HUMAN GENES

1. Human GenesHuman Genes
• By A.Arputha SelvarajBy A.Arputha Selvaraj

2. • What is Bioinformatics?What is Bioinformatics?
• Availability of information about the human genomeAvailability of information about the human genome
and other genomesand other genomes
• Human health related databasesHuman health related databases
• Bioinformatics and Drug developmentBioinformatics and Drug development
• Ethical, Legal and Social Issues (ELSI)Ethical, Legal and Social Issues (ELSI)

3. What is Bioinformatics?What is Bioinformatics?
• One idea for a definition:One idea for a definition:
• (Molecular)(Molecular) Bio - informaticsBio - informatics ==
• is conceptualizing biology in terms of moleculesis conceptualizing biology in terms of molecules
(in the sense of physical-chemistry) and then(in the sense of physical-chemistry) and then
applying "informatics" techniques (derived fromapplying "informatics" techniques (derived from
disciplines such as applied math, CS, anddisciplines such as applied math, CS, and
statistics) to understand and organize thestatistics) to understand and organize the
information associated with these molecules, oninformation associated with these molecules, on
a large-scale.a large-scale.

4. • Bioinformatics is the field of science in which
biology, computer science, and information
technology merge into a single discipline. The
ultimate goal of the field is to enable the discovery
of new biological insights as well as to create
a global perspective from which unifying
principles in biology can be discerned. There
are three important sub-disciplines within
bioinformatics:

5. • the development of new algorithms and statisticsthe development of new algorithms and statistics
with which to assess relationships amongwith which to assess relationships among
members of large data sets;members of large data sets;
• the analysis and interpretation of various types ofthe analysis and interpretation of various types of
data including nucleotide and amino aciddata including nucleotide and amino acid
sequences, protein domains, and proteinsequences, protein domains, and protein
structures;structures;
• the development and implementation of tools thatthe development and implementation of tools that
enable efficient access and management ofenable efficient access and management of
different types of information.different types of information.

6. Biological Data + Computer Calculations
Bioinformatics

7. The Bioinformatics SpectrumThe Bioinformatics Spectrum

8. What is the Human Genome?What is the Human Genome?
•The entire genetic makeup of the human cell nucleus.
•Genes carry the information for making all of the proteins
required by the body for growth and maintenance.
•The genome also encodes rRNA and tRNA which are
involved in protein synthesis.

9. • Made up of ~35,000-50,000 genes which code forMade up of ~35,000-50,000 genes which code for
functional proteins in the bodyfunctional proteins in the body
• Includes non-coding sequences located betweenIncludes non-coding sequences located between
genes, which makes up the vast majority of the DNAgenes, which makes up the vast majority of the DNA
in the genome (~95%)in the genome (~95%)
• The particular order of nucleotide bases (As, Gs, Cs,The particular order of nucleotide bases (As, Gs, Cs,
and Ts) determines the amino acid composition ofand Ts) determines the amino acid composition of
proteinsproteins

10. • Information about DNA variations (polymorphisms)Information about DNA variations (polymorphisms)
among individuals can lend insight into newamong individuals can lend insight into new
technologies for diagnosing, treating, and preventingtechnologies for diagnosing, treating, and preventing
diseases that afflict humankind.diseases that afflict humankind.

11. What Goals Were Established for the HumanWhat Goals Were Established for the Human
Genome Project When it Began in 1990?Genome Project When it Began in 1990?
•Identify all of the genes in human DNA.
•Determine the sequence of the 3 billion chemical
nucleotide bases that make up human DNA.
•Store this information in data bases.
•Develop faster, more efficient sequencing technologies.
•Develop tools for data analysis.
•Address the ethical, legal, and social issues (ELSI) that
are arise form the project.

