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COMPLEX GENOME ANALYSIS Ikhide Imumorin, PhD Assistant Professor of Animal Molecular & Quantitative Genetics Cornell University Ithaca, NY 14853 USA
GENOMICS ANALYSIS
The genomes of living organisms vary enormously in size.
Genomicists look at two basic features of genomes:  sequence and polymorphism. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Divide and conquer strategy meets most challenges. ,[object Object],[object Object],[object Object],[object Object]
Fig. 10.2
Techniques for mapping and cloning ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Making a large scale linkage map ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Fig. 10.3
Genome wide identification of genetic markers ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object]
SNPs and SSRs for genome coverage ,[object Object],[object Object]
Genome wide typing of genetic markers ,[object Object],[object Object],[object Object],Fig. 10.4
Long range physical maps:  karyotypes and genomic libraries position markers on chromosomes. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Vectors used for clone large inserts for physical mapping ,[object Object],[object Object],[object Object],[object Object],[object Object]
How to determine order of clones across genome ,[object Object],[object Object],[object Object]
Identifying and isolating a set of overlapping fragments from a library ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Physical mapping by analysis of STSs Bottom-up approach Each STS represents a unique segment of the genome amplified by PCR. Fig. 10.5
Human Karyotype ,[object Object],[object Object],Fig. 10.6 a, b
Chromosome 7 at three levels of resolution Fig. 10. 6 c
FISH protocol for top-down approach Fig. 10.8
Sequence maps show order of nucleotides in  cloned piece of DNA. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Hierarchical shotgun strategy Used in publicly funded effort to sequence human genome ,[object Object],[object Object],[object Object],[object Object],[object Object],Fig. 10.9
Whole-genome shotgun sequencing Used by  Celera Genomics to sequence whole human genome.   ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Fig. 10.10
Limitations of whole genome sequencing ,[object Object],[object Object],[object Object],[object Object]
Sequencing of the human genome ,[object Object],[object Object],[object Object],[object Object]
Integration of linkage, physical, and sequence maps ,[object Object],[object Object],[object Object]
Changes in biology, genetics and genomics from human genome sequence ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Major insights from human and model organism sequences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Conserved segments of syntenic blocks in human and mouse genomes Fig. 10.12
Noncoding RNA genes ,[object Object],[object Object],[object Object],[object Object]
Protein coding genes generate the proteome. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Protein coding genes generate the proteome How transcription factor protein domains have expanded in specific lineages Fig. 10.11
Examples of domain accretions in chromatin proteins Fig. 10.13
Number of distinct domain architectures in four eukaryotic genomes Fig. 10.14
Repeat sequences fall into five classes. ,[object Object],[object Object],[object Object],[object Object],[object Object]
Repeat sequences constitute more than 50% of the genome. Fig. 10.15
Gene Organization of Genome ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Genome has a distinct organization.  Gene family – olfactory receptor gene family
Class II region of human major histocompatibility complex contains 60 genes in 700 kb Fig. 10.17
Combinatorial strategies ,[object Object],[object Object],Fig. 10.19a Fig. 10.18
Lateral transfer of genes ,[object Object],[object Object]
Twofold higher mutation rate in males ,[object Object],[object Object],[object Object],[object Object]
Human races have similar genes. ,[object Object],[object Object],[object Object],[object Object]
All living organisms are a single race. ,[object Object],[object Object],[object Object]
In the future, other features of chromosomes will become increasingly important. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
High-throughput instruments DNA sequencer Fig. 10.20
High-throughput instruments e.g, microarrays Fig. 10.21
Two color - DNA microarray Fig. 10.22
Analysis of genomic and RNA sequences ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Lynx therapeutics sequencing strategy of MPSS Fig. 10.24
Systems Biology – the global study of multiple components of biological systems and their interactions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Human Genome Project has changed the potential for predictive/preventive medicine. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Social, ethical, and legal issues ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Editor's Notes

  1. Figure 10.2
  2. Figure 10.3
  3. Figure 10.4
  4. Figure 10.5
  5. Figure 10.5 a, b
  6. Figure 10.5 c
  7. Figure 10.8
  8. Figure 10.9
  9. Figure 10.10
  10. Figure 10.12
  11. Figure 10.13
  12. Figure 10.16
  13. Figure 10.14
  14. Fig. 10.15
  15. Figure 10.20
  16. Figure 10.18 (top) / Figure 10.19a (bottom)
  17. Figure 10.20
  18. Figure 10.21
  19. Figure 10.22
  20. Figure 10.24