Something related to genetics ?

1. Somethingrelated to genetics? Dr. Lars Eijssen

2. Image: http://www.bio.georgiasouthern.edu

3. Contents • Basics of genetic variation • Technology to measure variation • Linking SNPs to traits

4. Part 1 Basics of geneticvariation

5. DNA 1 DNA 2 Variations in genes • Only 0.1% of the bases are unique! • Effect onuniquetraits • Butalsoonsusceptibility to disease

6. Effects of variations • Variations can be: • Harmless • Harmful • Latent • A variation is called a mutation if a disadvantageous effect on disease has been proven

7. Basic types of geneticvariation

8. Definition • A SNP (single nucleotide polymorphism) is defined as a single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population • SNPsoccuronce in 500-1000 bases • Currently, dbSNP at NCBI (build 132) has about 6.9M human SNPs (4.5M validated)

9. VariationsotherthanSNPs • Largervariations • Hypervariableregions • Repeatlengthpolymorphism • Differences in the number of repeatswithin a repetetivesequence  ATATATATAT  ATATATATATATATATATAT  ATATATATATATAT

10. Alleles – Genotypes - Inheritance

11. Red dominant – Green recessive

12. Green dominant – Red recessive

13. A gene can have more than 2 alleles

14. 55% 35% Allelefrequency 10%

15. Definition • Penetrance: the number of people with a certain genotype that also develop the associated phenotype Red: 75%

16. Haplotype: the combination of alleles (SNPs) one has

17. Recombinationand cross-over

18. Recombinationand cross-over Haplotype block

19. Types of SNP in a gene Exon Intron Gene Non-coding SNP > Coding SNP

20. (coding) SNPs in a protein Coding SNP mRNA Synonymous SNP Protein Non-synonymous SNP Truncating SNP

21. Effect of SNPsonproteincomposition

22. SNPs in NCBI (Entrez SNP)

23. Functionaleffects of SNPs • When amino acid (AA) changes, is the change relevant? • Type of AA • Site of the change • Functional domain • Conservation in other species • Truncatingmutation http://avonapbio.pbworks.com

24. Are non-codingSNPs relevant? • Also non-coding SNPs may have an effect: • Effect on target sites of Transcription Factors (regulation of transcription) • Effect on target sites of miRNAs (regulation of transcript decay) • Effect on splice donor or acceptor sites (regulation of – alternative – splicing) • Other…

25. Non-geneticvariations • Apart fromvariations in the sequence of the genes, otherinheritablevariationsoccur • These are calledepigeneticvariations

26. Part 2 Technology to measyrevariation

27. Sangersequencing • Terminates the chain with incorporation of a ddNT http://www.mrc-lmb.cam.ac.uk

28. Pyrosequencing • Detectsformation of pyrophosphate (light) Images from: http://www.har.mrc.ac.uk (left) and http://www.ercim.eu (right)

29. Largescalemeasurement of SNPs • Affymetrix SNP chip • 500,000 or 1M SNPs • Genome wide studyof SNPs • Data analysis? • (SM Carr et al. 2008. Comp. Biochem. Physiol. D, 3:11)

30. http://www.mun.ca/biology/scarr/DNA_Chips.html (after SM Carr et al. 2008. Comp. Biochem. Physiol. D, 3:11)

31. Resequencing chips • Another type of chip allowssequencinggenesorgenomicregions of interest • Similartechnology • Onecan design the chips dependingon the genes of interest • As suchonecanmeasure all knownmutationsrelated to a disease

32. Sequencing the whole genome • NextGenerationSequecing (NGS) has made itpossible to sequence the whole genome of anorganism • In principle, all variationsbetweenindividualscanbedetermined • Methodological details willnotbecovered in thiscourse(several platforms available) • In any case: massiveamounts of dataare generated (Gbs per sample) http://seqanswers.com

33. Sequencing the whole genome • Data analysis is notthat easy • Aligning • Calling (‘peak’ calling) • Realchangesorsequencingerrors • Error file • Same issue with ‘regular’ sequencing,butthereonecanevaluatebyeyesight • Howmanyfoldcoverage is needed? http://seqanswers.com http://www.genomics.agilent.com

34. Part 3 LinkingSNPs to traits

35. SNPs as markers • SNPs close to a particular gene acts as a genetic polymorphic marker for that gene • No functionalconnectionneeded!

36. More on markers • The more variation the better • Equallylikelyalleles • SNPswith more thantwoalleles • Repeatlengthvariations • Longer variabele sequences of DNA • SNPsstillveryuseful • Abundant and easy to measureon a largescale

37. SNP maps Example:

38. SNP profiles Personalized - medicine - nutrition

39. Trait • A trait is just a characteristic • Length, weights, eye color, sex, … • Traitscanbe discrete (sex, …) orcontinuous (weight, …) • Discrete = ‘quantitative’ • Continuous = ‘qualitative’ http://phe.rockefeller.edu

40. Heritability • OftenMISinterpreted • The heritability of a traitmeanshowmuch of itsvariationcanbeexplainedbygeneticvariation • …in the population in whichit is measured • Thus high heritability does notmeanthat the trait is geneticallydetermined in general • Itonlytellswhether the population is informative to studygeneticcontributions to a phenotype

41. Heritability > Heritability Images: varioussources

42. Genome wideassociation studies • GWAS (‘association’) tries to link SNPs to traits (diseases) in a genome wideway • Makesuse of unrelatedindividuals • Sonofamilymembers • Tries to findwhichallelicvariants, correlatewith the phenotype of interest • If a complete haplotypegoestogetherwith the phenotype, this is consideredassociation

43. Each color indicates a different haplotype in the studypopulation Patient 1 Patient 2 Patient 3 Patient 4 Patient 5 Patient 6 Control 1 Control 2 Control 3 Region of interest (determine in more detail, or check genesitcontains)

44. http://www.htbiology.com

45. Linkage studies • Linkagemakesuse of relatedindividuals • familymembers • Adantage is higher power as compared to GWAS • Butoneneedslargeenough families withenough (informative) ‘cross overs’ and preferablyseveralgenerations • Principle is the same as with GWAS, using markers orSNPs

46. http://www.molvis.org

47. Computations • The linkagedisequilibrium(D or LD) indicated the deviation of a haplotype’sfrequencyfromitsexpectedfrequency • The LOD score (10log of the odds) indicates the likelihood of obtaining the data giventhat the loci are indeed linked, versus obtaining the data bychance • A score higherthan 3 (whichmeans a 1000:1 odds) is consideredevidence of linkage

48. Limitations • A very large sample size is needed but also population uniformity • Trade-off • To most common diseases, many SNPs/genes contribute for a few percent each • Difficult to detect • Often many genes in haplotype blocks • Rare alleles make sampling even more difficult often discrepancy even between large studies

49. What’s more? • Always realise that the SNPs linked to the phenotype are not (neccesarily) the functional or causing SNPs, they are just close enough to be markers • Now we only discussed genetic contributions to a phenotype • Other aspects to study: • Genes modifying the effects ofother genes (epistatis) • Gene-environment interactions • Specific study of interactions is very difficult • Even more possibilities • Even smaller effects Images: http://theosophical.wordpress.com (left) and http://www.foodfacts.info (right)

50. Questions? Thankyou!