12. Two Different Groups Worked to Obtain theTwo Different Groups Worked to Obtain the
DNA Sequence of the Human GenomeDNA Sequence of the Human Genome
•The HGP is a multinational consortium established by
government research agencies and funded publicly
•Celera Genomics is a private company whose former
CEO, J. Craig Venter, ran an independent sequencing
project
•Differences arose regarding who should receive the
credit for this scientific milestone
•June 6, 2000, the HGP and Celera Genomics held a
joint press conference to announce that TOGETHER
they had completed ~97% of the human genome

13. PublishedPublished
•The International Human Genome Sequencing
Consortium published their results in Nature, 409
(6822): 860-921, 2001.”Initial Sequencing and Analysis
of the Human Genome”
•Celera Genomics published their results in Science,
Vol 291(5507): 1304-1351, 2001.“The Sequence of the
Human Genome”

14. Banking on Genome dataBanking on Genome data
• Britain is about embark on the world’s largestBritain is about embark on the world’s largest
genome data project focussed on middle aged peoplegenome data project focussed on middle aged people
which may shed light on the interaction betweenwhich may shed light on the interaction between
genes, health and the environmentgenes, health and the environment
• Studies of families affected by genetic diseaseStudies of families affected by genetic disease
have proven useful for genetic linkage analyses (e.g.have proven useful for genetic linkage analyses (e.g.
Huntington’s disease, neurofibramatosis, cysticHuntington’s disease, neurofibramatosis, cystic
fibrosis, Duchenne’s muscular dystrophy).fibrosis, Duchenne’s muscular dystrophy).

15. Organism Genome size(basepairs)Organism Genome size(basepairs)
• Epstein-Barr virusEpstein-Barr virus 0.172 *0.172 *106
• BacteriumBacterium (E.coli)(E.coli) 4.6 *4.6 *106
• YeastYeast (S.cerevisiae)(S.cerevisiae) 12.1 *12.1 * 106
• Nematode wormNematode worm (C.elegans)(C.elegans) 95.5 *95.5 * 106
• Thale cressThale cress (A.thaliana)(A.thaliana) 117 *117 * 106
• Fruit flyFruit fly (D.melanogaster)(D.melanogaster) 180 *180 * 106
• HumanHuman (H.sapiens)(H.sapiens) 3200 *3200 * 106

16. Gene Sequence Protein SequencesGene Sequence Protein Sequences
• Supposed to be raw data .Supposed to be raw data .
• One has to add layers of information to theOne has to add layers of information to the
sequence datasequence data
• Annotation of the data becomes very importantAnnotation of the data becomes very important
• Annotation : Theoretical methodsAnnotation : Theoretical methods
Experimental methodsExperimental methods
• Bioinformatics / Statistics / MathematicsBioinformatics / Statistics / Mathematics

17. Complete Genome Sequences From SeveralComplete Genome Sequences From Several
Organisms Are KnownOrganisms Are Known
• Comparative GenomicsComparative Genomics
• Structural GenomicsStructural Genomics
• Functional GenomicsFunctional Genomics
• Cellular GenomicsCellular Genomics
• Network GenomicsNetwork Genomics
• Ethical GenomicsEthical Genomics
• Moral GenomicsMoral Genomics

18. Other Completed GenomesOther Completed Genomes
• Haemophilus influenzaeHaemophilus influenzae
• Escherichia coliEscherichia coli
• Bacillus subtilusBacillus subtilus
• Helicobacter pyloriHelicobacter pylori
• Borrelia burgdorferiBorrelia burgdorferi
• Streptococcus pneumoniaeStreptococcus pneumoniae
• Saccharomyces cerevisiaeSaccharomyces cerevisiae

19. • Caenorhabditis elegansCaenorhabditis elegans
• Arabidopsis thalianaArabidopsis thaliana
• Archaeoglobus fulgidusArchaeoglobus fulgidus
• Methanobacterium thermoautotrophicumMethanobacterium thermoautotrophicum
• Methanococcus jannaschiiMethanococcus jannaschii
• Mycoplasma pneumoniaeMycoplasma pneumoniae
• Mycoplasm genitaliuMycoplasm genitaliu
• Rickettsia prowazekiiRickettsia prowazekii
• Mycobacterium tuberculosisMycobacterium tuberculosis

20. • Treponema pallidumTreponema pallidum
• Staphylococcus aureusStaphylococcus aureus
• And more!And more!

