1. Fig. 12-1 Chapter 12: Genomics

2. Genomics: the study of whole-genome structure, organization, and function Structural genomics: the physical genome; whole genome mapping Functional genomics: the proteome, expression patterns, networks

3. Creating a physical map of the genome Create a comprehensive genomic library (use a vector that incorporates huge fragments) Order the clones by identifying overlapping groups (e.g., sequencing ends to determine “contigs”) Sequence each contig Identify genes and chromosomal rearrangements within each contig (correlates the genetic and physical maps)

4. Fig. 12-2 Overview of genome sequencing

5. Fig. 12-4 Sequencing the ends of clones in a library

6. Fig. 12-2 Overview of genome sequencing

7. Fig. 12-5

8. Fig. 12-6

9. Fig. 12-3 Overview of genome sequencing

10. Fig. 12-7

11. Fig. 12-8

12. Fig. 12-9 Several orders of magnitude resolution separates cytogenetic from gene-level understanding

13. Creating a high-resolution genetic map of the genome requires many “markers” Classic mutations and allelic variations (too few) Molecular polymorphisms; selectively neutral DNA sequence variations are common in genomes Example: Restriction Fragment Length Polymorphisms (RFLP markers)

14. Fig. 12-10 Inheritance of an RFLP:

15. Fig. 12-10 Inheritance of an RFLP: Determining linkage to a known gene

16. Fig. 12-10 Inheritance of an RFLP: Determining linkage to a known gene

17. Fig. 12-11 Linkage analysis of a gene and VNTR markers

18. Creating a high-resolution genetic map of the genome requires many “markers” Classic mutations and allelic variations Molecular polymorphisms; selectively neutral DNA sequence variations are common in genomes Example: Restriction Fragment Length Polymorphisms (RFLP markers) Example: Simple Sequence Length Polymorphisms (SSLP markers)

19. SSLP: Simple sequence length polymorphism VNTR repeat clusters (minisatellite markers) dinucleotide repeats (microsatellite markers) VNTRs can be detected by restriction/Southern blot analysis; both detected by PCR using primers for each end of the repeat tract

20. Variable number tandem repeats (VNTRs) “minisatellite” DNA 15-100 bp units; repeated in 1-5 kb blocks expansion/contraction of the block due to meiotic unequal crossingover crossingover so frequent that each individual has unique pattern (revealed by genomic Southern blot/hybridization analysis)

21. Fig. 12-12 Using a SSLP marker to map a disease

22. Fig. 12-12 Using a SSLP marker to map a disease Unlinked Linked to P Linked to p Unlinked

23. Fig. 12-13 Polymorphism markers can provide a high resolution map Linkage map of human chromosome 1

24. High-resolution cytogenetic mapping is based on: In situ hybridization: hybridization of known sequences directly to chromosome preparations Rearrangement break mapping Radiation hybrid mapping

25. Fig. 12-14 FISH analysis using a probe for a muscle protein gene

26. Fig. 12-16 Survey clones from the region of the break to determine one that spans the break

27. Fig. 12-16 FISH analysis locates the sequence and the breakpoint cytogenetically Survey clones from the region of the break to determine one that spans the break

28. Fig. 12-24 Cytogenetic map of human chromosome 7

29. Fig. 12-17 Determining the sequence map sites of rearrangement breakpoints and other mutations

30. Mapping & determining a gene of interest Fig. 12-18

31. Genome sequencing projects Sequence individual clones and subclones (extensive use of robotics) Identify overlaps to assemble sequence contigs (extensive use of computer-assisted analysis) Identify putative genes by identifying open reading frames, consensus sequences and other bioinformatic tools

32. Once a genomic sequence is obtained, it is subjected to bioinformatic analysis to determine structure and function Identify apparent ORFs and consensus regulatory sequences to identify potential genes Identify corresponding cDNA (and EST) sequences to identify genuine coding regions Polypeptide similarity analysis (similarity to polypeptides encoded in other genomes)

33. Fig. 12-19 Genes and their components have characteristic sequences Bioinformatic analysis of raw sequences can suggest possible features

34. Fig. 12-20 Confirmation of genes and their architecture is obtained by analysis of cDNAs cDNA subprojects are key facets of a genome project

35. Fig. 12-21 High-resolution genomics arises through the combination of bioinformatics and experimentation

36. Fig. 12-22 Using bioinformatics to make detailed gene predictions

37. Fig. 12-23 Complete sequence and partial interpretation of a complete human chromosome

38. Fig. 12-26 Comparative genomics reveals ancestral chromosome rearrangements

39. Fig. 12-27 Microarray analysis – a form of functional genomics 1046 cDNA array 65,000 oligo array (representing 1641 genes) Arrays hybridized to cDNAs prepared from total RNA Relative intensity (color-coded) reflects abundance of individual RNAs

40. Fig. 12-