losses of large chunks of DNA sequence (10kB – 5Mb) 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

21. Copy Number Variation Normal cell deletion amplification CN=0 CN=1 CN=3 CN=4 CN=2

22. 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

23. Today’s focus 1.Copy number variations (CNV) 2.Single Nucleotide Polymorphisms (SNPs) 3.Alternative transcripts

24. Alternative splicing

25. Defects of the machinery of 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

26. Introduction to genomes & genome browsers Content  Introduction  The human genome  Human genetic variation CNVs SNPs Alternative splicing  Browsing the human genome

27. Annotating the genome A genome sequence is of limited use without functional annotation. Genome annotation is the process of attaching biological information to sequences. It consists of two main steps: identifying elements on the genome attaching biological information to these elements. Annotating the genome – Bioinformatics! The genome browser is a tool for visualizing genome annotation. It provides context to understand genomic regions of interest

28. Basic & Advanced Genome Annotation Basic: – 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)

29. Possible research questions P. Schattner, Genomics 93 (2009):187-195

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

31. Other Ensembl Installations http://www.ensemblgenomes.org/

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

33. Ensembl Genes – biological basis All Ensembl transcripts are based on proteins and mRNAs in: – UniProt/Swiss-Prot (manually curated) – UniProt/TrEMBL – NCBI RefSeq (manually curated)

34. 34 Ensembl Homepage ↔

36. HGNC – a unique name and symbol for every gene in human http://www.genenames.org/ ENSG### Ensembl Gene ID ENST### Ensembl Transcript ID ENSP### Ensembl Peptide ID ENSE### Ensembl Exon ID

37. Ensembl: An Example Click for more details tracks

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

41. 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