21. Completed Plant GenomesCompleted Plant Genomes
• Arabidopsis thalianaArabidopsis thaliana
Completed Insect GenomesCompleted Insect Genomes
• Drosophila melanogasterDrosophila melanogaster
Completed Rodent GenomesCompleted Rodent Genomes
• Mus musculusMus musculus

22. Which Branches of Biology will Benefit from thisWhich Branches of Biology will Benefit from this
Knowledge?Knowledge?
•Medicine
•PharmacogenomicsPharmacogenomics
•Biotechnology
•Bioinformatics
•Proteomics

23. MedicineMedicine
Diagnosis of disease and disease riskDiagnosis of disease and disease risk
(a) when a patient presents with symptoms(a) when a patient presents with symptoms
(b) in advance of apperance of symptoms(b) in advance of apperance of symptoms
[eg]Huntigton disease (an inherited[eg]Huntigton disease (an inherited
neurodegenerative disorder)neurodegenerative disorder)
• symptoms:uncontrollable dance-like (choreatic)symptoms:uncontrollable dance-like (choreatic)
movements,mental disturbance,personalitymovements,mental disturbance,personality
changes and intellectual impairmentchanges and intellectual impairment
• repeats of the trinucleotide CAG,correspondingrepeats of the trinucleotide CAG,corresponding
to polyglutamine blocks in the correspondingto polyglutamine blocks in the corresponding
protein,huntinginprotein,huntingin

24. • 11-28 CAG repeats -->normal11-28 CAG repeats -->normal
• 29-34 CAG repeats---->likely to develop disease29-34 CAG repeats---->likely to develop disease
• 35-41 CAG repeats develop mild symptoms35-41 CAG repeats develop mild symptoms
• morethan 41 CAG repeats suffer full huntingtonmorethan 41 CAG repeats suffer full huntington
diseasedisease
(c) for in utero diagnosis of potential abnormalities(c) for in utero diagnosis of potential abnormalities
such as cystic fibrosis, asthma etc.such as cystic fibrosis, asthma etc.
(d) for genetic counselling of couples contemplating(d) for genetic counselling of couples contemplating
having childrenhaving children

25. Online databases of disease-associatedOnline databases of disease-associated
mutationsmutations

26. Online database of Mendelian Inheritance inOnline database of Mendelian Inheritance in
Man (OMIM)Man (OMIM)

27. Human Gene Mutation Database (HGMD)Human Gene Mutation Database (HGMD)

28. IARC p53 databaseIARC p53 database

29. Haemophilia B databaseHaemophilia B database

30. Von Willebrand factor databaseVon Willebrand factor database

31. Amyotrophic lateral sclerosis databaseAmyotrophic lateral sclerosis database

32. Bioinformatics and Drug developmentBioinformatics and Drug development

33. CompoundCompound Target enzymeTarget enzyme Clinical useClinical use
AcetazolamideAcetazolamide Carbonic anhydraseCarbonic anhydrase GlaucomaGlaucoma
AspirinAspirin CylooxygenasesCylooxygenases InflammationInflammation
Amoxicillin Pencillin binding proteinsAmoxicillin Pencillin binding proteins Bacterial infectionsBacterial infections
DigoxinDigoxin Sodium,potassium ATPaseSodium,potassium ATPase Heart diseaseHeart disease
OmeprazoleOmeprazole HH++
,K,K++
-ATPase-ATPase Peptic ulcersPeptic ulcers
SorbinolSorbinol Aldose reductaseAldose reductase CancerCancer
VIAGRAVIAGRA PhosphodiesterasePhosphodiesterase Erectile DysfunctionErectile Dysfunction

34. RECEPTORSRECEPTORS
• G-protein coupled receptorsG-protein coupled receptors
• Ligand-gated ion channelsLigand-gated ion channels
• Tyrosine kinase receptorsTyrosine kinase receptors
• Nuclear receptorsNuclear receptors

