1. The Development of Personalized Medicine
(Molecular Medicine/Precision Medicine)

2. Science
February 2001
Human Genome Project
$3 billion
1990
2003

3. Genes
Environment
Normal
Physiology
Disease
Chance

4. The Human Genome
Previous Estimates
?100, ,000 Genes

6. 1,600 genes
397 genes

8. Fred Sanger 1918 – Nov 2013 Double Nobel Laureate in Chemistry
"just a chap who messed about in a lab"

9. Sanger Institute, Hinxton, Cambridge, UK

10. X174 bacteriophage
5,386 nucleotides
1977 Fred Sanger

11. Genomic/cDNA libraries
Early 1980s
Genomic/cDNA libraries
Factor IX gene (34,000 bp – 3+ years)

12. in 2015 - 1 day Early 1980s Genomic/cDNA libraries
Factor IX gene (34,000 bp – 3+ years)
in day

14. 1983 Sonoma Valley Revelation
Dr. Kary Mullis -
1983 Sonoma Valley Revelation
(Scientific American April 1990)

16. Kary Mullis: Nobel Laureate 1993
AIDS denialist
Global warming dissenter
LSD supporter
Polymerase Chain Reaction - PCR
(Nucleic acid amplification technique)

18. Francis Collins
National Human Genome
Research Institute
Craig Ventor
Celera Genomics

19. Dr. Francis Collins
Dr. Craig Ventor

20. Human Genes
20, ,000
Occupy ~2% of the genome

21. Human Phenotypic Complexity

22. Human Phenotypic Complexity
Alternative RNA forms
- alternative splicing
Protein modifications
ie -
a) Phosphorylation
b) Glycosylation

23. the new genetic knowledge?
How have we used
the new genetic knowledge?

24. Initial Genetic Characterizations
Sickle cell anemia
Hemophilia
Cystic Fibrosis

25. Sickle Cell Anemia Initial Genetic Characterizations
Synthesis of an abnormal form of hemoglobin
β globin gene mutation
Amino Acid 6
Glutamic Valine
Acid

26. Genetic Knowledge Application
Molecular genetic diagnosis
Cystic fibrosis
Muscular dystrophy
Hemochromatosis
2. Production of recombinant therapeutic proteins
Hormones - insulin, erythropoietin
Clotting factors
3. Gene Therapy

27. Larger genes responsible for less common single gene
Genetic Characterizations:
Larger genes responsible for
less common single gene
(monogenic) disorders

28. Common Complex Genetic Traits
Genetic Characterizations:
Common Complex Genetic Traits

30. November 2014

31. Nature Genetics
December 2014

32. Complex Genetic Diseases
Contribution of Genetics
Rare monogenic cases (<5%)
- strong family history/earlier onset
Common forms
a) variable onset
b) many genes involved
c) environmental influences
d) chance

33. The New Age of
DNA Sequencing

34. Standard “Sanger” Sequencing
Single template molecule
Read lengths nucleotides

35. Next generation sequencing
DNA Sequencing
Resequencing
Deep sequencing
Massively parallel DNA sequencing
Next generation sequencing

36. Next Generation Sequencing
100,000 parallel sequencing reactions
nucleotide read lengths
1-2.5 billion nucleotides/day
Resulting Bioinformatic Challenge

37. 1,000 Genomes Sequence Project
Nature April 2008
1,000 Genomes Sequence Project
UK NHS 100,000 Genomes Project
DNA Sequence of James Watson

39. Illumina launched its HiSeq X Ten Sequencer
January 2014
Illumina launched its HiSeq X Ten Sequencer
first $1,000 genome at 30x coverage

40. (single nucleotide variants - SNVs)
Human DNA Sequence Variability
Single nucleotide polymorphisms - SNPs
3 million SNPs
(single nucleotide variants - SNVs)
10,000 SNPs change amino-acid sequences

41. Genome-Wide Association Analysis (GWAS) ~10,000 subjects
Asparagus Anosmia
Genome-Wide Association Analysis (GWAS)
~10,000 subjects
535,000 Single nucleotide variants (SNVs)

42. Freckling

43. ENCODE Study - Nature 2012 The Role of Regulatory Sequence Variability
80% of genome involved in regulation of
gene expression patterns
“Junk (intergenic) DNA” critical

44. Multiple dimmer switch analogy
Normal
Level of gene expression
Disease

45. Coffee Break

46. Human Molecular Genetic Pathology
Thalassemia
Cystic Fibrosis
Hemochromatosis
Highly prevalent
Monogenic traits
Significant progress with diagnostic
and therapeutic issues

47. Red Blood Cells (erythrocytes)
Anucleate “protein bags” - 70% hemoglobin
Synthesized in bone marrow
Circulate for 120 days
Removal by the reticuloendothelial system
liver
spleen
lymph nodes

48. Developmental Regulation of Globin Gene Expression

50. Hemoglobin Tetramer

51. Thalassemia Pathogenesis
Imbalance of Alpha:Beta chain globin synthesis
Excess globin chain precipitates
Results in
1. RBC precursor death in bone marrow
2. Premature removal of circulating RBCs

52. Thalassemia Pathogenesis
Hemoglobin concentration reduced in all RBCs
RBCs
Pale - Hypochromic
Small - Microcytic

53. Normal Blood Smear

54. Thalassemic Blood Smear

55. Red Blood Cell Effects of Unbalanced Globin Chain Synthesis

56. Clinical Features of Thalassemia
Severe anemia
Failure to develop in infants
Heart failure
Treatment
Blood (RBC) transfusions - iron deposition
Iron chelation therapy
Bone marrow transplant

57. Pathology of Excessive Iron Deposition
Skin - increased pigment
Pancreas - late-onset diabetes
Liver - cirrhosis/ liver cell cancer
Heart - Cardiac failure
Pituitary - reduced libido/ impotence
Treatment – Phlebotomy/Iron Chelation Therapy

58. Genetics of Thalassemia
Autosomal Recessive Traits
Mutational (allelic) heterogeneity

59. Alpha (chromosome 16) and Beta (chromosome 11)
Locus Organization

60. Beta Thalassemia Mutations +
Beta Globin Gene 1 2 3 + 5’ 3’
Transcription
Frameshift deletion
Deletion
Nonsense
Poly A site
Splicing
Beta Thalassemia Mutations +
Insertion