36. Workflow of a virtual screening run against a specific target

37. Genetics of responses to therapy-Genetics of responses to therapy-
customized treatmentcustomized treatment
• sequence analysis permits selecting drugs andsequence analysis permits selecting drugs and
dosages optimal for individual patients, a fast-dosages optimal for individual patients, a fast-
growing field called pharmacogenomics [eg] 6-growing field called pharmacogenomics [eg] 6-
mercaptopurine used in the treatment ofmercaptopurine used in the treatment of
childhood leukaemiachildhood leukaemia

38. Identification of drug targetsIdentification of drug targets
(a) drug design process(a) drug design process
(b) drugs act on targets such as receptors, enzymes,(b) drugs act on targets such as receptors, enzymes,
harmones and some unknown targetsharmones and some unknown targets
(c) differential genomics [eg] tumour cells(c) differential genomics [eg] tumour cells
Gene theraphyGene theraphy
(a) direct supply of proteins [eg] insulin(a) direct supply of proteins [eg] insulin
(b) antisense therapy [eg] crohn disease(b) antisense therapy [eg] crohn disease

39. Eliminating side effectsEliminating side effects
Developing revolutionary new drugs and treatmentsDeveloping revolutionary new drugs and treatments
for illness that previously couldn't befor illness that previously couldn't be
treated/preventing or avoiding serious diseasestreated/preventing or avoiding serious diseases
It is believed that we are approaching a new era ofIt is believed that we are approaching a new era of
‘personalized medicines’ medicine that understands‘personalized medicines’ medicine that understands
as individual patient at the genetic level and offers theas individual patient at the genetic level and offers the
optimum treatmentoptimum treatment

40. Rationales for Drug DesignRationales for Drug Design
 Tuberculosis is a global threat affecting 1/3 of
world population with latent infections. 50% of
HIV patients develop TB.
 TB cases are on the rise and approximately 2
million people each year die from the infection.
 The spread of HIV/AIDS and the emergence of
multidrug-resistant TB are contributing to the
worsening impact of this disease.
 It is estimated that between now and 2020,
approximately 1000 million people will be newly
infected, over 150 million people will get sick,
and 36 million will die of TB - if control is not
further strengthened.
2002

41. Drug Design CycleDrug Design Cycle

42. Realistic Design CycleRealistic Design Cycle

43. Blockbuster DrugsBlockbuster Drugs
Claritin
an anti-allergy
drug with sales
reaching $3
billion in 2000
(nearly 1/3 of
Schering
Plough’s
revenues .
Prilosec
an ulcer drug
produced by
Astra Zeneca,
sold over $6.2
billion worth
globally in
2000 alone.
Zantac
also an ulcer
drug. Glaxo sold
$9 billion worth
of globally, but
lost patent
protection in
1997.
Drug sales in
the US in 1997
totaled more
than $69.4
billion.
HIV drugs
In 1998 in the
US, NRTIs
accounted for
$885 million in
sales, PIs $865
million and
NNRTIs for $100
million.
The market in
the rest of the
world is about
$2 billion
(1998).

44. Cartoon representation ofCartoon representation of TATA xylanase along with thexylanase along with the
active site Glu 131 and Glu 237, the salt bridge (Arg 124active site Glu 131 and Glu 237, the salt bridge (Arg 124
- Glu 232) and disulphide bridge- Glu 232) and disulphide bridge

45. The “salad bowl” view showing the substrate bindingThe “salad bowl” view showing the substrate binding
cleft. The Active site is at the C-terminus of thecleft. The Active site is at the C-terminus of the ββ barrelbarrel
and the salt bridge is at the N-terminus of theand the salt bridge is at the N-terminus of the ββ barrelbarrel

46. Figure shows an example for the competition for polarFigure shows an example for the competition for polar
atoms by water molecules is more at low temperatureatoms by water molecules is more at low temperature

47. A Water dimer formed by Wat 533 (W1) and Wat 511 (W2) and itsA Water dimer formed by Wat 533 (W1) and Wat 511 (W2) and its
interactions.Conserved residues are labeled in red. Interactionsinteractions.Conserved residues are labeled in red. Interactions
involving water molecules appear to contribute to the stability ofinvolving water molecules appear to contribute to the stability of
residues in the active site region.residues in the active site region.ββ-strands 1 and 8 are not shown.-strands 1 and 8 are not shown.

48. HIV protease & inhibitor

49. (HIV protease dimer complexed with
protease inhibitor(red), GIF generated using
RasMol)

50. HIV protease & inhibitor (red)

51. BiotechnologyBiotechnology
– Production of useful protein products for use inProduction of useful protein products for use in
medicine, agriculture, bioremediation andmedicine, agriculture, bioremediation and
pharmaceutical industries.pharmaceutical industries.
• AntibioticsAntibiotics
• Protein replacement (factor VIII, TPA,Protein replacement (factor VIII, TPA,
streptokinase, insulin, interferon…)streptokinase, insulin, interferon…)
• BT insecticide toxin (fromBT insecticide toxin (from Bacillus thuringiensisBacillus thuringiensis))
• Herbicide resistance (glyphosate resistance)Herbicide resistance (glyphosate resistance)

52. • Bioengineered foods [e.g. Flavr Savr tomato
(antisense – polygalacturonase) to delay rotting]
• “Pharm” animals

53. ProteomicsProteomics
– Investigates patterns and levels of geneInvestigates patterns and levels of gene
expression in diseased cells that can be analyzedexpression in diseased cells that can be analyzed
to build databases of expression profiles.to build databases of expression profiles.

54. Developmental BiologyDevelopmental Biology
– Regulation of embryonic development.Regulation of embryonic development.
– Regulation of the aging processRegulation of the aging process..

55. Evolutionary and Comparative BiologistsEvolutionary and Comparative Biologists
– Because DNA mutates at a constant rate,Because DNA mutates at a constant rate,
comparisons of DNA between different organismscomparisons of DNA between different organisms
can provide evolutionary histories.can provide evolutionary histories.

56. Ethical, Legal and Social Issues (ELSI)Ethical, Legal and Social Issues (ELSI)
•Privacy legislation
•Gene testing
•Patenting
•Forensics
•Behavioral Genetics
•Genetics in the Courtroom

57. Philosophical ImplicationsPhilosophical Implications
Human responsibility
Free will versus genetic determinism

58. Psychological Impact and igmatizationPsychological Impact and igmatization
– Affects on the individualAffects on the individual
– Affects on society’s perceptions and expectationsAffects on society’s perceptions and expectations
of the individualof the individual

59. Clinical IssuesClinical Issues
– Growing demand to educate health care workers toGrowing demand to educate health care workers to
accurately evaluate genetic tests.accurately evaluate genetic tests.
– Public needs to gain scientific literacy andPublic needs to gain scientific literacy and
understand the capabilities, limitations and risks.understand the capabilities, limitations and risks.
– Standards need to be established including qualityStandards need to be established including quality
controls to ensure accuracy and reliability.controls to ensure accuracy and reliability.
– Federal regulation?Federal regulation?

60. Genetic CounselingGenetic Counseling
– Informed consent for complex proceduresInformed consent for complex procedures
– Counseling about the risks, limitations andCounseling about the risks, limitations and
reliability of genetic screening techniquesreliability of genetic screening techniques
– Reproductive decision making based on geneticReproductive decision making based on genetic
informationinformation
– Reproductive rightsReproductive rights

61. Multifactorial Diseases and EnvironmentalMultifactorial Diseases and Environmental
FactorsFactors
– Genetic predispositions do not mandate diseaseGenetic predispositions do not mandate disease
developmentdevelopment
– Caution must be exercised when correlatingCaution must be exercised when correlating
genetic tests with predictionsgenetic tests with predictions

62. SummarySummary
•The significance of the completion of the human
genome project cannot be overstated.
•With the dictionary of the genome available, the
molecular mechanisms of human health and disease
will be resolved.
•Armed with this knowledge a transformation in medical
diagnostics and therapy is underway and will continue
into the next few decades.
•The application of this knowledge needs to be
regulated and restricted to practices deemed ethically
sound.

63. Thank youThank you